飯田　慶 （イイダ　ケイ）

コミュニケーション情報 byコメンテータガイド

• コメント

  RNAが関与する生命現象を対象に、コンピュータを使って研究をする、基礎生物学分野の研究者です（トランスクリプトーム解析など）。ただし、AI領域、シミュレーション領域は専門外となります。

研究者情報

学位

• 博士（理学）（名古屋大学）

ホームページURL

https://orcid.org/0000-0001-7130-8705

ORCID ID

•  https://orcid.org/0000-0001-7130-8705

J-Global ID

• 200901087903479252

研究キーワード

• 筋萎縮性側索硬化症（ALS）   一細胞RNA-seq   RNA結合タンパク質   エピトランスクリプトーム   トランスクリプトーム   選択的スプライシング   情報生物学   

現在の研究分野（キーワード）

RNAが関与する生命現象を対象に、コンピュータを使って研究をする、基礎生物学分野の研究者です（トランスクリプトーム解析など）。ただし、AI領域、シミュレーション領域は専門外となります。

研究分野

• ライフサイエンス / システムゲノム科学 / データサイエンス

経歴

• 2024年04月 - 現在  京都大学医学研究科附属 がん免疫総合研究センター特定准教授（クロスアポイントメント）
• 2022年04月 - 現在  京都大学大学院医学研究科客員研究員
• 2022年04月 - 現在  近畿大学理工学部講師
• 2022年06月 - 2024年03月  京都大学 iPS細胞研究所研究員(非常勤)
• 2012年09月 - 2022年03月  京都大学医学研究科特定助教
• 2008年12月 - 2012年08月  理化学研究所生命情報基盤研究部門
• 2007年04月 - 2008年11月  University of California, Riverside
• 2004年04月 - 2007年03月  長浜バイオ大学バイオサイエンス学部
• 2002年04月 - 2004年03月  理化学研究所ゲノム科学研究センター

所属学協会

• 日本メディカルAI学会   日本RNA学会   

研究活動情報

論文

• Secretory GFP reconstitution labeling of neighboring cells interrogates cell–cell interactions in metastatic niches

  Misa Minegishi; Takahiro Kuchimaru; Kaori Nishikawa; Takayuki Isagawa; Satoshi Iwano; Kei Iida; Hiromasa Hara; Shizuka Miura; Marika Sato; Shigeaki Watanabe; Akifumi Shiomi; Yo Mabuchi; Hiroshi Hamana; Hiroyuki Kishi; Tatsuyuki Sato; Daigo Sawaki; Shigeru Sato; Yutaka Hanazono; Atsushi Suzuki; Takahide Kohro; Tetsuya Kadonosono; Tomomi Shimogori; Atsushi Miyawaki; Norihiko Takeda; Hirofumi Shintaku; Shinae Kizaka-Kondoh; Satoshi Nishimura

  Nature Communications 14 1 2023年12月 

  Abstract Cancer cells inevitably interact with neighboring host tissue-resident cells during the process of metastatic colonization, establishing a metastatic niche to fuel their survival, growth, and invasion. However, the underlying mechanisms in the metastatic niche are yet to be fully elucidated owing to the lack of methodologies for comprehensively studying the mechanisms of cell–cell interactions in the niche. Here, we improve a split green fluorescent protein (GFP)-based genetically encoded system to develop secretory glycosylphosphatidylinositol-anchored reconstitution-activated proteins to highlight intercellular connections (sGRAPHIC) for efficient fluorescent labeling of tissue-resident cells that neighbor on and putatively interact with cancer cells in deep tissues. The sGRAPHIC system enables the isolation of metastatic niche-associated tissue-resident cells for their characterization using a single-cell RNA sequencing platform. We use this sGRAPHIC-leveraged transcriptomic platform to uncover gene expression patterns in metastatic niche-associated hepatocytes in a murine model of liver metastasis. Among the marker genes of metastatic niche-associated hepatocytes, we identify Lgals3, encoding galectin-3, as a potential pro-metastatic factor that accelerates metastatic growth and invasion.
• CCL21‐Ser expression in melanoma cells recruits CCR7+ naïve T cells to tumor tissues and promotes tumor growth

  Megumi Miyamoto; Yuki Kawato; Ryonosuke Fujie; Kaoru Kurowarabe; Kakeru Fujiwara; Reika Nobusawa; Ryota Hayashi; Kei Iida; Izumi Ohigashi; Haruko Hayasaka

  Cancer Science 2023年07月 [査読有り]
   

  Abstract CCL21‐Ser, a chemokine encoded by the Ccl21a gene, is constitutively expressed in the thymic epithelial cells and stromal cells of secondary lymphoid organs. It regulates immune cell migration and survival through its receptor CCR7. Herein, using CCL21‐Ser‐expressing melanoma cells and the Ccl21a‐deficient mice, we demonstrated the functional role of cancer cell‐derived CCL21‐Ser in melanoma growth in vivo. The B16‐F10 tumor growth was significantly decreased in Ccl21a‐deficient mice compared with that in wild‐type mice, indicating that host‐derived CCL21‐Ser contributes to melanoma proliferation in vivo. In Ccl21a‐deficient mice, tumor growth of melanoma cells expressing CCL21‐Ser was significantly enhanced, suggesting that CCL21‐Ser from melanoma cells promotes tumor growth in the absence of host‐derived CCL21‐Ser. The increase in tumor growth was associated with an increase in the CCR7⁺ CD62L⁺ T cell frequency in the tumor tissue but was inversely correlated with Treg frequency, suggesting that naïve T cells primarily promote tumor growth. Adoptive transfer experiments demonstrated that naïve T cells are preferentially recruited from the blood into tumors with melanoma cell‐derived CCL21‐Ser expression. These results suggest that CCL21‐Ser from melanoma cells promotes the infiltration of CCR7⁺ naïve T cells into the tumor tissues and creates a tumor microenvironment favorable for melanoma growth.
• Integrated-gut-liver-on-a-chip platform as an in vitro human model of non-alcoholic fatty liver disease

  Jiandong Yang; Yoshikazu Hirai; Kei Iida; Shinji Ito; Marika Trumm; Shiho Terada; Risako Sakai; Toshiyuki Tsuchiya; Osamu Tabata; Ken-ichiro Kamei

  Communications Biology 6 1 2023年03月 [査読有り]
   

  Abstract Non-alcoholic fatty liver disease (NAFLD) afflicts a significant percentage of the population; however, no effective treatments have yet been established because of the unsuitability of in vitro assays and animal experimental models. Here, we present an integrated-gut-liver-on-a-chip (iGLC) platform as an in vitro human model of the gut-liver axis (GLA) by co-culturing human gut and liver cell lines interconnected via microfluidics in a closed circulation loop, for the initiation and progression of NAFLD by treatment with free fatty acids (FFAs) for 1 and 7 days, respectively. Co-cultured Caco-2 gut-mimicking cells and HepG2 hepatocyte-like cells demonstrate the protective effects from apoptosis against FFAs treatment, whereas mono-cultured cells exhibit induced apoptosis. Phenotype and gene expression analyses reveal that the FFAs-treated gut and liver cells accumulated intracellular lipid droplets and show an increase in gene expression associated with a cellular response to copper ions and endoplasmic reticulum stress. As an in vitro human GLA model, the iGLC platform may serve as an alternative to animal experiments for investigating the mechanisms of NAFLD.
• Chemical induction of splice-neoantigens attenuates tumor growth in a preclinical model of colorectal cancer

  Shingo Matsushima; Masahiko Ajiro; Kei Iida; Kenji Chamoto; Tasuku Honjo; Masatoshi Hagiwara

  Science Translational Medicine 14 673 2022年11月 

  Neoantigen production is a determinant of cancer immunotherapy. However, the expansion of neoantigen abundance for cancer therapeutics is technically challenging. Here, we report that the synthetic compound RECTAS can induce the production of splice-neoantigens that could be used to boost antitumor immune responses. RECTAS suppressed tumor growth in a CD8 ⁺ T cell– and tumor major histocompatibility complex class I–dependent manner and enhanced immune checkpoint blockade efficacy. Subsequent transcriptome analysis and validation for immunogenicity identified six splice-neoantigen candidates whose expression was induced by RECTAS treatment. Vaccination of the identified neoepitopes elicited T cell responses capable of killing cancer cells in vitro, in addition to suppression of tumor growth in vivo upon sensitization with RECTAS. Collectively, these results provide support for the further development of splice variant–inducing treatments for cancer immunotherapy.
• Involvement of endothelins in neuroprotection of valosin-containing protein modulators against retinal ganglion cell damage

  Mami Kusaka; Tomoko Hasegawa; Hanako Ohashi Ikeda; Yumi Inoue; Sachiko Iwai; Kei Iida; Akitaka Tsujikawa

  Scientific Reports 12 1 2022年09月 

  Abstract We have previously shown that Kyoto University Substances (KUSs), valosin-containing protein (VCP) modulators, suppress cell death in retinal ganglion cells of glaucoma mouse models through alterations of various genes expressions. In this study, among the genes whose expression in retinal ganglion cells was altered by KUS treatment in the N-methyl-d-aspartic acid (NMDA) injury model, we focused on two genes, endothelin-1 (Edn1) and endothelin receptor type B (Ednrb), whose expression was up-regulated by NMDA and down-regulated by KUS treatment. First, we confirmed that the expression of Edn1 and Ednrb was upregulated by NMDA and suppressed by KUS administration in mice retinae. Next, to clarify the influence of KUSs on cell viability in relation to the endothelin signaling, cell viability was examined with or without antagonists or agonists of endothelin and with or without KUS in 661W retinal cells under stress conditions. KUS showed a significant protective effect under glucose-free conditions and tunicamycin-induced stress. This protective effect was partially attenuated in the presence of an endothelin antagonist or agonist under glucose-free conditions. These results suggest that KUSs protect cells partially by suppressing the upregulated endothelin signaling under stress conditions.
• Method for Identifying Sequence Motifs in Pre-miRNAs for Small-Molecule Binding

  Yusuke Takashima; Asako Murata; Kei Iida; Ayako Sugai; Masatoshi Hagiwara; Kazuhiko Nakatani

  ACS CHEMICAL BIOLOGY 2022年09月 

  Non-coding RNAs are emerging targets for drug development because they are involved in various cellular processes. However, there are a few reliable design strategies for small molecules that can target RNAs. This paper reports a simple and efficient method to comprehensively analyze RNA motifs that can be bound by a specific small molecule. The method involves Dicer-mediated pre-miRNA cleavage and subsequent analysis of the reaction products by high-throughput sequencing. A pre-miRNA mutant library containing a randomized region at the Dicer deavage site was used as the substrate for the reaction. Sequencing analysis of the products of the reaction carried out in the presence or absence of a synthetic small molecule identified the pre-miRNA mutants whose Dicer-mediated deavage was significantly altered b y the addition of the small molecule. The binding of the small molecule to the identified pre-miRNA mutants was confirmed by surface plasmon resonance, demonstrating the feasibility of our method.
• Identification of the α2 chain of interleukin‐13 receptor as a potential biomarker for predicting castration resistance of prostate cancer using patient‐derived xenograft models

  Takahiro Nagai; Naoki Terada; Masato Fujii; Yasuhisa Nagata; Kozue Nakahara; Shoichiro Mukai; Kosuke Okasho; Yuki Kamiyama; Shusuke Akamatsu; Takashi Kobayashi; Kei Iida; Masatsugu Denawa; Masatoshi Hagiwara; Takahiro Inoue; Osamu Ogawa; Toshiyuki Kamoto

  Cancer Reports 6 2 2022年08月
• Therapeutic manipulation of IKBKAP mis-splicing with a small molecule to cure familial dysautonomia.

  Masahiko Ajiro; Tomonari Awaya; Young Jin Kim; Kei Iida; Masatsugu Denawa; Nobuo Tanaka; Ryo Kurosawa; Shingo Matsushima; Saiko Shibata; Tetsunori Sakamoto; Rolenz Studer; Adrian R Krainer; Masatoshi Hagiwara

  Nature communications 12 1 4507 - 4507 2021年07月 

  Approximately half of genetic disease-associated mutations cause aberrant splicing. However, a widely applicable therapeutic strategy to splicing diseases is yet to be developed. Here, we analyze the mechanism whereby IKBKAP-familial dysautonomia (FD) exon 20 inclusion is specifically promoted by a small molecule splice modulator, RECTAS, even though IKBKAP-FD exon 20 has a suboptimal 5' splice site due to the IVS20 + 6 T > C mutation. Knockdown experiments reveal that exon 20 inclusion is suppressed in the absence of serine/arginine-rich splicing factor 6 (SRSF6) binding to an intronic splicing enhancer in intron 20. We show that RECTAS directly interacts with CDC-like kinases (CLKs) and enhances SRSF6 phosphorylation. Consistently, exon 20 splicing is bidirectionally manipulated by targeting cellular CLK activity with RECTAS versus CLK inhibitors. The therapeutic potential of RECTAS is validated in multiple FD disease models. Our study indicates that small synthetic molecules affecting phosphorylation state of SRSFs is available as a new therapeutic modality for mechanism-oriented precision medicine of splicing diseases.
• CDC2-like (CLK) protein kinase inhibition as a novel targeted therapeutic strategy in prostate cancer

  Simon Uzor; Sean R. Porazinski; Ling Li; Bethany Clark; Masahiko Ajiro; Kei Iida; Masatoshi Hagiwara; Abdullah A. Alqasem; Claire M. Perks; Ian D. Wilson; Sebastian Oltean; Michael R. Ladomery

  Scientific Reports 11 1 7963 - 7963 2021年04月 [査読有り]
   

  Dysregulation of alternative splicing is a feature of cancer, both in aetiology and progression. It occurs because of mutations in splice sites or sites that regulate splicing, or because of the altered expression and activity of splice factors and of splice factor kinases that regulate splice factor activity. Recently the CDC2-like kinases (CLKs) have attracted attention due to their increasing involvement in cancer. We measured the effect of the CLK inhibitor, the benzothiazole TG003, on two prostate cancer cell lines. TG003 reduced cell proliferation and increased apoptosis in PC3 and DU145 cells. Conversely, the overexpression of CLK1 in PC3 cells prevented TG003 from reducing cell proliferation. TG003 slowed scratch closure and reduced cell migration and invasion in a transwell assay. TG003 decisively inhibited the growth of a PC3 cell line xenograft in nude mice. We performed a transcriptomic analysis of cells treated with TG003. We report widespread and consistent changes in alternative splicing of cancer-associated genes including CENPE, ESCO2, CKAP2, MELK, ASPH and CD164 in both HeLa and PC3 cells. Together these findings suggest that targeting CLKs will provide novel therapeutic opportunities in prostate cancer.
• 急性網膜神経節細胞障害モデルを用いたVCP ATPase阻害剤の神経保護メカニズム

  日下 真実; 長谷川 智子; 池田 華子; 岩井 祥子; 飯田 慶; 垣塚 彰; 辻川 明孝

  日本眼科学会雑誌 125 臨増 174 - 174 (公財)日本眼科学会 2021年03月
• Improvement of Moloney murine leukemia virus reverse transcriptase thermostability by introducing a disulfide bridge in the ribonuclease H region

  Yutaro Narukawa; Mako Kandabashi; Tongyang Li; Misato Baba; Haruka Hara; Kenji Kojima; Kei Iida; Takayoshi Hiyama; Sho Yokoe; Tomomi Yamazaki; Teisuke Takita; Kiyoshi Yasukawa

  Protein Engineering, Design and Selection 34 gzab006  2021年02月 [査読有り]
   

  Moloney murine leukemia virus (MMLV) reverse transcriptase (RT) is widely used in research and clinical diagnosis. Improvement of MMLV RT thermostability has been an important topic of research for increasing the efficiency of cDNA synthesis. In this study, we attempted to increase MMLV RT thermostability by introducing a disulfide bridge in its RNase H region using site-directed mutagenesis. Five variants were designed, focusing on the distance between the two residues to be mutated into cysteine. The variants were expressed in Escherichia coli and purified. A551C/T662C was determined to be the most thermostable variant.
• S1PR3–G12-biased agonist ALESIA targets cancer metabolism and promotes glucose starvation

  Masayasu Toyomoto; Asuka Inoue; Kei Iida; Masatsugu Denawa; Isao Kii; Francois Marie Ngako Kadji; Takayuki Kishi; Dohyun Im; Tatsuro Shimamura; Hiroshi Onogi; Suguru Yoshida; So Iwata; Junken Aoki; Takamitsu Hosoya; Masatoshi Hagiwara

  Cell Chemical Biology S2451-9456 21 00004  2021年02月 [査読有り]
  
• Identification of Qk as a Glial Precursor Cell Marker that Governs the Fate Specification of Neural Stem Cells to a Glial Cell Lineage

  Akihide Takeuchi; Yuji Takahashi; Kei Iida; Motoyasu Hosokawa; Koichiro Irie; Mikako Ito; J.B. Brown; Kinji Ohno; Kinichi Nakashima; Masatoshi Hagiwara

  Stem Cell Reports 15 4 883 - 897 2020年10月 [査読有り]
   

  During brain development, neural stem cells (NSCs) initially produce neurons and change their fate to generate glias. While the regulation of neurogenesis is well characterized, specific markers for glial precursor cells (GPCs) and the master regulators for gliogenesis remain unidentified. Accumulating evidence suggests that RNA-binding proteins (RBPs) have significant roles in neuronal development and function, as they comprehensively regulate the expression of target genes in a cell-type-specific manner. We systematically investigated the expression profiles of 1,436 murine RBPs in the developing mouse brain and identified quaking (Qk) as a marker of the putative GPC population. Functional analysis of the NSC-specific Qk-null mutant mouse revealed the key role of Qk in astrocyte and oligodendrocyte generation and differentiation from NSCs. Mechanistically, Qk upregulates gliogenic genes via quaking response elements in their 3' untranslated regions. These results provide crucial directions for identifying GPCs and deciphering the regulatory mechanisms of gliogenesis from NSCs.
• Multilateral Bioinformatics Analyses Reveal the Function-Oriented Target Specificities and Recognition of the RNA-Binding Protein SFPQ

  Kei Iida; Masatoshi Hagiwara; Akihide Takeuchi

  iScience 23 7 101325 - 101325 2020年07月 [査読有り]
  
• Effect of VCP modulators on gene expression profiles of retinal ganglion cells in an acute injury mouse model.

  Tomoko Hasegawa; Hanako Ohashi Ikeda; Norimoto Gotoh; Kei Iida; Sachiko Iwai; Noriko Nakano; Akira Kakizuka; Akitaka Tsujikawa

  Scientific reports 10 1 4251 - 4251 2020年03月 [査読有り]
   

  In glaucoma, retinal ganglion cells are damaged, leading to the progressive constriction of the visual field. We have previously shown that the valosin-containing protein (VCP) modulators, Kyoto University Substance (KUS)121 and KUS187, prevent the death of retinal ganglion cells in animal models of glaucoma, including the one generated by N-methyl-D-aspartate (NMDA)-induced neurotoxicity. KUSs appeared to avert endoplasmic reticulum (ER) stress by maintaining ATP levels, resulting in the protection of ganglion cells from cell death. To further elucidate the protective mechanisms of KUSs, we examined gene expression profiles in affected ganglion cells. We first injected KUS-treated mice with NMDA and then isolated the affected retinal ganglion cells using fluorescence-activated cell sorting. Gene expression in the cells was quantified using a next-generation sequencer. Resultantly, we found that KUS121 upregulated several genes involved in energy metabolism. In addition, we observed the upregulation of Zfp667, which has been reported to suppress apoptosis-related genes and prevent cell death. These results further support the suitability of KUS121 as a therapeutic drug in protecting retinal ganglion cells in ophthalmic disorders, such as glaucoma.
• Sfpq-KOマウスをモデルとした骨格筋代謝-筋量制御ネットワークの解析

  細川 元靖; 武内 章英; 谷端 淳; 飯田 慶; 武田 伸一; 萩原 正敏

  日本筋学会学術集会プログラム・抄録集 5回 157 - 157 (一社)日本筋学会 2019年08月
• Integrative network analysis reveals biological pathways associated with Williams syndrome

  Ryo Kimura; Vivek Swarup; Kiyotaka Tomiwa; Michael J. Gandal; Neelroop N. Parikshak; Yasuko Funabiki; Masatoshi Nakata; Tomonari Awaya; Takeo Kato; Kei Iida; Shin Okazaki; Kanae Matsushima; Toshihiro Kato; Toshiya Murai; Toshio Heike; Daniel H. Geschwind; Masatoshi Hagiwara

  Journal of Child Psychology and Psychiatry 60 5 585 - 598 2019年05月 [査読有り]
   

  BACKGROUND: Williams syndrome (WS) is a neurodevelopmental disorder that has been attributed to heterozygous deletions in chromosome 7q11.23 and exhibits a variety of physical, cognitive, and behavioral features. However, the genetic basis of this phenotypic variability is unclear. In this study, we identified genetic clues underlying these complex phenotypes. METHODS: Neurobehavioral function was assessed in WS patients and healthy controls. Total RNA was extracted from peripheral blood and subjected to microarray analysis, RNA-sequencing, and qRT-PCR. Weighted gene co-expression network analysis was performed to identify specific alterations related to intermediate disease phenotypes. To functionally interpret each WS-related module, gene ontology and disease-related gene enrichment were examined. We also investigated the micro (mi)RNA expression profiles and miRNA co-expression networks to better explain the regulation of the transcriptome in WS. RESULTS: Our analysis identified four significant co-expression modules related to intermediate WS phenotypes. Notably, the three upregulated WS-related modules were composed exclusively of genes located outside the 7q11.23 region. They were significantly enriched in genes related to B-cell activation, RNA processing, and RNA transport. BCL11A, which is known for its association with speech disorders and intellectual disabilities, was identified as one of the hub genes in the top WS-related module. Finally, these key upregulated mRNA co-expression modules appear to be inversely correlated with a specific downregulated WS-related miRNA co-expression module. CONCLUSIONS: Dysregulation of the mRNA/miRNA network involving genes outside of the 7q11.23 region is likely related to the complex phenotypes observed in WS patients.
• Loss of RNA-Binding Protein Sfpq Causes Long-Gene Transcriptopathy in Skeletal Muscle and Severe Muscle Mass Reduction with Metabolic Myopathy

  Motoyasu Hosokawa; Akihide Takeuchi; Jun Tanihata; Kei Iida; Shin'ichi Takeda; Masatoshi Hagiwara

  iScience 13 229 - 242 2019年03月 [査読有り]
   

  Growing evidences are suggesting that extra-long genes in mammals are vulnerable for full-gene length transcription and dysregulation of long genes is a mechanism underlying human genetic disorders. How long-distance transcription is achieved is a fundamental question to be elucidated. In previous study, we had discovered that RNA-binding protein SFPQ preferentially binds to long pre-mRNAs and specifically regulates the cluster of neuronal genes >100 kbp. Here we investigated the roles of SFPQ for long gene expression, target specificities, and also physiological functions in skeletal muscle. Loss of Sfpq selectively downregulated genes >100 kbp including Dystrophin, which is 2.26 Mbp in length. Sfpq knockout (KO) mice showed progressive muscle mass reduction and metabolic myopathy characterized by glycogen accumulation and decreased abundance of mitochondrial oxidative phosphorylation complexes. Functional clustering analysis identified energy metabolism pathway genes as SFPQ's targets. These findings indicate target gene specificities and tissue-specific physiological functions of SFPQ in skeletal muscle.
• Versatility of RNA-Binding Proteins in Living Cells

  Riki Kurokawa; Akihide Takeuchi; Nobuyuki Shiina; Masato Katahira; Takefumi Yamashita; Yoko Matsuno; Keisuke Hitachi; Shinsuke Ishigaki; Nesreen Haamad; Ryoma Yoneda; Naomi Ueda; Kei Iida; Motoyasu Hosokawa; Masatoshi Hagiwara; Mamiko Iida; Tsukasa Mashima; Yudai Yamaoki; Masatomo So; Takashi Nagata; Gen Sobue; Keiko Kondo; Hiroki Watanabe; Takayuki Uchihashi

  Biomedical Sciences 5 1 7 - 7 2019年 [査読有り]
  
• Accurate fidelity analysis of the reverse transcriptase by a modified next-generation sequencing.

  Hiroyuki Okano; Misato Baba; Ryota Hidese; Kei Iida; Tongyang Li; Kenji Kojima; Teisuke Takita; Itaru Yanagihara; Shinsuke Fujiwara; Kiyoshi Yasukawa

  Enzyme and microbial technology 115 81 - 85 2018年08月 [査読有り]
   

  We evaluated fidelity of various reverse transcriptases (RTs) by a novel method with modified next-generation sequencing (NGS). In the optimized condition, one NGS run could handle cDNA products from multiple cDNA synthesis reactions performed at different conditions. This was achieved using a primer containing not only the tag of 14 randomized bases to label each cDNA molecule but also a tag of five bases to label each reaction condition. With this method, we quantitated the error rates of 44 cDNA synthesis reactions by retroviral RTs or genetically engineered DNA polymerases with RT activity under different conditions. The results indicated that high concentrations of MgCl2, Mn(OCOCH3)2, and dNTP decrease the fidelity and that these effects are more pronounced in reactions using RT from human immunodeficiency virus type 1. This is the first report about a precise fidelity monitoring of various RTs by a direct sequence determination.
• Synaptic N6-methyladenosine (m6A) epitranscriptome reveals functional partitioning of localized transcripts

  Daria Merkurjev; Wan-Ting Hong; Kei Iida; Ikumi Oomoto; Belinda J. Goldie; Hitoshi Yamaguti; Takayuki Ohara; Shin-ya Kawaguchi; Tomoo Hirano; Kelsey C. Martin; Matteo Pellegrini; Dan Ohtan Wang

  Nature Neuroscience 1 - 11 2018年06月 [査読有り]
   

  A localized transcriptome at the synapse facilitates synapse-, stimulus- and transcript-specific local protein synthesis in response to neuronal activity. While enzyme-mediated mRNA modifications are known to regulate cellular mRNA turnover, the role of these modifications in regulating synaptic RNA has not been studied. We established low-input m6A-sequencing of synaptosomal RNA to determine the chemically modified local transcriptome in healthy adult mouse forebrains and identified 4,469 selectively enriched m6A sites in 2,921 genes as the synaptic m6A epitranscriptome (SME). The SME is functionally enriched in synthesis and modulation of tripartite synapses and in pathways implicated in neurodevelopmental and neuropsychiatric diseases. Interrupting m6A-mediated regulation via knockdown of readers in hippocampal neurons altered expression of SME member Apc, resulting in synaptic dysfunction including immature spine morphology and dampened excitatory synaptic transmission concomitant with decreased clusters of postsynaptic density-95 (PSD-95) and decreased surface expression of AMPA receptor subunit GluA1. Our findings indicate that chemical modifications of synaptic mRNAs critically contribute to synaptic function.
• SINC-seq: correlation of transient gene expressions between nucleus and cytoplasm reflects single-cell physiology.

  Mahmoud N Abdelmoez; Kei Iida; Yusuke Oguchi; Hidekazu Nishikii; Ryuji Yokokawa; Hidetoshi Kotera; Sotaro Uemura; Juan G Santiago; Hirofumi Shintaku

  Genome biology 19 1 66 - 66 2018年06月 [査読有り]
   

  We report a microfluidic system that physically separates nuclear RNA (nucRNA) and cytoplasmic RNA (cytRNA) from a single cell and enables single-cell integrated nucRNA and cytRNA-sequencing (SINC-seq). SINC-seq constructs two individual RNA-seq libraries, nucRNA and cytRNA, per cell, quantifies gene expression in the subcellular compartments, and combines them to create novel single-cell RNA-seq data. Leveraging SINC-seq, we discover distinct natures of correlation among cytRNA and nucRNA that reflect the transient physiological state of single cells. These data provide unique insights into the regulatory network of messenger RNA from the nucleus toward the cytoplasm at the single-cell level.
• SINC-seq: correlation of transient gene expressions between nucleus and cytoplasm reflects single-cell physiology.

  Abdelmoez MN; Iida K; Oguchi Y; Nishikii H; Yokokawa R; Kotera H; Uemura S; Santiago JG; Shintaku H

  Genome biology 19 1 66 - 66 2018年06月 [査読有り]
   

  We report a microfluidic system that physically separates nuclear RNA (nucRNA) and cytoplasmic RNA (cytRNA) from a single cell and enables single-cell integrated nucRNA and cytRNA-sequencing (SINC-seq). SINC-seq constructs two individual RNA-seq libraries, nucRNA and cytRNA, per cell, quantifies gene expression in the subcellular compartments, and combines them to create novel single-cell RNA-seq data. Leveraging SINC-seq, we discover distinct natures of correlation among cytRNA and nucRNA that reflect the transient physiological state of single cells. These data provide unique insights into the regulatory network of messenger RNA from the nucleus toward the cytoplasm at the single-cell level.
• Loss of Sfpq Causes Long-Gene Transcriptopathy in the Brain.

  Akihide Takeuchi; Kei Iida; Toshiaki Tsubota; Motoyasu Hosokawa; Masatsugu Denawa; J B Brown; Kensuke Ninomiya; Mikako Ito; Hiroshi Kimura; Takaya Abe; Hiroshi Kiyonari; Kinji Ohno; Masatoshi Hagiwara

  Cell reports 23 5 1326 - 1341 2018年05月 [査読有り]
   

  Genes specifically expressed in neurons contain members with extended long introns. Longer genes present a problem with respect to fulfilment of gene length transcription, and evidence suggests that dysregulation of long genes is a mechanism underlying neurodegenerative and psychiatric disorders. Here, we report the discovery that RNA-binding protein Sfpq is a critical factor for maintaining transcriptional elongation of long genes. We demonstrate that Sfpq co-transcriptionally binds to long introns and is required for sustaining long-gene transcription by RNA polymerase II through mediating the interaction of cyclin-dependent kinase 9 with the elongation complex. Phenotypically, Sfpq disruption caused neuronal apoptosis in developing mouse brains. Expression analysis of Sfpq-regulated genes revealed specific downregulation of developmentally essential neuronal genes longer than 100 kb in Sfpq-disrupted brains; those genes are enriched in associations with neurodegenerative and psychiatric diseases. The identified molecular machinery yields directions for targeted investigations of the association between long-gene transcriptopathy and neuronal diseases.
• Next-generation sequencing-based analysis of reverse transcriptase fidelity.

  Kiyoshi Yasukawa; Kei Iida; Hiroyuki Okano; Ryota Hidese; Misato Baba; Itaru Yanagihara; Kenji Kojima; Teisuke Takita; Shinsuke Fujiwara

  Biochemical and biophysical research communications 492 2 147 - 153 2017年10月 [査読有り]
   

  In this study, we devised a simple and rapid method to analyze fidelity of reverse transcriptase (RT) using next-generation sequencing (NGS). The method comprises a cDNA synthesis reaction from standard RNA with a primer containing a tag of 14 randomized bases and the RT to be tested, PCR using high-fidelity DNA polymerase, and NGS. By comparing the sequence of each read with the reference sequence, mutations were identified. The mutation can be identified to be due to an error introduced by either cDNA synthesis, PCR, or NGS based on whether the sequence reads with the same tag contain the same mutation or not. The error rates in cDNA synthesis with Moloney murine leukemia virus (MMLV) RT thermostable variant MM4 or the recently developed 16-tuple variant of family B DNA polymerase with RT activity, RTX, from Thermococcus kodakarensis, were 0.75-1.0 × 10-4 errors/base, while that in the reaction with the wild-type human immunodeficiency virus type 1 (HIV-1) RT was 2.6 × 10-4 errors/base. Overall, our method could precisely evaluate the fidelity of various RTs with different reaction conditions in a high-throughput manner without the use of expensive optics and troublesome adaptor ligation.
• Novel Stress-Inducible Antisense RNAs of Protein-Coding Loci Are Synthesized by RNA-Dependent RNA Polymerase.

  Akihiro Matsui; Kei Iida; Maho Tanaka; Katsushi Yamaguchi; Kayoko Mizuhashi; Jong-Myong Kim; Satoshi Takahashi; Norio Kobayashi; Shuji Shigenobu; Kazuo Shinozaki; Motoaki Seki

  Plant physiology 175 1 457 - 472 2017年09月 [査読有り]
   

  Our previous study identified approximately 6,000 abiotic stress-responsive noncoding transcripts existing on the antisense strand of protein-coding genes and implied that a type of antisense RNA was synthesized from a sense RNA template by RNA-dependent RNA polymerase (RDR). Expression analyses revealed that the expression of novel abiotic stress-induced antisense RNA on 1,136 gene loci was reduced in the rdr1/2/6 mutants. RNase protection indicated that the RD29A antisense RNA and other RDR1/2/6-dependent antisense RNAs are involved in the formation of dsRNA. The accumulation of stress-inducible antisense RNA was decreased and increased in dcp5 and xrn4, respectively, but not changed in dcl2/3/4, nrpd1a and nrpd1b RNA-seq analyses revealed that the majority of the RDR1/2/6-dependent antisense RNA loci did not overlap with RDR1/2/6-dependent 20-30 nt RNA loci. Additionally, rdr1/2/6 mutants decreased the degradation rate of the sense RNA and exhibited arrested root growth during the recovery stage following a drought stress, whereas dcl2/3/4 mutants did not. Collectively, these results indicate that RDRs have stress-inducible antisense RNA synthesis activity and a novel biological function that is different from the known endogenous small RNA pathways from protein-coding genes. These data reveal a novel mechanism of RNA regulation during abiotic stress response that involves complex RNA degradation pathways.
• DNA hypermethyation and silencing of PITX1 correlated with advanced stage and poor postoperative prognosis of esophageal squamous cell carcinoma.

  Otsubo T; Yamada K; Hagiwara T; Oshima K; Iida K; Nishikata K; Toyoda T; Igari T; Nohara K; Yamashita S; Hattori M; Dohi T; Kawamura YI

  Oncotarget 8 48 84434 - 84448 2017年09月 [査読有り]
   

  Esophageal squamous cell carcinoma (ESCC) is associated with the accumulation of genetic and epigenetic changes in the background mucosa. Dysregulated DNA methylation is known to lead to the inactivation of tumor suppressor genes and the activation of oncogenes. To identify the genes whose expression is perturbed by abnormal DNA methylation in ESCC, integrative transcriptomics by serial analysis of gene expression (SAGE) and methylome sequencing by methyl-DNA immunoprecipitation (MeDIP) analysis were performed. We found 159 genes with significantly decreased expression in ESCC compared to that in noncancerous esophageal mucosa. MeDIP-seq analysis identified hypermethylation in the promoter region of 56 of these genes. Using surgically resected tissues of 40 cases, we confirmed that the paired-like homeodomain 1 (PITX1) gene was hypermethylated in ESCC compared to that in normal tissues (P < 0.0001) by pyrosequencing. PITX1 overexpression in ESCC cell lines inhibited cell growth and colony formation, whereas PITX1 knockdown accelerated cell growth. A PITX1-transfected ESCC cell line, KYSE30, formed smaller tumors in nude mice than in mock-transfected cells. Hypermethylation of PITX1 was associated with tumor depth (P = 0.0011) and advanced tumor stage (P = 0.0052) and predicted poor survival in ESCC (hazard ratio, 0.1538; 95% confidence interval, 0.03159-0.7488; P = 0.0169). In this study, we found a novel tumor suppressor gene of ESCC, PITX1, which is silenced by DNA hypermethylation. Downregulation of PITX1 contributes to the growth and progression of ESCC. Hypermethylation of the PITX1 in ESCC correlated with tumor progression and advanced stage cancer, and may predict a poor prognosis.
• Retinoid derivative Tp80 exhibits anti-hepatitis C virus activity through restoration of GI-GPx expression

  Bao Ngoc Nguyen; Yukiko Okuno; Masahiko Ajiro; Kei Iida; Masatsugu Denawa; Makoto Yamamoto; Naoya Sakamoto; Hiroyuki Kagechika; Masatoshi Hagiwara

  Journal of Medical Virology 89 7 1224 - 1234 2017年07月 [査読有り]
   

  Hepatitis C virus (HCV) is a positive-sense single-stranded RNA virus with an estimated infection in ∼180 million people worldwide, and its chronic infection leads to development of cirrhosis and hepatocellular carcinoma. Although recent development of direct acting antiviral (DAA) compounds improved anti-HCV regimens, alternative therapeutic compounds are still demanded due to an expected emergence of escape mutants for those DAAs. In order to identify novel anti-HCV agents, we conducted chemical library screening for 2086 compounds using HCV Rep-Feo reporter replicon in Huh7 hepatoma cells. Our screening identified retinoid derivative Tp80, which inhibits replication of HCV Rep-Feo (genotype 1b) and JFH1 HCV (genotype 2a) with 0.62 μM and 1.0 μM, respectively, of 50% effective concentration (EC50), at which cytotoxicity is not evident for host hepatocytes. Subsequent transcriptome profiling revealed Tp80 exhibits anti-HCV activity through restoration of gastrointestinal glutathione peroxidase (GI-GPx), suppression of which is responsible for HCV-induced oxidative stress to facilitate HCV replication. Furthermore, comparison of Tp80 with other retinoid derivatives revealed Tp80 shows best potency in both GI-GPx restoration and anti-HCV activity among compounds we examined. In conclusion, our current study provides Tp80 as a promising candidate of anti-HCV compound, suppressing host cellular oxidative stress through a restoration of GI-GPx.
• Synthetic ligand promotes gene expression by affecting GC sequence in promoter

  Saki Matsumoto; Kei Iida; Asako Murata; Masatsugu Denawa; Masatoshi Hagiwara; Kazuhiko Nakatani

  Bioorganic and Medicinal Chemistry Letters 27 15 3391 - 3394 2017年 [査読有り]
   

  A naphthyridine carbamate tetramer (NCT8) is a synthetic compound, which selectively binds to nucleic acids containing CGG/CGG sequence. Although NCT8 is a promising compound for a wide range of DNA and RNA based biotechnology such as modulation of specific gene expression, little is known about its behavior in human cells. In the present study, we investigated the changes induced in gene expression by NCT8. Genes differentially expressed in the presence of NCT8 in HeLa cells were identified by whole-transcriptome analysis. The whole-transcriptome analysis showed that NCT8 significantly induced up-regulation of specific genes, whose promoter region has GC-rich sequence.
• Sm-like protein-mediated RNA metabolism is required for heat stress tolerance in Arabidopsis

  Masanori Okamoto; Akihiro Matsui; Maho Tanaka; Taeko Morosawa; Junko Ishida; Kei Iida; Yoshiki Mochizuki; Tetsuro Toyoda; Motoaki Seki

  Frontiers in Plant Science 7 2016 2016年07月 [査読有り]
   

  Sm-like proteins play multiple functions in RNA metabolism, which is essential for biological processes such as stress responses in eukaryotes. The Arabidopsis thaliana sad1 mutant has a mutation of sm-like protein 5 (LSM5) and shows impaired drought and salt stress tolerances. The lsm5/sad1 mutant also showed hypersensitivity to heat stress. GFP-fused LSM5/SAD1 was localized in the nucleus under optimal growth conditions. After heat stress treatment, GFP-fused LSM5/SAD1 fluorescence was also observed as small cytoplasmic dots, in addition to nuclear localization. Whole genome transcriptome analysis revealed that many genes in Arabidopsis were drastically changed in response to heat stress. More heat-responsive genes were highly expressed in lsm5/sad1 mutant at both 2 and 6 h after heat stress treatment. Additionally, intron-retained and capped transcripts accumulated in the lsm5/sad1 mutant after heat stress treatment. In this study, we also identified non-Arabidopsis Genome Initiative transcripts that were expressed from unannotated regions. Most of these transcripts were antisense transcripts, and many capped non-AGI transcripts accumulated in the lsm5/sad1 mutant during heat stress treatment. These results indicated that LSM5/SAD1 functions to degrade aberrant transcripts through appropriate mRNA splicing and decapping, and precise RNA metabolic machinery is required for heat stress tolerance.
• On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase

  Hans Ienasescu; Kang Li; Robin Andersson; Morana Vitezic; Sarah Rennie; Yun Chen; Kristoffer Vitting-Seerup; Emil Lagoni; Mette Boyd; Jette Bornholdt; Michiel J. L. De Hoon; Hideya Kawaji; Timo Lassmann; Yoshihide Hayashizaki; Alistair R. R. Forrest; Piero Carninci; Albin Sandelin

  Database 2016 1 - 10 2016年01月 [査読有り]
   

  Genomics consortia have produced large datasets profiling the expression of genes, micro-RNAs, enhancers and more across human tissues or cells. There is a need for intuitive tools to select subsets of such data that is the most relevant for specific studies. To this end, we present SlideBase, a web tool which offers a new way of selecting genes, promoters, enhancers and microRNAs that are preferentially expressed/used in a specified set of cells/tissues, based on the use of interactive sliders. With the help of sliders, SlideBase enables users to define custom expression thresholds for individual cell types/ tissues, producing sets of genes, enhancers etc. which satisfy these constraints. Changes in slider settings result in simultaneous changes in the selected sets, updated in real time. SlideBase is linked to major databases from genomics consortia, including FANTOM, GTEx, The Human Protein Atlas and BioGPS.
• Next-generation sequencing-based comprehensive molecular analysis of 43 Japanese patients with cone and cone-rod dystrophies.

  Maho Oishi, Akio Oishi, Norimoto Gotoh, Ken Ogino, Koichiro Higasa, Kei Iida, Yukiko Makiyama, Satoshi Morooka, Fumihiko Matsuda, Nagahisa Yoshimura

  Molecular vision 22 150 - 160 2016年 [査読有り]
   

  Purpose: To investigate the efficacy of targeted exome sequencing for mutational screening of Japanese patients with cone dystrophy (CD) or cone-rod dystrophy (CRD). Methods: DNA samples from 43 Japanese patients with CD or CRD were sequenced using an exome-sequencing panel targeting all 193 known inherited eye disease genes and next-generation sequencing methodologies. Subsequently, candidate variants were screened using systematic data analyses, and their potential pathogenicity was assessed using distinct filtering approaches, which included the frequency of the variants in normal populations, in silico prediction tools, and cosegregation. Results: Causative mutations were detected in 12 patients with CD or CRD (27.9%). In total, 14 distinct mutations were identified in the genes ABCA4, CDHR1, CRB1, CRX, GUCY2D, KCNV2, PROM1, PRPH2, and RDH5, including four novel mutations, c.3050+1G>A in ABCA4, c.386A>G in CDHR1, c.652+1_652+4del in CRB1, and c.454G>A in KCNV2. Moreover, a putative pathogenic mutation was identified in RGS9BP, a gene recognized as the source of bradyopsia. Conclusions: Targeted exome sequencing effectively identified causative mutations in Japanese patients with CD or CRD. The results confirmed the heterogeneity of the genes responsible for CD and CRD in Japanese populations, as well as the efficacy of targeted exome sequencing-based screening of patients with inherited retinal degeneration.
• The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome

  Laurence D. Hurst; Avazeh T. Ghanbarian; Alistair R. R. Forrest; FANTOM consortium; Lukasz Huminiecki; Michael Rehli; J. Kenneth Baillie; Michiel J. L. de Hoon; Vanja Haberle; Timo Lassmann; Ivan V. Kulakovskiy; Marina Lizio; Masayoshi Itoh; Robin Andersson; Christopher J. Mungall; Terrence F. Meehan; Sebastian Schmeier; Nicolas Bertin; Mette Jørgensen; Emmanuel Dimont; Erik Arner; Christian Schmidl; Ulf Schaefer; Yulia A. Medvedeva; Charles Plessy; Morana Vitezic; Jessica Severin; Colin A. Semple; Yuri Ishizu; Robert S. Young; Margherita Francescatto; Intikhab Alam; Davide Albanese; Gabriel M. Altschuler; Takahiro Arakawa; John A.C. Archer; Peter Arner; Magda Babina; Sarah Baker; Piotr J. Balwierz; Anthony G. Beckhouse; Swati-Bhatt Pradhan; Judith A. Blake; Antje Blumenthal; Beatrice Bodega; Alessandro Bonetti; James Briggs; Frank Brombacher; A. Maxwell Burroughs; Andrea Califano; Carlo V. Cannistraci; Daniel Carbajo; Yun Chen; Marco Chierici; Yari Ciani; Hans C. Clevers; Emiliano Dalla; Carrie A. Davis; Michael Detmar; Alexander D. Diehl; Taeko Dohi; Finn Drabløs; Albert S.B. Edge; Matthias Edinger; Karl Ekwall; Mitsuhiro Endoh; Hideki Enomoto; Michela Fagiolini; Lynsey Fairbairn; Hai Fang; Mary C. Farach-Carson; Geoffrey J. Faulkner; Alexander V. Favorov; Malcolm E. Fisher; Martin C. Frith; Rie Fujita; Shiro Fukuda; Cesare Furlanello; Masaaki Furuno; Jun-ichi Furusawa; Teunis B. Geijtenbeek; Andrew Gibson; Thomas Gingeras; Daniel Goldowitz; Julian Gough; Sven Guhl; Reto Guler; Stefano Gustincich; Thomas J. Ha; Masahide Hamaguchi; Mitsuko Hara; Matthias Harbers; Jayson Harshbarger; Akira Hasegawa; Yuki Hasegawa; Takehiro Hashimoto; Meenhard Herlyn; Kelly J. Hitchens; Shannan J. Ho Sui; Oliver M. Hofmann; Ilka Hoof; Fumi Hori; Lukasz Huminiecki; Kei Iida; Tomokatsu Ikawa; Boris R. Jankovic; Hui Jia; Anagha Joshi; Giuseppe Jurman; Bogumil Kaczkowski; Chieko Kai; Kaoru Kaida; Ai Kaiho; Kazuhiro Kajiyama; Mutsumi-Katayama Kanamori; Artem S. Kasianov; Takeya Kasukawa; Shintaro Katayama; Sachi Kato; Shuji Kawaguchi; Hiroshi Kawamoto; Yuki I. Kawamura; Tsugumi Kawashima; Judith S. Kempfle; Tony J. Kenna; Juha Kere; Levon M. Khachigian; Toshio Kitamura; S. Peter Klinken; Alan J. Knox; Miki Kojima; Soichi Kojima; Naoto Kondo; Haruhiko Koseki; Shigeo Koyasu; Sarah Krampitz; Atsutaka Kubosaki; Andrew T. Kwon; Jeroen F.J. Laros; Weonju Lee; Andreas Lennartsson; Kang Li; Berit Lilje; Leonard Lipovich; Alan-sim Mackay; Riichiroh Manabe; Jessica C. Mar; Benoit Marchand; Anthony Mathelier; Niklas Mejhert; Alison Meynert; Yosuke Mizuno; David A. de Lima Morais; Hiromasa Morikawa; Mitsuru Morimoto; Kazuyo Moro; Efthymios Motakis; Hozumi Motohashi; Christine L. Mummery; Mitsuyoshi Murata; Sayaka-Sato Nagao; Yutaka Nakachi; Fumio Nakahara; Toshiyuki Nakamura; Yukio Nakamura; Kenichi Nakazato; Erik van Nimwegen; Noriko Ninomiya; Hiromi Nishiyori; Shohei Noma; Tadasuke Nozaki; Soichi Ogishima; Naganari Ohkura; Hiroko Ohmiya; Hiroshi Ohno; Mitsuhiro Ohshima; Mariko-Hatakeyama Okada; Yasushi Okazaki; Valerio Orlando; Dmitry A. Ovchinnikov; Arnab Pain; Robert Passier; Margaret Patrikakis; Helena Persson; Silvano Piazza; James G.D. Prendergast; Owen J.L. Rackham; Jordan A. Ramilowski; Mamoon Rashid; Timothy Ravasi; Patrizia Rizzu; Marco Roncador; Sugata Roy; Morten B. Rye; Eri Saijyo; Antti Sajantila; Akiko Saka; Shimon Sakaguchi; Mizuho Sakai; Hiroki Sato; Hironori Satoh; Suzana Savvi; Alka Saxena; Claudio Schneider; Erik A. Schultes; Gundula G. Schulze-Tanzil; Anita Schwegmann; Thierry Sengstag; Guojun Sheng; Hisashi Shimoji; Yishai Shimoni; Jay W. Shin; Christophe Simon; Daisuke Sugiyama; Takaaki Sugiyama; Masanori Suzuki; Naoko Suzuki; Rolf K. Swoboda; Peter A.C. 't Hoen; Michihira Tagami; Naoko Takahashi; Jun Takai; Hiroshi Tanaka; Hideki Tatsukawa; Zuotian Tatum; Mark Thompson; Hiroo Toyoda; Tetsuro Toyoda; Eivind Valen; Marc van de Wetering; Linda M. van den Berg; Roberto Verardo; Dipti Vijayan; Ilya E. Vorontsov; Wyeth W. Wasserman; Shoko Watanabe; Christine A. Wells; Louise N. Winteringham; Ernst Wolvetang; Emily J. Wood; Yoko Yamaguchi; Masayuki Yamamoto; Misako Yoneda; Yohei Yonekura; Shigehiro Yoshida; Suzan E. Zabierowski; Peter G. Zhang; Xiaobei Zhao; Silvia Zucchelli; Kim M. Summers; Harukazu Suzuki; Carsten O. Daub; Jun Kawai; Peter Heutink; Winston Hide; Tom C. Freeman; Boris Lenhard; Vladimir B. Bajic; Martin S. Taylor; Vsevolod J. Makeev; Albin Sandelin; David A. Hume; Piero Carninci; Yoshihide Hayashizaki

  PLoS Biology 13 12 e1002315 - e1002315 2015年12月 [査読有り]
   

  X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression profiles of X-linked genes. Tissues whose tissue-specific genes are very highly expressed (e.g., secretory tissues, tissues abundant in structural proteins) are also tissues in which gene expression is relatively rare on the X chromosome. These trends cannot be fully accounted for in terms of alternative models of biased expression. In conclusion, the notion that it is hard for genes on the Therian X to be highly expressed, owing to transcriptional traffic jams, provides a simple yet robustly supported rationale of many peculiar features of X’s gene content, gene expression, and evolution.
• Deciphering targeting rules of splicing modulator compounds: Case of TG003

  Maki Sakuma; Kei Iida; Masatoshi Hagiwara

  BMC Molecular Biology 16 1 2015年09月 [査読有り]
   

  Background: Recent advances in the development of small chemical compounds that can modulate RNA splicing brought excitement to the field of splicing-targeting therapy. Splicing-targeting therapy tries to ameliorate the disease by altering the exon combination of transcripts to reduce the undesired effect of genetic mutations. However, the knowledge and tools to understand factors contributing to splicing modulator compound sensitivity have been lacking. Our goal was to establish a method to characterize sequence features found in compound sensitive exons. Results: Here we developed a comparative transcriptomic approach to explore features that make an exon sensitive to a chemical compound. In this study, we chose TG003, a potential drug for Duchenne muscular dystrophy, and performed RNA-sequencing on samples from human and mouse skeletal muscle cells, with and without TG003 treatments. We compared TG003 responsiveness between homologous exon pairs and identified 21 pairs in which human exons were skip-enhanced but not mouse exons. We compared the sequence features splice site scores, number of splicing factor binding sites, and properties of branch sequence and polypyrimidine tracts, and found that polypyrimidine tracts were stronger (longer stretches and richer content of consecutive polypyrimidine) in the mouse TG003 insensitive exons. We also compared the features between TG003 skip-enhanced and insensitive exons within the species, and discovered that human TG003 skip-enhanced exons were shorter and had less splicing factor binding sites than the group of human TG003 insensitive exons. Mouse insensitive exons homologous to human TG003 skip-enhanced exons shared these properties. Our results suggested that these features are prerequisites for TG003 skip-enhanced exons and weak polypyrimidine tracts are defining features, which were supported by a decision tree analysis on all cassette exons in human. Conclusions: In this study we established a comparative transcriptomic approach, which shed lights on how small chemical compounds modulate RNA splicing. The results described here was the first attempt to decipher the targeting rules of a splicing modulator compound. We expect that this approach would contribute to the precise understanding of the mechanism of TG003-induced splicing modulation, expand target diseases of splicing modulators in general, as well as the development of new splicing modulators.
• Loss of Arabidopsis 5′–3′ Exoribonuclease AtXRN4 Function Enhances Heat Stress Tolerance of Plants Subjected to Severe Heat Stress

  Anh Hai Nguyen; Akihiro Matsui; Maho Tanaka; Kayoko Mizunashi; Kentaro Nakaminami; Makoto Hayashi; Kei Iida; Tetsuro Toyoda; Dong Van Nguyen; Motoaki Seki

  Plant and Cell Physiology 56 9 1762 - 1772 2015年09月 [査読有り]
  
• Rectifier of aberrant mRNA splicing recovers tRNA modification in familial dysautonomia

  Mayumi Yoshida; Naoyuki Kataoka; Kenjyo Miyauchi; Kenji Ohe; Kei Iida; Suguru Yoshida; Takayuki Nojima; Yukiko Okuno; Hiroshi Onogi; Tomomi Usui; Akihide Takeuchi; Takamitsu Hosoya; Tsutomu Suzuki; Masatoshi Hagiwara

  Proceedings of the National Academy of Sciences of the United States of America 112 9 2764 - 2769 2015年03月 [査読有り]
   

  Familial dysautonomia (FD), a hereditary sensory and autonomic neuropathy, is caused by missplicing of exon 20, resulting from an intronic mutation in the inhibitor of kappa light polypeptide gene enhancer in B cells, kinase complex-associated protein (IKBKAP) gene encoding IKK complex-associated protein (IKAP)/elongator protein 1 (ELP1). A newly established splicing reporter assay allowed us to visualize pathogenic splicing in cells and to screen small chemicals for the ability to correct the aberrant splicing of IKBKAP. Using this splicing reporter, we screened our chemical libraries and identified a compound, rectifier of aberrant splicing (RECTAS), that rectifies the aberrant IKBKAP splicing in cells from patients with FD. Here, we found that the levels of modified uridine at the wobble position in cytoplasmic tRNAs are reduced in cells from patients with FD and that treatment with RECTAS increases the expression of IKAP and recovers the tRNA modifications. These findings suggest that the missplicing of IKBKAP results in reduced tRNA modifications in patients with FD and that RECTAS is a promising therapeutic drug candidate for FD.
• Comprehensive Molecular Diagnosis of a Large Cohort of Japanese Retinitis Pigmentosa and Usher Syndrome Patients by Next-Generation Sequencing

  Maho Oishi; Akio Oishi; Norimoto Gotoh; Ken Ogino; Koichiro Higasa; Kei Iida; Yukiko Makiyama; Satoshi Morooka; Fumihiko Matsuda; Nagahisa Yoshimura

  Investigative Opthalmology & Visual Science 55 11 7369 - 7369 2014年11月 [査読有り]
   

  PURPOSE: Retinitis pigmentosa (RP), a major cause of blindness in developed countries, has multiple causative genes; its prevalence differs by ethnicity. Usher syndrome is the most common form of syndromic RP and is accompanied by hearing impairment. Although molecular diagnosis is challenging, recent technological advances such as targeted high-throughput resequencing are efficient screening tools. METHODS: We performed comprehensive molecular testing in 329 Japanese RP and Usher syndrome patients by using a custom capture panel that covered the coding exons and exon/intron boundaries of all 193 known inherited eye disease genes combined with Illumina HiSequation 2500. Candidate variants were screened using systematic data analyses, and their potential pathogenicity was assessed according to the frequency of the variants in normal populations, in silico prediction tools, and compatibility with known phenotypes or inheritance patterns. RESULTS: Molecular diagnoses were made in 115/317 RP patients (36.3%) and 6/12 Usher syndrome patients (50%). We identified 104 distinct mutations, including 66 novel mutations. EYS, USH2A, and RHO were common causative genes. In particular, mutations in EYS accounted for 15.0% of the autosomal recessive/simplex RP patients or 10.7% of the entire RP cohort. Among the 189 previously reported mutations detected in the current study, 55 (29.1%) were found commonly in Japanese or other public databases and were excluded from molecular diagnoses. CONCLUSIONS: By screening a large cohort of patients, this study catalogued the genetic variations involved in RP and Usher syndrome in a Japanese population and highlighted the different distribution of causative genes among populations.
• CDK9 inhibitor FIT-039 prevents replication of multiple DNA viruses

  Makoto Yamamoto; Hiroshi Onogi; Isao Kii; Suguru Yoshida; Kei Iida; Hiroyuki Sakai; Minako Abe; Toshiaki Tsubota; Nobutoshi Ito; Takamitsu Hosoya; Masatoshi Hagiwara

  Journal of Clinical Investigation 124 8 3479 - 3488 2014年08月 [査読有り]
   

  A wide range of antiviral drugs is currently available however, drug-resistant viruses have begun to emerge and represent a potential public health risk. Here, we explored the use of compounds that inhibit or interfere with the action of essential host factors to prevent virus replication. In particular, we focused on the cyclin-dependent kinase 9 (CDK9) inhibitor, FIT-039, which suppressed replication of a broad spectrum of DNA viruses through inhibition of mRNA transcription. Specifically, FIT-039 inhibited replication of herpes simplex virus 1 (HSV-1), HSV-2, human adenovirus, and human cytomegalovirus in cultured cells, and topical application of FIT-039 ointment suppressed skin legion formation in a murine HSV-1 infection model. FIT-039 did not affect cell cycle progression or cellular proliferation in host cells. Compared with the general CDK inhibitor flavopiridol, transcriptome analyses of FIT-039-treated cells revealed that FIT-039 specifically inhibited CDK9. Given at concentrations above the inhibitory concentration, FIT-039 did not have a cytotoxic effect on mammalian cells. Importantly, administration of FIT-039 ameliorated the severity of skin lesion formation in mice infected with an acyclovir-resistant HSV-1, without noticeable adverse effects. Together, these data indicate that FIT-039 has potential as an antiviral agent for clinical therapeutics.
• A promoter-level mammalian expression atlas.

  Alistair R R Forrest; Hideya Kawaji; Michael Rehli; J Kenneth Baillie; Michiel J L de Hoon; Vanja Haberle; Timo Lassmann; Ivan V Kulakovskiy; Marina Lizio; Masayoshi Itoh; Robin Andersson; Christopher J Mungall; Terrence F Meehan; Sebastian Schmeier; Nicolas Bertin; Mette Jørgensen; Emmanuel Dimont; Erik Arner; Christian Schmidl; Ulf Schaefer; Yulia A Medvedeva; Charles Plessy; Morana Vitezic; Jessica Severin; Colin A Semple; Yuri Ishizu; Robert S Young; Margherita Francescatto; Intikhab Alam; Davide Albanese; Gabriel M Altschuler; Takahiro Arakawa; John A C Archer; Peter Arner; Magda Babina; Sarah Rennie; Piotr J Balwierz; Anthony G Beckhouse; Swati Pradhan-Bhatt; Judith A Blake; Antje Blumenthal; Beatrice Bodega; Alessandro Bonetti; James Briggs; Frank Brombacher; A Maxwell Burroughs; Andrea Califano; Carlo V Cannistraci; Daniel Carbajo; Yun Chen; Marco Chierici; Yari Ciani; Hans C Clevers; Emiliano Dalla; Carrie A Davis; Michael Detmar; Alexander D Diehl; Taeko Dohi; Finn Drabløs; Albert S B Edge; Matthias Edinger; Karl Ekwall; Mitsuhiro Endoh; Hideki Enomoto; Michela Fagiolini; Lynsey Fairbairn; Hai Fang; Mary C Farach-Carson; Geoffrey J Faulkner; Alexander V Favorov; Malcolm E Fisher; Martin C Frith; Rie Fujita; Shiro Fukuda; Cesare Furlanello; Masaaki Furino; Jun-ichi Furusawa; Teunis B Geijtenbeek; Andrew P Gibson; Thomas Gingeras; Daniel Goldowitz; Julian Gough; Sven Guhl; Reto Guler; Stefano Gustincich; Thomas J Ha; Masahide Hamaguchi; Mitsuko Hara; Matthias Harbers; Jayson Harshbarger; Akira Hasegawa; Yuki Hasegawa; Takehiro Hashimoto; Meenhard Herlyn; Kelly J Hitchens; Shannan J Ho Sui; Oliver M Hofmann; Ilka Hoof; Furni Hori; Lukasz Huminiecki; Kei Iida; Tomokatsu Ikawa; Boris R Jankovic; Hui Jia; Anagha Joshi; Giuseppe Jurman; Bogumil Kaczkowski; Chieko Kai; Kaoru Kaida; Ai Kaiho; Kazuhiro Kajiyama; Mutsumi Kanamori-Katayama; Artem S Kasianov; Takeya Kasukawa; Shintaro Katayama; Sachi Kato; Shuji Kawaguchi; Hiroshi Kawamoto; Yuki I Kawamura; Tsugumi Kawashima; Judith S Kempfle; Tony J Kenna; Juha Kere; Levon M Khachigian; Toshio Kitamura; S Peter Klinken; Alan J Knox; Miki Kojima; Soichi Kojima; Naoto Kondo; Haruhiko Koseki; Shigeo Koyasu; Sarah Krampitz; Atsutaka Kubosaki; Andrew T Kwon; Jeroen F J Laros; Weonju Lee; Andreas Lennartsson; Kang Li; Berit Lilje; Leonard Lipovich; Alan Mackay-Sim; Ri-ichiroh Manabe; Jessica C Mar; Benoit Marchand; Anthony Mathelier; Niklas Mejhert; Alison Meynert; Yosuke Mizuno; David A de Lima Morais; Hiromasa Morikawa; Mitsuru Morimoto; Kazuyo Moro; Efthymios Motakis; Hozumi Motohashi; Christine L Mummery; Mitsuyoshi Murata; Sayaka Nagao-Sato; Yutaka Nakachi; Fumio Nakahara; Toshiyuki Nakamura; Yukio Nakamura; Kenichi Nakazato; Erik van Nimwegen; Noriko Ninomiya; Hiromi Nishiyori; Shohei Noma; Shohei Noma; Tadasuke Noazaki; Soichi Ogishima; Naganari Ohkura; Hiroko Ohimiya; Hiroshi Ohno; Mitsuhiro Ohshima; Mariko Okada-Hatakeyama; Yasushi Okazaki; Valerio Orlando; Dmitry A Ovchinnikov; Arnab Pain; Robert Passier; Margaret Patrikakis; Helena Persson; Silvano Piazza; James G D Prendergast; Owen J L Rackham; Jordan A Ramilowski; Mamoon Rashid; Timothy Ravasi; Patrizia Rizzu; Marco Roncador; Sugata Roy; Morten B Rye; Eri Saijyo; Antti Sajantila; Akiko Saka; Shimon Sakaguchi; Mizuho Sakai; Hiroki Sato; Suzana Savvi; Alka Saxena; Claudio Schneider; Erik A Schultes; Gundula G Schulze-Tanzil; Anita Schwegmann; Thierry Sengstag; Guojun Sheng; Hisashi Shimoji; Yishai Shimoni; Jay W Shin; Christophe Simon; Daisuke Sugiyama; Takaai Sugiyama; Masanori Suzuki; Naoko Suzuki; Rolf K Swoboda; Peter A C 't Hoen; Michihira Tagami; Naoko Takahashi; Jun Takai; Hiroshi Tanaka; Hideki Tatsukawa; Zuotian Tatum; Mark Thompson; Hiroo Toyodo; Tetsuro Toyoda; Elvind Valen; Marc van de Wetering; Linda M van den Berg; Roberto Verado; Dipti Vijayan; Ilya E Vorontsov; Wyeth W Wasserman; Shoko Watanabe; Christine A Wells; Louise N Winteringham; Ernst Wolvetang; Emily J Wood; Yoko Yamaguchi; Masayuki Yamamoto; Misako Yoneda; Yohei Yonekura; Shigehiro Yoshida; Susan E Zabierowski; Peter G Zhang; Xiaobei Zhao; Silvia Zucchelli; Kim M Summers; Harukazu Suzuki; Carsten O Daub; Jun Kawai; Peter Heutink; Winston Hide; Tom C Freeman; Boris Lenhard; Vladimir B Bajic; Martin S Taylor; Vsevolod J Makeev; Albin Sandelin; David A Hume; Piero Carninci; Yoshihide Hayashizaki

  Nature 507 7493 462 - 70 2014年03月 [査読有り]
   

  Regulated transcription controls the diversity, developmental pathways and spatial organization of the hundreds of cell types that make up a mammal. Using single-molecule cDNA sequencing, we mapped transcription start sites (TSSs) and their usage in human and mouse primary cells, cell lines and tissues to produce a comprehensive overview of mammalian gene expression across the human body. We find that few genes are truly 'housekeeping', whereas many mammalian promoters are composite entities composed of several closely separated TSSs, with independent cell-type-specific expression profiles. TSSs specific to different cell types evolve at different rates, whereas promoters of broadly expressed genes are the most conserved. Promoter-based expression analysis reveals key transcription factors defining cell states and links them to binding-site motifs. The functions of identified novel transcripts can be predicted by coexpression and sample ontology enrichment analyses. The functional annotation of the mammalian genome 5 (FANTOM5) project provides comprehensive expression profiles and functional annotation of mammalian cell-type-specific transcriptomes with wide applications in biomedical research.
• An atlas of active enhancers across human cell types and tissues

  Robin Andersson; Claudia Gebhard; Irene Miguel-Escalada; Ilka Hoof; Jette Bornholdt; Mette Boyd; Yun Chen; Xiaobei Zhao; Christian Schmidl; Takahiro Suzuki; Evgenia Ntini; Erik Arner; Eivind Valen; Kang Li; Lucia Schwarzfischer; Dagmar Glatz; Johanna Raithel; Berit Lilje; Nicolas Rapin; Frederik Otzen Bagger; Mette Jorgensen; Peter Refsing Andersen; Nicolas Bertin; Owen Rackham; A. Maxwell Burroughs; J. Kenneth Baillie; Yuri Ishizu; Yuri Shimizu; Erina Furuhata; Shiori Maeda; Yutaka Negishi; Christopher J. Mungall; Terrence F. Meehan; Timo Lassmann; Masayoshi Itoh; Hideya Kawaji; Naoto Kondo; Jun Kawai; Andreas Lennartsson; Carsten O. Daub; Peter Heutink; David A. Hume; Torben Heick Jensen; Harukazu Suzuki; Yoshihide Hayashizaki; Ferenc Mueller; Alistair R. R. Forrest; Piero Carninci; Michael Rehli; Albin Sandelin

  NATURE 507 7493 455 - + 2014年03月 [査読有り]
   

  Enhancers control the correct temporal and cell-type-specific activation of gene expression in multicellular eukaryotes. Knowing their properties, regulatory activity and targets is crucial to understand the regulation of differentiation and homeostasis. Here we use the FANTOM5 panel of samples, covering the majority of human tissues and cell types, to produce an atlas of active, in vivo-transcribed enhancers. We show that enhancers share properties with CpG-poor messenger RNA promoters but produce bidirectional, exosome-sensitive, relatively short unspliced RNAs, the generation of which is strongly related to enhancer activity. The atlas is used to compare regulatory programs between different cells at unprecedented depth, to identify disease-associated regulatory single nucleotide polymorphisms, and to classify cell-type-specific and ubiquitous enhancers. We further explore the utility of enhancer redundancy, which explains gene expression strength rather than expression patterns. The online FANTOM5 enhancer atlas represents a unique resource for studies on cell-type-specific enhancers and gene regulation.
• RARGE II: An integrated phenotype database of arabidopsis mutant traits using a controlled vocabulary

  Kenji Akiyama; Atsushi Kurotani; Kei Iida; Takashi Kuromori; Kazuo Shinozaki; Tetsuya Sakurai

  Plant and Cell Physiology 55 1 e4 - e4 2014年01月 [査読有り]
   

  Arabidopsis thaliana is one of the most popular experimental plants. However, only 40% of its genes have at least one experimental Gene Ontology (GO) annotation assigned. Systematic observation of mutant phenotypes is an important technique for elucidating gene functions. Indeed, several large-scale phenotypic analyses have been performed and have generated phenotypic data sets from many Arabidopsis mutant lines and overexpressing lines, which are freely available online. Since each Arabidopsis mutant line database uses individual phenotype expression, the differences in the structured term sets used by each database make it difficult to compare data sets and make it impossible to search across databases. Therefore, we obtained publicly available information for a total of 66,209 Arabidopsis mutant lines, including loss-of-function (RATM and TARAPPER) and gain-of-function (AtFOX and OsFOX) lines, and integrated the phenotype data by mapping the descriptions onto Plant Ontology (PO) and Phenotypic Quality Ontology (PATO) terms. This approach made it possible to manage the four different phenotype databases as one large data set. Here, we report a publicly accessible web-based database, the RIKEN Arabidopsis Genome Encyclopedia II (RARGE II http://rarge-v2.psc.riken.jp/), in which all of the data described in this study are included. Using the database, we demonstrated consistency (in terms of protein function) with a previous study and identified the presumed function of an unknown gene. We provide examples of AT1G21600, which is a subunit in the plastid-encoded RNA polymerase complex, and AT5G56980, which is related to the jasmonic acid signaling pathway. © 2013 The Author.
• Small open reading frames associated with morphogenesis are hidden in plant genomes

  K. Hanada; M. Higuchi-Takeuchi; M. Okamoto; T. Yoshizumi; M. Shimizu; K. Nakaminami; R. Nishi; C. Ohashi; K. Iida; M. Tanaka; Y. Horii; M. Kawashima; K. Matsui; T. Toyoda; K. Shinozaki; M. Seki; M. Matsui

  Proceedings of the National Academy of Sciences 110 6 2395 - 2400 2013年02月 [査読有り]
  
• Positional correlation analysis improves reconstruction of full-length transcripts and alternative isoforms from noisy array signals or short reads

  Shuji Kawaguchi; Kei Iida; Erimi Harada; Kousuke Hanada; Akihiro Matsui; Masanori Okamoto; Kazuo Shinozaki; Motoaki Seki; Tetsuro Toyoda

  Bioinformatics 28 7 929 - 937 2012年04月 [査読有り]
   

  Motivation: A reconstruction of full-length transcripts observed by next-generation sequencer or tiling arrays is an essential technique to know all phenomena of transcriptomes. Several techniques of the reconstruction have been developed. However, problems of high-level noises and biases still remain and interrupt the reconstruction. A method is required that is robust against noise and bias and correctly reconstructs transcripts regardless of equipment used.Results: We propose a completely new statistical method that reconstructs full-length transcripts and can be applied on both next-generation sequencers and tiling arrays. The method called ARTADE2 analyzes 'positional correlation', meaning correlations of expression values for every combination on genomic positions of multiple transcriptional data. ARTADE2 then reconstructs full-length transcripts using a logistic model based on the positional correlation and the Markov model. ARTADE2 elucidated 17 591 full-length transcripts from 55 transcriptome datasets and showed notable performance compared with other recent prediction methods. Moreover, 1489 novel transcripts were discovered. We experimentally tested 16 novel transcripts, among which 14 were confirmed by reverse transcription-polymerase chain reaction and sequence mapping. The method also showed notable performance for reconstructing of mRNA observed by a next-generation sequencer. Moreover, the positional correlation and factor analysis embedded in ARTADE2 successfully detected regions at which alternative isoforms may exist, and thus are expected to be applied for discovering transcript biomarkers for a wide range of disciplines including preemptive medicine. © The Author(s) 2012. Published by Oxford University Press.
• ARTADE2DB: Improved statistical inferences for arabidopsis gene functions and structure predictions by dynamic structure-based dynamic expression (DSDE) analyses

  Kei Iida; Shuji Kawaguchi; Norio Kobayashi; Yuko Yoshida; Manabu Ishii; Erimi Harada; Kousuke Hanada; Akihiro Matsui; Masanori Okamoto; Junko Ishida; Maho Tanaka; Taeko Morosawa; Motoaki Seki; Tetsuro Toyoda

  Plant and Cell Physiology 52 2 254 - 264 2011年02月 [査読有り]
   

  Recent advances in technologies for observing high-resolution genomic activities, such as whole-genome tiling arrays and high-throughput sequencers, provide detailed information for understanding genome functions. However, the functions of 50 of known Arabidopsis thaliana genes remain unknown or are annotated only on the basis of static analyses such as protein motifs or similarities. In this paper, we describe dynamic structure-based dynamic expression (DSDE) analysis, which sequentially predicts both structural and functional features of transcripts. We show that DSDE analysis inferred gene functions 12 more precisely than static structure-based dynamic expression (SSDE) analysis or conventional co-expression analysis based on previously determined gene structures of A. thaliana. This result suggests that more precise structural information than the fixed conventional annotated structures is crucial for co-expression analysis in systems biology of transcriptional regulation and dynamics. Our DSDE method, ARabidopsis Tiling-Array-based Detection of Exons version 2 and over-representation analysis (ARTADE2-ORA), precisely predicts each gene structure by combining two statistical analyses: a probe-wise co-expression analysis of multiple transcriptome measurements and a Markov model analysis of genome sequences. ARTADE2-ORA successfully identified the true functions of about 90 of functionally annotated genes, inferred the functions of 98 of functionally unknown genes and predicted 1,489 new gene structures and functions. We developed a database ARTADE2DB that integrates not only the information predicted by ARTADE2-ORA but also annotations and other functional information, such as phenotypes and literature citations, and is expected to contribute to the study of the functional genomics of A. thaliana. URL: http://artade.org. © 2011 The Author.
• RAS1, a quantitative trait locus for salt tolerance and ABA sensitivity in Arabidopsis

  Z. Ren; Z. Zheng; V. Chinnusamy; J. Zhu; X. Cui; K. Iida; J.-K. Zhu

  Proceedings of the National Academy of Sciences 107 12 5669 - 5674 2010年03月 [査読有り]
  
• Posmed-plus: An intelligent search engine that inferentially integrates cross-species information resources for molecular breeding of plants

  Yuko Makita; Norio Kobayashi; Yoshiki Mochizuki; Yuko Yoshida; Satomi Asano; Naohiko Heida; Mrinalini Deshpande; Rinki Bhatia; Akihiro Matsushima; Manabu Ishii; Shuji Kawaguchi; Kei Iida; Kosuke Hanada; Takashi Kuromori; Motoaki Seki; Kazuo Shinozaki; Tetsuro Toyoda

  Plant and Cell Physiology 50 7 1249 - 1259 2009年07月 [査読有り]
   

  Molecular breeding of crops is an efficient way to upgrade plant functions useful to mankind. A key step is forward genetics or positional cloning to identify the genes that confer useful functions. In order to accelerate the whole research process, we have developed an integrated database system powered by an intelligent data-retrieval engine termed PosMed-plus (Positional Medline for plant upgrading science), allowing us to prioritize highly promising candidate genes in a given chromosomal interval(s) of Arabidopsis thaliana and rice, Oryza sativa. By inferentially integrating cross-species information resources including genomes, transcriptomes, proteomes, localizomes, phenomes and literature, the system compares a user's query, such as phenotypic or functional keywords, with the literature associated with the relevant genes located within the interval. By utilizing orthologous and paralogous correspondences, PosMed-plus efficiently integrates cross-species information to facilitate the ranking of rice candidate genes based on evidence from other model species such as Arabidopsis. PosMed-plus is a plant science version of the PosMed system widely used by mammalian researchers, and provides both a powerful integrative search function and a rich integrative display of the integrated databases. PosMed-plus is the first cross-species integrated database that inferentially prioritizes candidate genes for forward genetics approaches in plant science, and will be expanded for wider use in plant upgrading in many species.
• Analysis of multiple occurrences of alternative splicing events in arabidopsis thaliana using novel sequenced full-length cDNAs

  Kei Iida; Kaoru Fukami-Kobayashi; Atsushi Toyoda; Yoshiyuki Sakaki; Masatomo Kobayashi; Motoaki Seki; Kazuo Shinozaki

  DNA Research 16 3 155 - 164 2009年06月 [査読有り]
   

  Alternative splicing (AS) is a mechanism by which multiple types of mature mRNAs are generated from a single pre-mature mRNA. In this study, we completely sequenced 1800 full-length cDNAs from Arabidopsis thaliana, which had 5′ and/or 3′ sequences that were previously found to have AS events or alternative transcription start sites. Unexpectedly, these sequences gave us further evidence of AS, as 601 out of 1800 transcripts showed novel AS events. We focused on the combination patterns of multiple AS events within individual genes. Interestingly, some specific AS event combination patterns tended to appear more frequently than expected. The two most common patterns were: (i) alternative donor-0∼12 times of exon skips-alternative acceptor and (ii) several times (∼8) of retained introns. We also found that multiple AS events in a transcript tend to have the same effects concerning the length of the mature mRNA. Our current results are consistent with our previous observations, which showed changes in AS profiles under different conditions, and suggest the involvement of hypothetical cis- and trans-acting factors in the regulation of AS events.
• Bioinformatics analysis suggests base modifications of tRNAs and miRNAs in Arabidopsis thaliana

  Kei Iida; Hailing Jin; Jian-Kang Zhu

  BMC Genomics 10 1 155 - 155 2009年04月 [査読有り]
   

  Background: Modifications of RNA bases have been found in some mRNAs and non-coding RNAs including rRNAs, tRNAs, and snRNAs, where modified bases are important for RNA function. Little is known about RNA base modifications in Arabidopsis thaliana. Results: In the current work, we carried out a bioinformatics analysis of RNA base modifications in tRNAs and miRNAs using large numbers of cDNA sequences of small RNAs (sRNAs) generated with the 454 technology and the massively parallel signature sequencing (MPSS) method. We looked for sRNAs that map to the genome sequence with one-base mismatch (OMM), which indicate candidate modified nucleotides. We obtained 1,187 sites with possible RNA base modifications supported by both 454 and MPSS sequences. Seven hundred and three of these sites were within tRNA loci. Nucleotide substitutions were frequently located in the T arm (substitutions from A to U or G), upstream of the D arm (from G to C, U, or A), and downstream of the D arm (from G to U). The positions of major substitution sites corresponded with the following known RNA base modifications in tRNAs: N1-methyladenosine (m1A), N2-methylguanosine (m2G), and N2-N2-methylguanosine (m22G). Conclusion: These results indicate that our bioinformatics method successfully detected modified nucleotides in tRNAs. Using this method, we also found 147 substitution sites in miRNA loci. As with tRNAs, substitutions from A to U or G and from G to C, U, or A were common, suggesting that base modifications might be similar in tRNAs and miRNAs. We suggest that miRNAs contain modified bases and such modifications might be important for miRNA maturation and/or function. © 2009 Iida et al licensee BioMed Central Ltd.
• ROS3 is an RNA-binding protein required for DNA demethylation in Arabidopsis

  ZHENG X. W.

  Nature 455 7217 1259 - 1262 2008年10月 [査読有り]
  
• The Arabidopsis NFYA5 transcription factor is regulated transcription ally and posttranscriptionally to promote drought resistance

  LI W.X.

  Plant Cell 20 8 2238 - 2251 2008年08月 [査読有り]
  
• On the expansion of the pentatricopeptide repeat gene family in plants

  Nicholas O'Toole; Mitsuru Hattori; Charles Andres; Kei Iida; Claire Lurin; Christian Schmitz-Linneweber; Mamoru Sugita; Ian Small

  Molecular Biology and Evolution 25 6 1120 - 1128 2008年06月 [査読有り]
   

  Pentatricopeptide repeat (PPR) proteins form a huge family in plants (450 members in Arabidopsis and 477 in rice) defined by tandem repetitions of characteristic sequence motifs. Some of these proteins have been shown to play a role in posttranscriptional processes within organelles, and they are thought to be sequence-specific RNA-binding proteins. The origins of this family are obscure as they are lacking from almost all prokaryotes, and the spectacular expansion of the family in land plants is equally enigmatic. In this study, we investigate the growth of the family in plants by undertaking a genome-wide identification and comparison of the PPR genes of 3 organisms: the flowering plants Arabidopsis thaliana and Oryza sativa and the moss Physcomitrella patens. A large majority of the PPR genes in each of the flowering plants are intron less. In contrast, most of the 103 PPR genes in Physcomitrella are intron rich. A phylogenetic comparison of the PPR genes in all 3 species shows similarities between the intron-rich PPR genes in Physcomitrella and the few intron-rich PPR genes in higher plants. Intron-poor PPR genes in all 3 species also display a bias toward a position of their introns at their 5′ ends. These results provide compelling evidence that one or more waves of retrotransposition were responsible for the expansion of the PPR gene family in flowering plants. The differing numbers of PPR proteins are highly correlated with differences in organellar RNA editing between the 3 species. © The Author 2008. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved.
• Alternative splicing at NAGNAG acceptor sites shares common properties in land plants and mammals

  Kei Iida; Masafumi Shionyu; Yasuhiro Suso

  MOLECULAR BIOLOGY AND EVOLUTION 25 4 709 - 718 2008年04月 [査読有り]
   

  In recent years, several papers have reported that a special type of alternative splicing (AS) event occurs at the tandem 3' splice site, termed the "NAGNAG acceptor." This type of AS event (termed AS-NAGNAG) is well studied in both human and mouse. To illustrate the significance of AS-NAGNAG events, we focused on their occurrence in Arabidopsis thaliana and Oryza sativa (rice). Our study is the first genome-wide approach examining AS-NAGNAG events in land plants. Based on transcripts and genomic sequences, we found 321 and 372 AS-NAGNAG events in Arabidopsis and rice, respectively. These events were significantly enriched in genes encoding DNA-binding proteins, and more than half of all AS-NAGNAG events affected polar amino acid residues. The observed properties of AS-NAGNAG events in plants were similar to those seen in mammals. These results showed that AS-NAGNAG events may provide a mechanism for fine-tuning of DNA-binding proteins in both mammals and land plants. We found 7 gene groups of AS-NAGNAG events that were conserved between Arabidopsis and rice, including 2 groups for RNA-binding proteins. Conservation of the events for RNA-binding proteins is a property also seen in mammals. Furthermore, we found 23 gene groups containing AS-NAGNAG events that occurred in noncorresponding introns of homologous genes. They included 5 groups of DNA-binding proteins, whose number was larger than expected. We think there is a bias with which AS-NAGNAG events are fixed in genes for DNA-binding proteins. Our analysis showed that AS-NAGNAG events found in land plants share similar properties with those in mammals. Based on our results, we propose that AS-NAGNAG events are likely to be a common mechanism in the fine-tuning of protein functions, especially DNA/RNA-binding proteins, in both mammals and plants. Their role might contribute to the construction of complicated transcriptomes and proteomes in the evolutionary history of mammals and land plants.
• Genomic Analysis of Stress Respnse

  Motoaki Seki; Junko Ishida; Maiko Nakajima; Akiko Enju; Kei Iida; Masakazu Satou; Miki Fujita; Yoshihiro Narusaka; Mari Narusaka; Tetsuya Sakurai; Kenji Akiyama; Youko Oono; Ayako Kamei; Taishi Umezawa; Saho Mizukado; Kyonoshin Maruyama; Kazuko Yamaguchi-Shinozaki; Kazuo Shinozaki

  Plant Abiotic Stress 248 - 265 2007年11月 [査読有り]
  
• Assessing the monophyly of chlorophyll-c containing plastids by multi-gene phylogenies under the unlinked model conditions

  Kei Iida; Kiyotaka Takishita; Kazuhiko Ohshima; Yuji Inagaki

  MOLECULAR PHYLOGENETICS AND EVOLUTION 45 1 227 - 238 2007年10月 [査読有り]
   

  Recent multi-gene phylogenetic analyses of plastid-encoded genes have recovered a robust monophyly of chlorophyll-c containing plastids (Chl-c palstids) in cryptophytes, haptophytes, photosynthetic stramenopiles, and dinoflagellates. However, all the plast id multi-gene phylogenies published to date utilized the "linked" model, which ignores the heterogeneity of sequence evolution across genes in alignments. Both empirical and simulation studies show that, compared to the linked model, the "unlinked" model, which accounts for gene-specific evolution, can greatly improve multi-gene estimations. Here we newly sequenced 46 genes of Chl-c plastids, and examined the Chl-c plastid evolution by multi-gene analyses under the unlinked model. Unexpectedly, Chl-c plastid monophyly received only low to medium support in our analyses based on multi-gene data sets including up to 4829 alignment positions. Although we systematically surveyed and excluded the genes that could mislead estimation, the (inconclusive) support for Chl-c plastid monophyly was not significantly altered. We conclude that the estimates from the current plastid-encoded gene data are insufficient to resolve Chl-c plastid evolution with confidence, and are highly affected by genes subjected to the analyses, and methods for tree reconstruction applied. Thus, future data analyses of larger multi-gene data sets, preferentially under the unlinked model, are required to conclusively understand Chl-c plastid evolution. (c) 2007 Elsevier Inc. All rights reserved.
• Changes of alternative splicing profiles and its regulating system in Arabidopsis thaliana

  Kei Iida; Yasuhiro Suso; Mitiko Go

  PLANT AND CELL PHYSIOLOGY 48 S8 - S8 2007年
• Monitoring expression profiles of Arabidopsis genes during cold acclimation and deacclimation using DNA microarrays.

  Youko Oono; Motoaki Seki; Masakazu Satou; Kei Iida; Kenji Akiyama; Tetsuya Sakurai; Miki Fujita; Kazuko Yamaguchi-Shinozaki; Kazuo Shinozaki

  Functional & integrative genomics 6 3 212 - 34 2006年07月 [査読有り]
   

  A comparative analysis of gene expression profiles during cold acclimation and deacclimation is necessary to elucidate the molecular mechanisms of cold stress responses in higher plants. We analyzed gene expression profiles in the process of cold acclimation and deacclimation (recovery from cold stress) using two microarray systems, the 7K RAFL cDNA microarray and the Agilent 22K oligonucleotide array. By both microarray analyses, we identified 292 genes up-regulated and 320 genes down-regulated during deacclimation, and 445 cold up-regulated genes and 341 cold down-regulated genes during cold acclimation. Many genes up-regulated during deacclimation were found to be down-regulated during cold acclimation, and vice versa. The genes up-regulated during deacclimation were classified into (1) regulatory proteins involved in further regulation of signal transduction and gene expression and (2) functional proteins involved in the recovery process from cold-stress-induced damages and plant growth. We also applied expression profiling studies to identify the key genes involved in the biosynthesis of carbohydrates and amino acids that are known to play important roles in cold acclimation. We compared genes that are regulated during deacclimation with those regulated during rehydration after dehydration to discuss the similarity and difference of each recovery process.
• Survey of conserved alternative splicing events of mRNAs encoding SR proteins in land plants

  K Iida; M Go

  MOLECULAR BIOLOGY AND EVOLUTION 23 5 1085 - 1094 2006年05月 [査読有り]
   

  The serine/arginine-rich (SR) protein family plays an important role in constitutive and alternative splicing (AS). These proteins regulate AS in a tissue-specific and stress-responsive manner. Pre-mRNAs encoding SR proteins are often alternatively spliced, and these AS events may be important for the regulation of AS events of other pre-mRNAs. In this study, we analyzed AS events of SR proteins in Arabidopsis thaliana and Oryza sativa (rice). We found three sets of AS events conserved between Arabidopsis and rice. These conserved AS events were found in the plant-novel-SR protein, SC35-like (SCL), and two-Zn-knuckles-type 9G8 subfamilies. Each member of these subfamilies has at least one RNA recognition motif (RRM) and at least one intron in the RRM-encoded region. We found that the conserved AS events occurred in these introns and, in each case, the conserved AS events resulted in mature mRNAs encoding proteins with incomplete RRMs. To search for the evolutionary origin of these AS events, we analyzed SR proteins in Physcomitrella patens (moss) in addition to those in Arabidopsis and rice. We found moss homologues of the plant-novel-SR protein, SCL, and the two-Zn-knuckles-type 9G8 subfamilies in silico, and these homologues have long introns at the same location of the conserved AS sites in Arabidopsis and rice. Such long introns are quite specific for alternatively spliced introns concerning the Arabidopsis SR protein genes. The long introns found in the moss SR protein genes strongly suggested that conserved AS events in moss SR protein genes might be similar to those in Arabidopsis and rice. We traced the evolutionary origin of the conserved AS events to 400 MYA, when plants first invaded land. These events are likely important in the regulation of whole AS events and likely contribute to the complicated transcriptome described by AS. The complicated transcriptome created by regulated AS events might have provided plants tolerance against droughts or temperature shifts and given them the ability to live on land.
• Alternative splicing events of pre-mRNAs encoding transcription factors in Arabidopsis

  K Iida; M Go

  PLANT AND CELL PHYSIOLOGY 47 S49 - S49 2006年
• Arabidopsis whole genome expression profiling under abiotic stress conditions

  M Seki; J Ishida; T Morosawa; A Matsui; JM Kim; M Nakajima; A Enju; T To; K Iida; M Go; Y Mochizuki; Y Hasegawa; T Toyoda; K Shinozaki

  PLANT AND CELL PHYSIOLOGY 47 S49 - S49 2006年
• A flexible representation of omic knowledge for thorough analysis of microarray data

  Yoshikazu Hasegawa; Motoaki Seki; Yoshiki Mochizuki; Naohiko Heida; Katsura Hirosawa; Naoki Okamoto; Tetsuya Sakurai; Masakazu Satou; Kenji Akiyama; Kei Iida; Kisik Lee; Shigehiko Kanaya; Taku Demura; Kazuo Shinozaki; Akihiko Konagaya; Tetsuro Toyoda

  PLANT METHODS 2 1 2006年 [査読有り]
   

  Background: In order to understand microarray data reasonably in the context of other existing biological knowledge, it is necessary to conduct a thorough examination of the data utilizing every aspect of available omic knowledge libraries. So far, a number of bioinformatics tools have been developed. However, each of them is restricted to deal with one type of omic knowledge, e. g., pathways, interactions or gene ontology. Now that the varieties of omic knowledge are expanding, analysis tools need a way to deal with any type of omic knowledge. Hence, we have designed the Omic Space Markup Language (OSML) that can represent a wide range of omic knowledge, and also, we have developed a tool named GSCope3, which can statistically analyze microarray data in comparison with the OSML-formatted omic knowledge data. Results: In order to test the applicability of OSML to represent a variety of omic knowledge specifically useful for analysis of Arabidopsis thaliana microarray data, we have constructed a Biological Knowledge Library (BiKLi) by converting eight different types of omic knowledge into OSML-formatted datasets. We applied GSCope3 and BiKLi to previously reported A. thaliana microarray data, so as to extract any additional insights from the data. As a result, we have discovered a new insight that lignin formation resists drought stress and activates transcription of many water channel genes to oppose drought stress; and most of the 20S proteasome subunit genes show similar expression profiles under drought stress. In addition to this novel discovery, similar findings previously reported were also quickly confirmed using GSCope3 and BiKLi. Conclusion: GSCope3 can statistically analyze microarray data in the context of any OSML-represented omic knowledge. OSML is not restricted to a specific data type structure, but it can represent a wide range of omic knowledge. It allows us to convert new types of omic knowledge into datasets that can be used for microarray data analysis with GSCope3. In addition to BiKLi, by collecting various types of omic knowledge as OSML libraries, it becomes possible for us to conduct detailed thorough analysis from various biological viewpoints. GSCope3 and BiKLi are available for academic users at our web site http://omicspace.riken.jp.
• RARTF: Database and tools for complete sets of Arabidopsis transcription factors

  Kei Iida; Motoaki Seki; Tetsuya Sakurai; Masakazu Satou; Kenji Akiyama; Tetsuro Toyoda; Akihiko Konagaya; Kazuo Shinozaki

  DNA RESEARCH 12 4 247 - 256 2005年08月 [査読有り]
   

  More than 5% of all genes in the Arabidopsis thaliana genome have been assumed to code for transcription factors. However, it has been difficult to accurately identify them. To construct proper sets of transcription factors, we used PSI-BLAST and InterProScan, and also checked several families manually. Especially to determine major Arabidopsis transcription factors (MYB, AP2/EREBP, bHLH, NAC, MADS, bZIP, WRKY), we compared the PSI-BLAST search results with those in recent reports. Finally, we identified 1968 proteins as transcription factors (7.4% of all Arabidopsis genes). We established a database named RARTF (RIKEN Arabidopsis Transcription Factor database, http://rarge.gsc.riken.jp/rartf/) based on the identified transcription factors. In RARTF, we provide information on the functional motif of transcription factors, full-length cDNAs, alternative pre-mRNA splicing events and Ac/Ds transposon-tagged mutants. We also provide expression profiles of 400 transcription factor genes in six experiments. We will report expression profiles of all transcription factor genes in various plant tissues under various stress and hormone conditions in the near future.
• Function enhancement of RARGE

  K Akiyama; T Sakurai; M Satou; K Iida; M Seki; T Kuromori; T Ito; A Konagaya; T Toyoda; K Shinozaki

  PLANT AND CELL PHYSIOLOGY 46 S145 - S145 2005年
• Monitoring expression profiles of Arabidopsis Genes in the process of cold acclimation and deacclimation using DNA microarrays

  Y Oono; M Seki; M Satou; K Iida; K Akiyama; T Sakurai; M Fujita; K Yamaguchi-Shinozaki; K Shinozaki

  PLANT AND CELL PHYSIOLOGY 46 S118 - S118 2005年
• Expression profiling using Arabidopsis whole-genome regulatory gene oligo DNA microarray

  M Seki; J Ishida; K Iida; M Nakajima; A Enju; T Sakurai; A Kamei; Y Oono; T Umezawa; M Fujita; S Mizukado; Y Narusaka; M Narusaka; K Shinozaki

  PLANT AND CELL PHYSIOLOGY 46 S140 - S140 2005年
• RARGE: a large-scale database of RIKEN Arabidopsis resources ranging from transcriptome to phenome

  T Sakurai; M Satou; K Akiyama; K Iida; M Seki; T Kuromori; T Ito; A Konagaya; T Toyoda; K Shinozaki

  NUCLEIC ACIDS RESEARCH 33 DATABASE ISS. D647 - D650 2005年01月 [査読有り]
   

  The RIKEN Arabidopsis Genome Encyclopedia (RARGE) database houses information on biological resources ranging from transcriptome to phenome, including RIKEN Arabidopsis full-length (RAFL) complementary DNAs (cDNAs), their promoter regions, Dissociation (Ds) transposon-tagged lines and expression data from microarray experiments. RARGE provides tools for searching by resource code, sequence homology or keyword, and rapid access to detailed information on the resources. We have isolated 245946 RAFL cDNA clones and collected 11933 transposon-tagged lines, which are available from the RIKEN Bioresource Center and are stored in RARGE. The RARGE web interface can be accessed at http://rarge.gsc.riken.jp/. Additionally, we report 90 000 new RAFL cDNA clones here.
• 3P288 シロイヌナズナにおける低温ストレス下での選択的スプライシングの様相の変化(生命情報科学 B) 機能ゲノミクス)

  飯田 慶; 関 原明; 櫻井 哲也; 佐藤 将一; 秋山 顕治; 豊田 哲郎; 小長谷 明彦; 篠崎 一雄

  生物物理 44 S261  一般社団法人 日本生物物理学会 2004年
• Arabidopsis gene expression profiles during recovery process after low-temperature stress using microarray

  Y Oono; M Seki; M Satou; J Ishida; K Iida; T Sakurai; K Akiyama; K Yamaguchi-Shinozaki; K Shinozakib

  PLANT AND CELL PHYSIOLOGY 45 S120 - S120 2004年
• Full-length cDNAs for the discovery and annotation of genes in A. thaliana.

  Seki, M; Satou, M; Sakurai, T; Akiyama, K; Iida, K; Ishida, J; Nakajima, M; Enju, A; Narusaka, M; Fujita, M; Oono, Y; Yamaguchi-Shinozaki, K; Carninci, P; Kawai, J; Hayashizaki, Y; Shinozaki, K

  "Plant Functional Genomics (edited by Dario Leister)" Haworth's Food Products Press, Binghamton, New York. 3 - 22 2004年 [査読有り]
  
• RIKEN Arabidopsis full-length (RAFL) cDNA and its applications for expression profiling under abiotic stress conditions

  M Seki; M Satou; T Sakurai; K Akiyama; K Iida; J Ishida; M Nakajima; A Enju; M Narusaka; M Fujita; Y Oono; A Kamei; K Yamaguchi-Shinozaki; K Shinozaki

  JOURNAL OF EXPERIMENTAL BOTANY 55 395 213 - 223 2004年01月 [査読有り]
   

  Full-length cDNAs are essential for the correct annotation of genomic sequences and for the functional analysis of genes and their products. 155 144 RIKEN Arabidopsis full-length (RAFL) cDNA clones were isolated. The 3'-end expressed sequence tags (ESTs) of all 155 144 RAFL cDNAs were clustered into 14 668 non-redundant cDNA groups, about 60% of predicted genes. The sequence database of the RAFL cDNAs is useful for promoter analysis and the correct annotation of predicted transcription units and gene products. Recently, cDNA microarray analysis has been developed for quantitative analysis of global and simultaneous analysis of expression profiles. RAFL cDNA microarrays were prepared, containing independent full-length cDNA groups for analysing the expression profiles of genes under various stress- and hormone-treatment conditions and in various mutants and transgenic plants. In this review, recent progress on transcriptome analysis using the RAFL cDNA microarray is highlighted.
• Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences

  K Iida; M Seki; T Sakurai; M Satou; K Akiyama; T Toyoda; A Konagaya; K Shinozaki

  NUCLEIC ACIDS RESEARCH 32 17 5096 - 5103 2004年 [査読有り]
   

  We mapped RIKEN Arabidopsis full-length (RAFL) cDNAs to the Arabidopsis thaliana genome to search for alternative splicing events. We used 278 734 full-length and 3'/5' terminal reads of the sequences of 220 214 RAFL cDNA clones for the analysis. Eighty-nine percent of the cDNA sequences could be mapped to the genome and were clustered in 17 130 transcription units (TUs). Alternative splicing events were found in 1764 out of 15 214 TUs (11.6%) with multiple sequences. We collected full-length cDNA clones from plants grown under various environmental conditions or from various organs. We then analyzed the correlation between alternative splicing events and environmental stress conditions. Alternative splicing profiles changed according to environmental stress conditions and the various developmental stages of plant organs. In particular, cold-stress conditions affected alternative splicing profiles. The change in alternative splicing profiles under cold stress may be mediated by alternative splicing and transcriptional regulation of splicing factors.
• Het-PDB Navi.: A database for protein-small molecule interactions

  A Yamaguchi; K Iida; N Matsui; S Tomoda; K Yura; M Go

  JOURNAL OF BIOCHEMISTRY 135 1 79 - 84 2004年01月 [査読有り]
   

  The genomes of more than 100 species have been sequenced, and the biological functions of encoded proteins are now actively being researched. Protein function is based on interactions between proteins and other molecules. One approach to assuming protein function based on genomic sequence is to predict interactions between an encoded protein and other molecules. As a data source for such predictions, knowledge regarding known protein-small molecule interactions needs to be compiled. We have, therefore, surveyed interactions between proteins and other molecules in Protein Data Bank (PDB), the protein three-dimensional (3D) structure database. Among 20,685 entries in PDB (April, 2003), 4,189 types of small molecules were found to interact with proteins. Biologically relevant small molecules most often found in PDB were metal ions, such as calcium, zinc, and magnesium. Sugars and nucleotides were the next most common. These molecules are known to act as cofactors for enzymes and/or stabilizers of proteins. In each case of interactions between a protein and small molecule, we found preferred amino acid residues at the interaction sites. These preferences can be the basis for predicting protein function from genomic sequence and protein 3D structures. The data pertaining to these small molecules were collected in a database named Het-PDB Navi., which is freely available at http:// daisy.nagahama-i-bio.ac.jp/golab/hetpdbnavi.html and linked to the official PDB home page.
• [Arabidopsis functional genomics using full-length cDNAs].

  Seki M; Shinozaki K; Ishida J; Nakajima M; Enju A; Sakurai T; Satou M; Akiyama K; Iida K; Oono Y

  Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme 48 14 1890 - 1898 2003年11月 [査読有り]
  
• Empirical analysis of transcriptional activity in the Arabidopsis genome

  K Yamada; J Lim; JM Dale; HM Chen; P Shinn; CJ Palm; AM Southwick; HC Wu; C Kim; M Nguyen; P Pham; R Cheuk; G Karlin-Newmann; SX Liu; B Lam; H Sakano; T Wu; GX Yu; M Miranda; HL Quach; M Tripp; CH Chang; JM Lee; M Toriumi; MMH Chan; CC Tang; CS Onodera; JM Deng; K Akiyama; Y Ansari; T Arakawa; J Banh; F Banno; L Bowser; S Brooks; P Carninci; QM Chao; N Choy; A Enju; AD Goldsmith; M Gurjal; NF Hansen; Y Hayashizaki; C Johnson-Hopson; VW Hsuan; K Iida; M Karnes; S Khan; E Koesema; J Ishida; PX Jiang; T Jones; J Kawai; A Kamiya; C Meyers; M Nakajima; M Narusaka; M Seki; T Sakurai; M Satou; R Tamse; M Vaysberg; EK Wallender; C Wong; Y Yamamura; SL Yuan; K Shinozaki; RW Davis; A Theologis; Ecker, JR

  SCIENCE 302 5646 842 - 846 2003年10月 [査読有り]
   

  Functional analysis of a genome requires accurate gene structure information and a complete gene inventory. A dual experimental strategy was used to verify and correct the initial genome sequence annotation of the reference plant Arabidopsis. Sequencing full-length cDNAs and hybridizations using RNA populations from various tissues to a set of high-density oligonucleotide arrays spanning the entire genome allowed the accurate annotation of thousands of gene structures. We identified 5817 novel transcription units, including a substantial amount of antisense gene transcription, and 40 genes within the genetically defined centromeres. This approach resulted in completion of similar to30% of the Arabidopsis ORFeome as a resource for global functional experimentation of the plant proteome.
• Monitoring expression profiles of Arabidopsis gene expression during rehydration process after dehydration using ca 7000 full-length cDNA microarray.

  Youko Oono; Motoaki Seki; Tokihiko Nanjo; Mari Narusaka; Miki Fujita; Rie Satoh; Masakazu Satou; Tetsuya Sakurai; Junko Ishida; Kenji Akiyama; Kei Iida; Kyonoshin Maruyama; Shinobu Satoh; Kazuko Yamaguchi-Shinozaki; Kazuo Shinozaki

  The Plant journal : for cell and molecular biology 34 6 868 - 87 2003年06月 [査読有り]
   

  Plants respond and adapt to drought stress in order to survive under stress conditions. Several genes that respond to drought at the transcriptional level have been described, but there are few reports on genes involved in the recovery from dehydration. Analysis of rehydration-inducible genes should help not only to understand the molecular mechanisms of stress responses in higher plants, but also to improve the stress tolerance of crops by gene manipulation. We used a full-length cDNA microarray containing ca. 7000 Arabidopsis full-length cDNAs and identified 152 rehydration-inducible genes. Venn diagram analysis showed relationship of the rehydration-inducible genes to proline-inducible and water-treatment-inducible genes. Among the 152 rehydration-inducible genes, 58 genes contained the ACTCAT sequence involved in proline- and hypoosmolarity-inducible gene expression in their promoter regions, suggesting that ACTCAT sequence is a major cis-acting element involved in rehydration-inducible gene expression, and that some novel cis-acting elements are involved in rehydration-inducible gene expression. Functional analysis of rehydration-inducible and rehydration-repressed genes revealed their functions not only in the release from a stressed status but also in the recovery of growth in plants.
• Database of RIKEN Arabidopsis full-length cDNAs and Ds transposon insertion lines

  T Sakurai; M Satou; K Akiyama; K Iida; M Seki; T Kuromori; T Hirayama; T Ito; K Shinozaki

  PLANT AND CELL PHYSIOLOGY 44 S129 - S129 2003年
• 3H1315 カルシウム、亜鉛、マグネシウムイオン配位子のモジュールへの局在

  飯田 慶; 松井 信彰; 由良 敬; 郷 通子

  生物物理 40 S195  一般社団法人 日本生物物理学会 2000年

MISC

• Author Correction: Therapeutic manipulation of IKBKAP mis-splicing with a small molecule to cure familial dysautonomia.

  Masahiko Ajiro; Tomonari Awaya; Young Jin Kim; Kei Iida; Masatsugu Denawa; Nobuo Tanaka; Ryo Kurosawa; Shingo Matsushima; Saiko Shibata; Tetsunori Sakamoto; Lorenz Studer; Adrian R Krainer; Masatoshi Hagiwara Nature communications 12 (1) 6039 -6039 2021年10月
• Dicer切断反応産物の次世代シークエンス解析を利用した低分子化合物の標的RNA配列モチーフの網羅的探索

  村田亜沙子; 高島裕介; 飯田慶; 須貝亜矢子; 萩原正敏; 中谷和彦 日本分子生物学会年会プログラム・要旨集(Web) 43rd 2020年
• Monitoring transcriptomic changes in soil-grown roots and shoots of Arabidopsis thaliana subjected to a progressive drought stress

  Khurram Bashir; Sultana Rasheed; Akihiro Matsui; Kei Iida; Maho Tanaka; Motoaki Seki Methods in Molecular Biology 1761 223 -230 2018年 [査読有り]
  
• DNAメチル化亢進によるPITX1遺伝子発現抑制は食道扁平上皮癌の予後不良と関連する

  河村 由紀; 大坪 武史; 山田 和彦; 萩原 輝記; 大島 健志朗; 飯田 慶; 西方 公郎; 豊田 哲郎; 猪狩 亨; 野原 京子; 服部 正平; 土肥 多惠子 生命科学系学会合同年次大会 2017年度 [1P -1004] 2017年12月
• がん細胞の代謝がもたらす組織微小環境を標的にしたがん治療

  豊本 雅靖; 井上 飛鳥; 飯田 慶; 出縄 政嗣; 喜井 勲; 林 佳子; 岸 貴之; 小野木 博; 吉田 優; 細谷 孝充; 青木 淳賢; 萩原 正敏 生命科学系学会合同年次大会 2017年度 [3AT25 -1419)] 2017年12月
• 食道癌のメチロームおよびトランスクリプトーム統合解析により見出されたホメオボックス遺伝子の発現低下

  河村 由紀; 大坪 武史; 山田 和彦; 萩原 輝記; 大島 健志朗; 飯田 慶; 西方 公郎; 豊田 哲郎; 猪狩 亨; 山田 純; 野原 京子; 服部 正平; 土肥 多惠子 日本生化学会大会・日本分子生物学会年会合同大会講演要旨集 88回・38回 [2P1114] -[2P1114] 2015年12月
• 抗C型肝炎ウイルス能をもつ低分子化合物の同定

  奥野友紀子; NGUYEN Bao Ngoc; NGUYEN Bao Ngoc; 飯田慶; 出縄政嗣; 坂本直哉; 影近弘之; 萩原正敏 日本ウイルス学会学術集会プログラム・抄録集 61st 2013年
• 筋ジストロフィーに対するトランスレーショナル・リサーチ I.エクソン・スキップ ジストロフィンpre-mRNAのスプライシングを変化させる低分子化合物の探索

  萩原正敏; 松尾雅文; 片岡直行; 飯田慶; 西田篤史 筋ジストロフィーに対するトランスレーショナル・リサーチ 平成22-24年度 総括研究報告書 2013年
• 筋ジストロフィーに対するトランスクリプトーム創薬の試み

  飯田慶; 飯田慶; 片岡直行; 西田篤史; 川口修治; 豊田哲郎; 古野正朗; 松尾雅文; 林崎良英; 萩原正敏 日本RNA学会年会要旨集 15th 2013年
• シロイヌナズナ完全長cDNAエンサイクロペディアの作製と遺伝子の機能・発現解析への利用.

  関 原明; 佐藤将一; 石田順子; 櫻井哲也; 中嶋舞子; 秋山顕治; 槐 亜希子; 飯田 慶; 篠崎一雄 ゲノミクス・プロテオミクスの新展開（今中忠行 監修）. 株式会社 エヌ・ティー・エス. 328 -336 2004年
• シロイヌナズナ完全長cDNAエンサイクロペディアの作製と遺伝子の機能・発現解析への利用

  関 原明; 鳴坂 真理; 大野 陽子; 藤田 美紀; 水門 佐保; 楠城 時彦; 梅澤 泰史; 亀井 綾子; 藤 泰子; 篠崎 和子; Ecker Joseph R; 石田 順子; Davis Ronald W; Theologis Athanasios; Carninci Piero; 河合 純; 林崎 良英; 澤崎 達也; 金 鍾明; 長谷川 嘉則; 遠藤 弥重太; 横山 茂之; 佐藤 将一; 篠崎 一雄; 櫻井 哲也; 中嶋 舞子; 槐 亜希子; 神谷 麻子; 秋山 顕治; 飯田 慶 日本植物生理学会年会およびシンポジウム 講演要旨集 2003 (0) 86 -86 2003年
• シロイヌナズナ完全長cDNAを用いた植物ゲノムの機能・発現解析.

  関 原明; 佐藤将一; 石田順子; 櫻井哲也; 中嶋舞子; 秋山顕治; 槐 亜希子; 飯田 慶; 大野陽子; 篠崎一雄 蛋白質 核酸 酵素 48 (14) 1890 -1898 2003年

共同研究・競争的資金等の研究課題

• リアルタイム温度マッピング可能な生体外ヒト肝疾患モデル構築と疾病機序解明への応用

  日本学術振興会：科学研究費助成事業

  研究期間 : 2023年04月 -2027年03月 

  代表者 : 田畑 修; 飯田 慶; 亀井 謙一郎; 平井 義和; 四竈 泰一
• 鶏蝸牛有毛細胞再生過程における支持細胞reprogramming機構の解明

  日本学術振興会：科学研究費助成事業

  研究期間 : 2023年04月 -2026年03月 

  代表者 : 中川 隆之; 飯田 慶; 松永 麻美; 山本 典生
• スプライシング病克服を目指すRNA制御特化機械学習によるスプライシングコード解明

  日本学術振興会：科学研究費助成事業 基盤研究(C)

  研究期間 : 2020年04月 -2023年03月 

  代表者 : 飯田 慶

   

  本研究は、RNAスプライシングの異常に起因する疾患の高精度な探索および、バイオインフォマティクス解析に基づく治療介入方法の提案を行うことを目指して、スプライシング暗号の解読を目指すものである。この目標に対して、スプライシング研究分野でデファクトスタンダードとなりつつあるIllumina社の研究グループが開発したスプライシング評価システムであるSpliceAIを重要な研究ツールの1つと位置づけ、これを用いて、東北メガバンクが提供している800万件以上のSNPs情報に対する網羅的なスプライシング変化の評価を実施・完了した。 令和3年度の優先課題に設定していた、深層学習モデルからのスプライシング制御配列候補情報の抽出については、本件が塩基配列情報を取り扱っているという特性を生かし、入力情報のバリエーションを準備することで達成した。当初予定していた変分オートエンコーダの様要からは予定の変更となったが、より可視性・再利用性に優れた形で制御配列候補を提示する仕組みとなる。さらにこれを進め、個々のスプライスサイトにおいて制御配列候補を提示するシステムの開発を進めている。 また、低分子化合物によるスプライシング介入時における薬効・副反応の評価に用いるためのSpliceAIの深層学習モデルを再構築する試みについても、進展させることができた。 さらに本研究で得られた知見・解析ノウハウに基づき、自然免疫応答に重要な役割を持つOAS1遺伝子におけるsplicing QTLがCOVID-19の重症化に関与するメカニズムを解析し、低分子化合物を用いたスプライシング操作が、ヒト細胞にSARS-CoV-2感染への抵抗性を付与できることを示した。本成果は査読中論文としてbioRxivから公開され、またCold Spring Harbor Meetingや分子生物学会年会にて口頭発表での報告を行った。
• 鳥類内耳有毛細胞再生初期過程の解明：哺乳類における有毛細胞再生効率化への応用

  日本学術振興会：科学研究費助成事業

  研究期間 : 2020年04月 -2023年03月 

  代表者 : 中川 隆之; 飯田 慶; 喜多 知子; 西村 幸司; 大西 弘恵; 山本 典生

   

  哺乳類とは異なり、鳥類の聴覚器官である基底乳頭では、有毛細胞再生が自発的に誘導され、聴覚機能も再生される。鳥類とは異なり、哺乳類では有効性が期待できるレベルの聴覚機能再生は報告されていない。近年、鶏に関する遺伝子情報が充実し、網羅的遺伝子解析手法を用いて、これまで困難であった鳥類における有毛細胞再生に関連する遺伝子およびシグナルの詳細な分子生物学的解析が可能となった。本研究では、鶏蝸牛器官培養系を用い、支持細胞から有毛細胞への直接分化転換による有毛細胞再生過程の網羅的遺伝子解析を行い、支持細胞の活性化メカニズム、活性化した支持細胞の細胞生物学的特徴、活性化支持細胞から有毛細胞への分化転換の分子機構の解明に関する研究を実施した。支持細胞の活性化については、発現変動遺伝子群のプロモーター領域におけるモチーフ解析から候補となる転写因子9つを同定した。また、単一細胞レベルでの網羅的遺伝子発現解析結果のpseudotime trajectory analysisを行い、支持細胞活性化に係わる候補情報伝達系を同定し、阻害薬実験を実施し、その役割を明らかにした。また、活性化した支持細胞に特徴的に発現する遺伝子群、分化転換初期段階にある支持細胞に特徴的に発現する遺伝子群を同定した。これらの結果は、哺乳類蝸牛での有毛細胞再生実現に向け、哺乳類蝸牛支持細胞の活性化誘導の推進、支持細胞から有毛細胞への分化転換効率化、新生有毛細胞の機能的な成熟誘導に関連するものであり、今後マウス蝸牛器官培養系での応用実験への展開を行う。
• 神経幹細胞分化を司るニューロエピジェネティクスとその制御機構の解明

  日本学術振興会：科学研究費助成事業 基盤研究(C)

  研究期間 : 2019年04月 -2022年03月 

  代表者 : 武内 章英; 飯田 慶

   

  申請者はこれまでに、SfpqというRNA結合タンパク質が、神経発生の過程で神経分化に必須な100-2000kb長の超長鎖遺伝子群の発現を制御していることを見出しており、ここからSfpq依存性の転写伸長機構が、核内構造、染色体構造、クロマチン構造の制御機構とクロストークして上記のような非常に長い遺伝子の発現を制御している可能性につき検討を行っている。昨年度は、Sfpqの作る遺伝子発現制御複合体の同定のため、核抽出液からSfpqの作る巨大複合体（RNAヒストン構造）の単離の条件検討を行い、その実験系を確立した。今年度、確立した実験系を用いて免疫沈降と質量分析（IP-MS）による網羅的な解析を行い、Sfpqの作る巨大複合体の構成分子1908個の同定に成功した。これらの分子につきGO解析を行ったところ、Chromatin organization、Epigenetic regulation、RNA Polymerase II Transcription Elongationに関わる分子が同定されたことから、仮設通りSfpq依存性の転写伸長機構が、クロマチンダイナミックス制御とクロストークして神経幹細胞分化を制御していることが強く示唆され、その制御分子を同定できた。 さらに一昨年作成したクロマチンダイナミクス関連の全遺伝子リストの作成を行い、自身が作成したマウス胎児脳の時空間的トランスクリプトームデーターとのマージを行い、神経分化過程でのクロマチンダイナミクス関連の全遺伝子の網羅的な発現パターン解析を行った。その結果、神経分化に伴い、クロマチン構成分子および制御因子のパターンが大きく変動することを確認した。今年度は、さらに上記のIP-MSの結果同定された分子リストとのマージを行い、実際の脳形成に発現が変動するSfpqの作る巨大複合体構成因子を同定できた。
• 局所mRNAメチル化修飾による神経細胞遺伝情報「地方分権型」制御メカニズムの解明

  日本学術振興会：科学研究費助成事業 基盤研究(B)

  研究期間 : 2017年04月 -2020年03月 

  代表者 : 王 丹; 飯田 慶

   

  本プロジェクトの実施に初年度は健康なマウス成体脳のシナプスにおけるm6A-seqを行い、シナプスに局在するm6A修飾の全貌を明らかにするとともに特徴を捉えることを目標とした。その目標が達成され、シナプスに存在するm6A-RNAをおよそ3千種類およびメチル化サイトを5千箇所弱を同定した。メチル化される遺伝子群の機能的特徴としては、シナプス形成、形態、構造、およびコミュニケーションに大きく寄与する遺伝子がエンリッチされ、メチル化されたものとそうではないものの間に機能的な分業機構の存在が明らかになった。この分業システムは新規なRNA制御システムであり、本研究で初めて明らかになった。
  さらに、マウス海馬由来の神経培養系を用いて、メチル化酵素や、メチル化RNAターゲットを認識するタンパク質のノックダウンを行い、mRNA化学修飾経路の機能を調べた。その結果、メチル化酵素METTL3は神経細胞の生存に必須であることや、リーダータンパクが興奮性シナプスが座するスパインの形態や機能に必要とされることが明らかになった。さらに、メチル化されるmRNAのうち、Apc遺伝子に注目し、m6A修飾を認識するリーダータンパクの発現低下がAPCタンパク質の発現低下につながる結果が得られた。以上の研究結果から、神経シナプスには多くのmRNAはメチル化修飾を受け、その修飾は機能的である結論が得られた。Apc遺伝子は神経突起形成やシナプス機能に重要であることが先行研究で示され、m6A修飾はターゲット遺伝子の翻訳制御を通して、神経発達に役割を果たすことが示唆された。本研究はカリフォルニア大学ロサンゼルス校および京都大学理学部と医学支援センターとの共同研究で実施された。
• CRISPRによるRNA病モデルｉＰＳ細胞・動物の構築と病態解明・治療薬創製

  日本学術振興会：科学研究費助成事業 基盤研究(S)

  研究期間 : 2015年05月 -2020年03月 

  代表者 : 萩原 正敏; 鶴山 竜昭; 奥野 友紀子; 飯田 慶; 大江 賢治; 細谷 孝充; 武内 章英; 粟屋 智就; 網代 将彦

   

  本研究は、①スプライシング操作化合物TG003およびRECTASのスプライシング介入ルールの解明、② スプライシング操作により治療可能な遺伝性疾患に適応できる化合物の予測と合成展開、③ CRISPR/Cas9法等で作製した疾患モデルiPS細胞やモデル動物による化合物の作用機序解明と有用性の実証を行い、ポストゲノム治療薬を創製する新しいケミカルバイオロジー分野の創出を目指している。本年度は、スプライシング変動によりGFP/RFPの発現が切り替わるdual reporterシステム（SPREADD）を用いた実験から、TG003が深部イントロン変異を有するNEMO異常症患者の偽エクソン発現を抑制する効果を持つことを明らかにし、患者iPS細胞を病態モデルとしたTNFα応答機能障害がTG003処理により改善することを見出し報告した(2019 J Clin Invest.)。また同様に深部イントロン変異により偽エクソンが発現するV型嚢胞性線維症に対してもTG003が偽エクソンの発現を抑制することを見出し、TG003からの化合物展開により、患者iPS細胞で原因遺伝子CFTRの発現回復効果を有する治療薬候補化合物の取得に成功した（投稿準備中）。RECTASについても、家族性自律神経異常症患者の線維芽細胞を用いたmRNA-seq解析と生化学的解析から作用メカニズムを解明し、家族性自律神経異常症モデルマウスと患者iPS細胞でもRECTASがスプライシングを正常化する作用のあることを確認できた（投稿準備中）。RECTASは偽エクソンによる心ファブリー病や、QT延長症候群にも効果があることが見出されたため、標的遺伝子を組み込んだSPREADD により最適化合物を検索するとともに、CRISPR/Cas9法によりモデル動物・iPS細胞を使った評価系を構築した。
• 種間比較トランスクリプトーム解析に立脚したスプライシング操作薬の作用機序の解明

  日本学術振興会：科学研究費助成事業 若手研究(B)

  研究期間 : 2015年04月 -2018年03月 

  代表者 : 飯田 慶; 佐久間 真紀

   

  3年間の研究期間を通じて当初の目標として掲げたように、スプライシング操作化合物に対する応答を種間（ヒトーマウス）で比較トランスクリプトーム解析するという新しい手法を開発し、これによりスプライシング操作化合物の標的配列の推定や、組織特異性の解明につながる成果を得た。これらの解析成果は、本研究で扱ったTG003やRECTAS等の化合物が塩基配列依存的に特定のエキソン群に作用することを示しており、ヒトゲノム配列を入力とした「個人ゲノム配列―薬剤感受性スコアリングシステム」の構築につながった。さらに、種間比較情報はこのスコアリングシステムの精度の向上に寄与し得ることを示すことができた。
• トランスクリプトームの人為的操作による遺伝病の治療

  日本学術振興会：科学研究費助成事業 基盤研究(A)

  研究期間 : 2015年04月 -2016年03月 

  代表者 : 萩原 正敏; 武内 章英; 大江 賢治; 二宮 賢介; 飯田 慶; 奥野 友紀子

   

  本研究の目的は、スプライシング異常に起因するRNA 病を標的とした新規治療方法を創製することであり、関連する論文を２報、報告した。 一つ目は、加齢黄斑変性症における病的な脈絡膜血管新生を抑制する化合物SRPIN803を同定した論文である（Molecular Pharmacology May 20, 2015 mol.114.097345）。SRPIN803は、SRPK1(SRSF protein kinase 1)とCK2 (Casein kinase 2)を同時に抑制することにより、リード化合物であるSRPIN340よりも強い病的血管新生作用を示した。加齢黄斑変性症のモデルマウスにおいて点眼による効果であり、臨床応用の可能性が示唆される報告である。 二つ目は、メタボリックシンドロームにおける脂肪分化を抑制する化合物BINDYを同定した論文である（Bioorganic & Medicinal Chemistry 23:4434,2015)。BINDYは、リード化合物であるINDYよりも強いDYRK kinase阻害効果を有し、脂肪分化に重要な転写因子であるPPARγとC/EBPαの発現を抑制することにより、3T3-L1細胞の脂肪分化を抑制した。最近、DYRK1Bの機能獲得型の遺伝子変異がメタボリックシンドロームを増悪させる報告からも、BINDYがメタボリックシンドロームに効果を示す可能性が示唆された。
• 新型分割イントロンの切り出し因子同定に基づく真核生物ｍＲＮＡ成熟機構進化の解明

  日本学術振興会：科学研究費助成事業 基盤研究(A)

  研究期間 : 2011年04月 -2015年03月 

  代表者 : 橋本 哲男; 稲垣 祐司; 奈良 武司; 飯田 慶

   

  腸管寄生虫 Giardia intestinalis において我々が発見した新型分割イントロンに注目し、Giardiaゲノムの中での分割・通常イントロンの分布を明らかにするとともに、分割イントロンのスプライシングメカニズムの解明とスプライセオソーム構成因子の解明を目的として研究を進めた。研究開始当初に明らかであったイントロンに加え、3つの通常イントロンと1つの分割イントロンをゲノム上に発見し、それらの存在を実験的に示した。一方、Giardiaスプライセオソームを精製するために、スプライセオソームを構成する複数のタンパク質にタグをつけてGiardiaで発現させる形質転換系の確立に取り組んだ。

メディア報道

• RNAスプライシング制御による新規がん免疫療法―ネオ抗原を産生増強する治療薬候補の同定―

  報道 : 2022年12月

  発行元・放送局 : 京都大学

  　インターネットメディア　PD-1阻害抗体など免疫チェックポイント阻害剤は、T細胞の賦活化を抑制するPD-1などに結合することにより、がん細胞に対するT細胞の攻撃を活性化し、末期がん患者をも救済する画期的な治療薬で、がん治療戦略の中心的存在となりつつあります。残念ながら、免疫チェックポイント阻害剤が奉功しないがん患者も多数いらっしゃいますが、T細胞は、がん細胞に特異的に発現するネオ抗原を目印としてがん細胞を認識し攻撃しているので、がん細胞のネオ抗原の発現量や多様性を増やすことができれば、がん免疫療法の効果を劇的に高められると予想されます。
• RNA結合タンパク質の標的分子探索手法を開発 －複雑なRNA制御のメカニズム解明に期待－

  報道 : 2020年07月

  発行元・放送局 : 京都大学

  　インターネットメディア　飯田慶 医学研究科特定助教、武内章英 同准教授、萩原正敏 同教授らの研究グループは、RNA結合タンパク質の1つであるSFPQ（Splicing Factor Proline And Glutamine Rich）をモデルとして、「RNAの機能的制御につながる結合」を探索するバイオインフォマティクス手法を開発しました。
• 神経ネットワークの可塑性を支えるRNAの機能に即した化学修飾を明らかにしました

  報道 : 2018年07月

  発行元・放送局 : 京都大学

  　インターネットメディア　王丹 高等研究院物質ー細胞統合システム拠点（iCeMS＝アイセムス）特定拠点准教授、飯田慶 医学研究科特定助教らのグループは、マウス前脳領域の神経細胞と神経細胞の間に形成される接合部位（シナプス）を対象に、m6A（RNAへのメチル化の一種）修飾を受けたmRNAの存在を網羅的に調べ、シナプス形成にかかわるmRNAの多くがm6A修飾を受ける様子を明らかにしました。
• 1細胞RNA分画解読法の開発に成功

  報道 : 2018年06月

  発行元・放送局 : 理化学研究所

  　インターネットメディア　理化学研究所（理研）開拓研究本部新宅マイクロ流体工学理研白眉研究チームの新宅博文理研白眉研究チームリーダー、マハメッド・ナディ・アブデルモエズ研修生、東京大学大学院理学系研究科の小口祐伴特任助教、上村想太郎教授、京都大学大学院医学研究科飯田慶特定助教らの共同研究グループ※は、一つの細胞から核RNAと細胞質RNAを分画して、それぞれの遺伝子発現を解析できるマイクロ流体技術を基盤とする「1細胞RNA分画解読法（SINC-seq法)）」を開発しました。
• 神経巨大遺伝子の発現制御メカニズムの発見

  報道 : 2018年05月

  発行元・放送局 : 京都大学

  　インターネットメディア　武内章英 医学研究科准教授、飯田慶 同特定助教、萩原正敏 同教授らの研究グループは、名古屋大学、東京工業大学との共同研究で、RNA結合タンパク質「Sfpq」が、哺乳類の神経細胞で全長が100キロベースを超えるような、巨大な遺伝暗号の読み出しを制御するメカニズムを発見しました。
• 植物の新しい環境ストレス適応機構の発見

  報道 : 2017年08月

  発行元・放送局 : 京都大学
• 次世代シーケンサーのデータ解析精度を向上させる新手法を開発

  報道 : 2012年02月

  発行元・放送局 : 理化学研究所

  　インターネットメディア

その他のリンク

researchmap

https://researchmap.jp/read0118609