Integration and normalization method for improving the comparative epigenome pipeline

• Project/Area Number: 15K18465
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: System genome science
• Research Institution: The University of Tokyo
• Principal Investigator: Nakato Ryuichiro 東京大学, 分子細胞生物学研究所, 助教 (60583044)
• Project Period (FY): 2015-04-01 – 2018-03-31
• Project Status: Completed (Fiscal Year 2017)
• Budget Amount: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000); Fiscal Year 2017: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000); Fiscal Year 2016: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000); Fiscal Year 2015: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000)
• Keywords: ChIP-seq法 / Hi-C法 / 大規模解析 / エピゲノム / 品質評価 / ゲノム立体構造 / Spike-in解析 / ノイズ除去 / IHECプロジェクト

Outline of Final Research Achievements

Recent advances in sequencing analyses enable us to compare hundreds of ChIP-seq samples simultaneously; such large-scale analysis has potential to reveal the high-dimensional interrelationship level for regulatory elements and annotate novel functional genomic regions de novo. However, there are various factors that can affect the data quality of the sample preparation step, especially for tissue samples and low-input analyses. It is still difficult to eliminate or normalize biases in each sample. To overcome this problem, we have developed three programs: (i) DROMPA3, cost-effective ChIP-seq pipeline; (ii) SSP, a novel quality assessment tool of ChIP-seq data; and (iii) Hi-C analysis pipeline. These programs can provide us with more robust and effective large-scale epigenome analysis.

Research Products

• [Journal Article] Sensitive and robust assessment of ChIP-seq read distribution using a strand-shift profile (2018)
  • Author(s): Ryuichiro Nakato, Katsuhiko Shirahige
  • Journal Title: Bioinformatics Volume: 印刷中
  • Peer Reviewed
• [Journal Article] Statistical Analysis and Quality Assessment of ChIP-seq Data with DROMPA. (2018)
  • Author(s): Nakato R, Shirahige K.
  • Journal Title: Methods Mol Biol. Volume: 1672 Pages: 631-643
  • DOI: 10.1007/978-1-4939-7306-4_41
  • ISBN: 9781493973057, 9781493973064
  • Peer Reviewed
• [Journal Article] Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation. (2016)
  • Author(s): Nakato R, Shirahige K.
  • Journal Title: Brief Bioinform Volume: 12 Pages: 1-12
  • DOI: 10.1093/bib/bbw023
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Replication-Coupled PCNA Unloading by the Elg1 Complex Occurs Genome-wide and Requires Okazaki Fragment Ligation (2015)
  • Author(s): Takashi Kubota, Yuki Katou, Ryuichiro Nakato, Katsuhiko Shirahige, Anne D. Donaldson
  • Journal Title: Cell Reports Volume: 12 Issue: 5 Pages: 774-787
  • DOI: 10.1016/j.celrep.2015.06.066
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Condensin targets and reduces unwound DNA structures associated with transcription in mitotic chromosome condensation (2015)
  • Author(s): Takashi Sutani, Toyonori Sakata, Ryuichiro Nakato, Koji Masuda, Mai Ishibashi, Daisuke Yamashita, Yutaka Suzuki, Tatsuya Hirano, Masashige Bando, Katsuhiko Shirahige
  • Journal Title: Nature Communications Volume: 6 Issue: 1 Pages: 1-13
  • DOI: 10.1038/ncomms8815
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] The Deubiquitinating Enzyme USP7 Regulates Androgen Receptor Activity by Modulating Its Binding to Chromatin (2015)
  • Author(s): Shu-Ting Chen, Maiko Okada, Ryuichiro Nakato, Kosuke Izumi, Masashige Bando and Katsuhiko Shirahige
  • Journal Title: Journal of Biological Chemistry Volume: 290 Issue: 35 Pages: 21713-21723
  • DOI: 10.1074/jbc.m114.628255
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Assembly of Slx4 signaling complexes behind DNA replication forks (2015)
  • Author(s): Attila Balint, TaeHyung Kim, David Gallo, Jose Renato Cussiol, Francisco M Bastos de Oliveira, Askar Yimit, Jiongwen Ou, Ryuichiro Nakato, Alexey Gurevich, Katsuhiko Shirahige, Marcus B Smolka, Zhaolei Zhang, Grant W Brown
  • Journal Title: The EMBO Journal Volume: 34 Issue: 16 Pages: 2182-2197
  • DOI: 10.15252/embj.201591190
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Esco1 Acetylates Cohesin via a Mechanism Different from That of Esco2 (2015)
  • Author(s): Masashi Minamino, Mai Ishibashi, Ryuichiro Nakato, Kazuhiro Akiyama, Hiroshi Tanaka, Yuki Kato, Lumi Negishi, Toru Hirota, Takashi Sutani, Masashige Bando, Katsuhiko Shirahige
  • Journal Title: Current Biology Volume: 25 Issue: 13 Pages: 1694-1706
  • DOI: 10.1016/j.cub.2015.05.017
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Presentation] Characterization of chromatin folding mechanisms regulated by cohesin, cohesin loader and CTCF (2018)
  • Author(s): Ryuichiro Nakato, Toyonori Sakata, Soya Shinkai, Katsuhiko Shirahige.
  • Organizer: Keystone Symposia "Chromatin Architecture and Chromosome Organization (X5)"
  • Int'l Joint Research
• [Presentation] バイオインフォマティクスで切り開くエピゲノム解析 (2017)
  • Author(s): 中戸隆一郎
  • Organizer: Heart rhythm interdisciplinary Association (HEIAN) Forum
  • Invited
• [Presentation] ゲノムのダイナミズムを解き明かす大規模ChIP-seq解析 (2017)
  • Author(s): 中戸隆一郎
  • Organizer: 理研シンポジウム「細胞システムの動態と論理 IX」
  • Invited
• [Presentation] Method of identifying biased data for large-scale ChIP-seq analysis (2016)
  • Author(s): Ryuichiro Nakato
  • Organizer: The EMBO Meeting "From Functional Genomics to Systems Biology"
  • Place of Presentation: Heidelberg, Germany
  • Year and Date: 2016-11-12
  • Int'l Joint Research
• [Book] 「実験医学」2016年6月増刊号：エピゲノムのダイナミズムを解き明かす大規模比較解析 ―血管内皮細胞を例に (2016)
  • Author(s): 中戸隆一郎, 和田洋一郎, 白髭克彦
  • Total Pages: 7
  • Publisher: 羊土社
• [Remarks] DROMPA3
  • URL: https://github.com/rnakato/DROMPA3
• [Remarks] SSP
  • URL: https://github.com/rnakato/SSP
• [Remarks] Palmsonntagmorgen
  • URL: http://rnakato.hatenablog.jp/
• [Remarks] SSP (github)
  • URL: https://github.com/rnakato/SSP