Development of bioinformatics platform for analyzing chromosome dynamics and comparative genomics.

• Project Area: Systematic study of chromosome adaptation
• Project/Area Number: 22125008
• Research Category: Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: Tokyo Institute of Technology
• Principal Investigator: ITOH TAKEHIKO 東京工業大学, 生命理工学研究科, 教授 (90501106)
• Co-Investigator(Kenkyū-buntansha): SHIRAHIGE Katsuhiko 東京大学, 分子細胞学研究所, 教授 (90273854)
• Project Period (FY): 2010-04-01 – 2015-03-31
• Project Status: Completed (Fiscal Year 2014)
• Budget Amount: ¥146,250,000 (Direct Cost: ¥112,500,000、Indirect Cost: ¥33,750,000); Fiscal Year 2014: ¥27,170,000 (Direct Cost: ¥20,900,000、Indirect Cost: ¥6,270,000); Fiscal Year 2013: ¥28,600,000 (Direct Cost: ¥22,000,000、Indirect Cost: ¥6,600,000); Fiscal Year 2012: ¥30,030,000 (Direct Cost: ¥23,100,000、Indirect Cost: ¥6,930,000); Fiscal Year 2011: ¥29,770,000 (Direct Cost: ¥22,900,000、Indirect Cost: ¥6,870,000); Fiscal Year 2010: ¥30,680,000 (Direct Cost: ¥23,600,000、Indirect Cost: ¥7,080,000)
• Keywords: 染色体動態 / バイオインフォマティクス / ゲノム情報解析 / ゲノム情報 / 新型シークエンサ / 新型シークエンサー

Outline of Final Research Achievements

We developed novel ChIP-seq analysis, genome assembling and detecting point or structural variation algorithms from NGS (illumina) sequence data. These algorithms were built up as individual programs and opened to the public via paper or our HP.
And we also performed analysis of the distribution of protein localization, denovo assembling of genomes, and SNPs or structural variation detection against S.cerevisiae, S.pombe, Human. Mouse and some bacterias with other many researchers.

Research Products

• [Journal Article] A genetic mechanism for female-limited Batesian mimicry in Papilio butterfly (2015)
  • Author(s): H. Nishikawa, T Iijima, R Kajitani, et. al.
  • Journal Title: Nature Genetics Volume: 47 Issue: 4 Pages: 405-409
  • DOI: 10.1038/ng.3241
  • Peer Reviewed / Open Access
• [Journal Article] Dimeric combinations of MafB, cFos and cJun control the apoptosis-survival balance in limb morphogenesis (2014)
  • Author(s): N. suda, T. Itoh, R. Nakato et. al.
  • Journal Title: Development Volume: 141 Issue: 14 Pages: 2885-2894
  • DOI: 10.1242/dev.099150
  • Peer Reviewed / Open Access
• [Journal Article] Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. (2014)
  • Author(s): R. Kajitani, K. Toshimoto, H. Noguchi, A. Toyoda, Y. Ogura, M. Okuno, M. Yabana, M. Harada, E. Nagayasu, H. Maruyama, Y. Kohara, A. Fujiyama, T. Hayashi and T.Itoh
  • Journal Title: Genome Research, Volume: 24 Issue: 8 Pages: 1384-1384
  • DOI: 10.1101/gr.170720.113
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] DROMPA: easy‐to‐handle peak calling and visualization software for the computational analysis and validation of ChIP‐seq data (2013)
  • Author(s): Ryuichiro Nakato
  • Journal Title: Genes to Cells Volume: 18 Issue: 7 Pages: 589-601
  • DOI: 10.1111/gtc.12058
  • Peer Reviewed
• [Journal Article] Coelacanth genomes reveal a variety of signatures for evolutionary transition from water to land (2013)
  • Author(s): Nikaido M, Noguchi, H, Nishihara H, Toyoda A, Suzuki Y, Kajitani R, Suzuki H, Okuno M, Aibara M, Ngatunga BP, Mzighani SI, Kalombo HW, Masengi KW, Tuda J, Nogami S, Maeda R, Iwata M, Abe Y, Fujimura K, Okabe M, Amano T, Maeno A, Shiroishi T, Itoh T, Sugano S, Kohara Y, Fujiyama A, Okada N.
  • Journal Title: Genome Research Volume: 23巻10号 Issue: 10 Pages: 1740-1748
  • DOI: 10.1101/gr.158105.113
  • Peer Reviewed
• [Journal Article] Sensory-neuron subtype-specific transcriptional programs controlling dendrite morphogenesis: genome-wide analysis of Abrupt and Knot/Collier. (2013)
  • Author(s): Yukako Hattori, Tadao Usui, Daisuke Satoh, Sanefumi Moriyama, Kohei Shimono, Takehiko Itoh, Katsuhiko Shirahige, Tadashi Uemura.
  • Journal Title: Developmental Cell Volume: 27(5) Issue: 5 Pages: 530-544
  • DOI: 10.1016/j.devcel.2013.10.024
  • NAID: 120005348995
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Transcriptomic analysis of four developmental stages of Strongyloides venezuelensis (2013)
  • Author(s): Nagayasu E, Ogura Y, Itoh T, Yoshida A, Chakraborty G, Hayashi T, Maruyama H
  • Journal Title: Parasitology International Volume: 62(1) Issue: 1 Pages: 57-65
  • DOI: 10.1016/j.parint.2012.09.006
  • Peer Reviewed
• [Journal Article] HDAC8 mutations in Cornelia de Lange syndrome affect the cohesin acetylation cycle. (2012)
  • Author(s): Deardorff MA
  • Journal Title: Nature Volume: 489(7415) Issue: 7415 Pages: 313-7
  • DOI: 10.1038/nature11316
  • Peer Reviewed
• [Journal Article] The Prereplication Complex Recruits XEco2 to Chromatin to Promote Cohesin Acetylation in Xenopus Egg Extracts (2012)
  • Author(s): Torahiko L. Higashi
  • Journal Title: Current Biology Volume: 22 Issue: 11 Pages: 977-988
  • DOI: 10.1016/j.cub.2012.04.013
  • Peer Reviewed
• [Journal Article] Replisome stability at defective DNA replication forks is independent of S phase checkpoint kinases (2012)
  • Author(s): De Piccoli G, 他
  • Journal Title: Mol Cell Volume: 45 Pages: 696-704
  • Peer Reviewed
• [Journal Article] The replication checkpoint protects fork stability by releasing transcribed genes from nuclear pores (2011)
  • Author(s): Bermejo R, 他
  • Journal Title: Cell Volume: 146 Pages: 372-83
  • Peer Reviewed
• [Journal Article] ATP hydrolysis is required for relocating cohesin from sites occupied by its Scc2/4 loading complex. (2011)
  • Author(s): Hu B, Itoh T, Mishra A, Katoh Y, Chan KL, Upcher W, Godlee C, Roig MB, Shirahige K, Nasmyth K.
  • Journal Title: Current Biology Volume: 21(1) Pages: 12-24
  • Peer Reviewed
• [Journal Article] Chromosome length influences replication-induced topological stress. (2011)
  • Author(s): Kegel A, Betts-Lindroos H, Kanno T, Jeppsson K, Strom L, Katou Y, Itoh T, Shirahige K, Sjogren C.
  • Journal Title: Nature Volume: 471(7338) Pages: 392-6
  • Peer Reviewed
• [Journal Article] An Smc3 acetylation cycle is essential for establishment of sister chromatid cohesion. (2010)
  • Author(s): Beckouet F, Hu B, Roig MB, Sutani T, Komata M, Uluocak P, Katis VL, Shirahige K, Nasmyth K.
  • Journal Title: Molecular Cell. Volume: 39(5) Pages: 689-99
  • Peer Reviewed
• [Presentation] Single Nucleotide Variation (SNV)を考慮したラガービール酵母のゲノム再解析 (2014)
  • Author(s): 奥野未来
  • Organizer: 日本農芸化学会
  • Place of Presentation: 明治大学
• [Presentation] Whole Genome Shotgunを用いた病原菌に関する疫学研究のための解析手法の開発 (2014)
  • Author(s): 吉村大
  • Organizer: ゲノム微生物学会
  • Place of Presentation: 東京農工大学
• [Presentation] A whole genome comparison between lager brewing yeast Weihenstephan 34/70 and its ancestral strains (2013)
  • Author(s): Miki Okuno
  • Organizer: Yeast 2013
  • Place of Presentation: Westend of Goethe University