The accurate determination of gene loci by genome-wide approach

2012 Fiscal Year Final Research Report

• Project/Area Number: 23651195
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: Medical genome science
• Research Institution: Kyushu University
• Principal Investigator: OHKAWA Yasuyuki 九州大学, 医学研究院, 准教授 (80448430)
• Project Period (FY): 2011 – 2012
• Keywords: クロマチン / 転写 / RNA ポリメラーゼII / 発現プロファイリング / リン酸化

Research Abstract

Cellular function is regulated by the balance of stringently regulated amounts of mRNA. Previous reports revealed that RNA polymerase II (RNAPII), which transcribes mRNA, c an be classified into the pausing state and the active transcription state according to the phosphorylation state of RPB1, the catalytic subunit of RNAPII. We examined the correlation between the phosphorylation of RNAPII and mRNA expression levels using acombined analysis by ChIPseq and RNAseq. We could visualized the recruitment of various phosphorylated RNAPIIs. Our analysis indicated that the complexity of quantitative regulation of mRNA levels could be classified into three categories according to thephosphorylation state of RNAPII.

Research Products

• [Journal Article] A co-localization model of paired ChIP-seq data using a large ENCODE data set enables comparison of multiple samples (2013)
  • Author(s): Maehara K, Odawara J, Harada A, Yoshimi T, Nagao K, Obuse C, Akashi K, Tachibana T, Sakata T, Ohkawa Y
  • Journal Title: Nucleic Acids Res Volume: Vol.41、No.1 Pages: 54-62
  • DOI: DOI:10.1093/nar/gks1010
  • Peer Reviewed
• [Journal Article] Ly6C(+) Ly6G(-) Myeloid-derived suppressor cells play a critical role in the resolution of acute inflammation and the subsequent tissue repair process after spinal cord injury (2013)
  • Author(s): Saiwai H, Kumamaru H, Ohkawa Y, Kubota K, Kobayakawa K, Yamada H, Yokomizo T, Iwamoto Y, Okada S
  • Journal Title: J Neurochem Volume: Vol.125、No.1 Pages: 74-88
  • DOI: DOI:10.1111/jnc.12135
  • Peer Reviewed
• [Journal Article] Chd2 interacts with H3.3 to determine myogenic cell fate (2012)
  • Author(s): Harada A, Okada S, Konno D, Odawara J, Yoshimi T, Yoshimura S, Kumamaru H, Saiwai H, Tsubota T, Kurumizaka H, Akashi K, Tachibana T, Imbalzano AN, Ohkawa Y
  • Journal Title: EMBO J Volume: Vol.31、No.13 Pages: 2994-3007
  • DOI: DOI:10.1038/emboj.2012.136
  • Peer Reviewed
• [Journal Article] Direct isolation and RNA-seq reveal environment-dependent properties of engrafted neural stem/progenitor cells (2012)
  • Author(s): Kumamaru H, Ohkawa Y, Saiwai H, Yamada H, Kubota K, Kobayakawa K, Akashi K, Okano H, Iwamoto Y, Okada S
  • Journal Title: Nat Commun Volume: Vol.3 Pages: 1140
  • DOI: DOI:10.1038/ncomms2132
  • Peer Reviewed
• [Journal Article] Surf4 modulates STIM1-dependent calcium entry (2012)
  • Author(s): Fujii Y, Shiota M, Ohkawa Y, Baba A, Wanibuchi H, Kinashi T, Kurosaki T, Baba Y
  • Journal Title: Biochem Biophys Res Commun Volume: Vol.422、No.4 Pages: 615-620
  • DOI: DOI:10.1016/j.bbrc.2012.05.037
  • Peer Reviewed
• [Journal Article] Age-related differences in cellular and molecular profiles of inflammatory responses after spinal cord injury (2012)
  • Author(s): Kumamaru H, Saiwai H, Ohkawa Y, Yamada H, Iwamoto Y, Okada S
  • Journal Title: J Cell Physiol Volume: Vol.227、No.4 Pages: 1335-1346
  • DOI: DOI:10.1002/jcp.22845
  • Peer Reviewed
• [Journal Article] Chromatin accessibility and transcription factor binding at the PPARγ2promoter during adipogenesis is protein kinase A-dependent (2011)
  • Author(s): Xiao H, Leblanc SE, Wu Q, Konda S, Salma N, Marfella CG, Ohkawa Y,Imbalzano AN
  • Journal Title: J Cell Physiol Volume: Vol.226、NO.1 Pages: 86-93
  • DOI: DOI:10.1002/jcp.22308
  • Peer Reviewed
• [Journal Article] Flow cytometric sorting of neuronal and glial nuclei from central nervous system tissue (2011)
  • Author(s): Okada S, Saiwai H, Kumamaru H, Kubota K, Harada A, Yamaguchi M, Iwamoto Y,Ohkawa Y
  • Journal Title: J Cell Physiol Volume: Vol.226、No.2 Pages: 552-558
  • DOI: DOI:10.1002/jcp.22365
  • Peer Reviewed
• [Journal Article] The classification of mRNA expression levels by the phosphorylation state of RNAPII CTD based on a combined genome-wide approach (2011)
  • Author(s): Odawara J, Harada A, Yoshimi T, Maehara K, Tachibana T, Okada S, Akashi K, Ohkawa Y
  • Journal Title: BMC Genomics Volume: Vo.12 Pages: 516
  • DOI: DOI:10.1186/1471-2164-12-516
  • Peer Reviewed
• [Presentation] ヒストンバリアントによる骨格筋分化制御機構 (2013)
  • Author(s): 大川 恭行
  • Organizer: 第1回ヒストンバリアント研究会
  • Place of Presentation: 九州大学総合研究棟、福岡
  • Year and Date: 2013-03-08
• [Presentation] Cd2 incorporates H3.3 to mark myogenic genes (2013)
  • Author(s): 大川 恭行
  • Organizer: 新学術領域「ゲノム支援」国際シンポジウム"Expanding Frontiers of Genome Science"
  • Place of Presentation: 東京大学 伊藤国際学術研究センター、東京
  • Year and Date: 2013-01-10
• [Presentation] 共局在回帰モデルと ENCODE データセットを介した ChIP-seq データの多サンプル比較解析 (2012)
  • Author(s): 前原 一満, 小田原 淳, 原田 哲仁, 吉見 智彦, 長尾 恒治, 小布施 力史, 立花 太郎, 坂田 年男, 大川 恭行
  • Organizer: 第35回日本分子生物学会年会
  • Place of Presentation: 福岡国際会議場・マリンメッセ福岡、福岡
  • Year and Date: 2012-12-14
• [Presentation] CHD5(Chromodomain helicase DNA binding protein 5)はマウスの胚性幹細胞において H3.1 と結合して遺伝子発現を抑制しうる (2012)
  • Author(s): 林 正康, 小田原 淳, 原田 哲仁, 前原一満, 立花 太郎, 赤司 浩一, 大川 恭行
  • Organizer: 第35回日本分子生物学会年会
  • Place of Presentation: 福岡国際会議場・マリンメッセ福岡、福岡
  • Year and Date: 2012-12-13
• [Presentation] 高次クロマチン構造制御による骨格筋分化制御 (2012)
  • Author(s): 大川 恭行
  • Organizer: 第35回日本分子生物学会年会
  • Place of Presentation: 福岡国際会議場・マリンメッセ福岡、福岡
  • Year and Date: 2012-12-12
• [Presentation] Chd-2 dependent deposition of H3.3 is required for myogenic cell fate (2012)
  • Author(s): Akihito Harada, Anthony N. Imbalzano, Yasuyuki Ohkawa
  • Organizer: KEYSTONE SYMPOSIA
  • Place of Presentation: コロラド,USA
  • Year and Date: 2012-01-19
• [Presentation] Control of gene expression through the phosphorylation of Ser2 and Ser5 of RNAP II : A combined analysis for ChIPseq and RNAseq (2012)
  • Author(s): Jun Odawara, Akihito Harada, Yasuyuki Ohkawa
  • Organizer: KEYSTONE SYMPOSIA
  • Place of Presentation: コロラド,USA
  • Year and Date: 2012-01-19
• [Presentation] The deposition of histone varients is the basis of chromatin structual changes in cell fate decision (2011)
  • Author(s): Yasuyuki Ohkawa, Jun Odawara, Akihito Harada
  • Organizer: 第34回日本分子生物学会年会
  • Place of Presentation: パシフィコ横浜、神奈川
  • Year and Date: 2011-12-16
• [Presentation] Chd-2 dependent deposition of H3.3 is crucial for Brg1 recruitment in myogenesis (2011)
  • Author(s): Akihito Harada, Jun Odawara, Kazumitu Maehara, Tomohiko Yoshimi, Saori Yoshimura, Taro Tachibana, Hitoshi Kurumizaka, Hiroshi Kimura, Yasuyuki Ohkawa
  • Organizer: 第34回日本分子生物学会年会
  • Place of Presentation: パシフィコ横浜、神奈川
  • Year and Date: 2011-12-15
• [Book] 実験医学 (2013)
  • Author(s): 大川 恭行, 小田原 淳, 原田 哲仁
  • Total Pages: 577-582
  • Publisher: 羊土社
• [Book] 細胞工学 (2012)
  • Author(s): 原田 哲仁, 大川 恭行
  • Total Pages: 877-881
  • Publisher: 秀潤社
• [Book] Methods Mol Biol"Isolation of nuclei from skeletal muscle satellite cells and myofibers for use in chromatin immunoprecipitation assays." (2012)
  • Author(s): Ohkawa Y, Mallappa C, Vallaster CS, Imbalzano AN
  • Total Pages: 517-530
  • Publisher: Springer 社
• [Book] Methods Mol Biol"An improved restriction enzyme accessibility assay for analyzing changes in chromatin structure insamples of limited cell number." (2012)
  • Author(s): Ohkawa Y, Mallappa C, Vallaster CS, Imbalzano AN
  • Total Pages: 531-542
  • Publisher: Springer 社
• [Remarks] 九州大学 医学研究院 先端医療医学部門エピジェネティクス分野 / 大川研究室
  • URL: http://chromatin.med.kyushu-u.ac.jp/