Comparative genome analysis of functional endogenous viral elements using massive nucleotide sequence data

• Project/Area Number: 16K21386
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Genome biology; Genetics/Chromosome dynamics
• Research Institution: Tokai University
• Principal Investigator: NAKAGAWA So 東海大学, 医学部, 助教 (70510014)
• Project Period (FY): 2016-04-01 – 2018-03-31
• Project Status: Completed (Fiscal Year 2017)
• Budget Amount: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000); Fiscal Year 2017: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000); Fiscal Year 2016: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
• Keywords: レトロウイルス / レトロトランスポゾン / 比較ゲノム / 分子進化 / データベース / 機能ゲノム / 内在性ウイルス様配列 / トランスポゾン / 内在性レトロウイルス / ゲノム進化 / 新規機能性配列探索 / バイオインフォマティクス

Outline of Final Research Achievements

The aim of this research project is to clarify various new functions gained by endogenous viral elements (EVEs) in mammalian genomes and their genome evolution. I have developed an annotation database called gEVE for possible protein-coding sequences derived from EVEs. In this study, we have identified various new functional sequences derived from EVE using NGS data analyzed with this database. For example, we discovered a novel structural protein Gag-like retroviral gene expressed in bovine placenta by collaborative research. We also identified non-coding regions derived from EVE and predicted that it might have acquired the function such as promoters.

Research Products

• [Journal Article] Novel endogenous retrovirus-derived transcript expressed in the bovine placenta is regulated by WNT signaling. (2017)
  • Author(s): Sakurai T, Nakagawa S, Bai H, Bai R, Kusama K, Ideta A, Aoyagi Y, Kaneko K, Iga K, Yasuda J, Miyazawa T, Imakawa K.
  • Journal Title: Biochemical Journal Volume: 474 Issue: 20 Pages: 3499-3512
  • DOI: 10.1042/bcj20170531
  • NAID: 120006649525
  • Peer Reviewed / Open Access
• [Journal Article] The Phylogeny of Placental Evolution Through Dynamic Integrations of Retrotransposons (2017)
  • Author(s): Kazuhiko Imakawa, So Nakagawa
  • Journal Title: Progress in Molecular Biology and Translational Science Volume: 145 Pages: 89-109
  • DOI: 10.1016/bs.pmbts.2016.12.004
  • Peer Reviewed
• [Journal Article] gEVE: a genome-based endogenous viral element database provides comprehensive viral protein-coding sequences in mammalian genomes (2016)
  • Author(s): So Nakagawa, Mahoko Ueda Takahashi
  • Journal Title: Database (Oxford) Volume: 2016 Pages: baw087-baw087
  • DOI: 10.1093/database/baw087
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Placental Development and Endogenous Retroviruses (2016)
  • Author(s): 今川和彦、中川草、草間和哉
  • Journal Title: Uirusu Volume: 66 Issue: 1 Pages: 1-10
  • DOI: 10.2222/jsv.66.1
  • NAID: 130006882854
  • ISSN: 0042-6857, 1884-3433
  • Peer Reviewed / Open Access
• [Journal Article] RD-114 virus story: from RNA rumor virus to a useful viral tool for elucidating the world cats' journey (2016)
  • Author(s): 宮沢孝幸、下出紗弓、中川草
  • Journal Title: Uirusu Volume: 66 Issue: 1 Pages: 21-30
  • DOI: 10.2222/jsv.66.21
  • NAID: 130006882840
  • ISSN: 0042-6857, 1884-3433
  • Open Access
• [Presentation] NGSを活用したゲノムに内在化するウイルス由来機能配列の探索 (2017)
  • Author(s): 中川草、上田真保子
  • Organizer: NGS現場の会 第五回研究会
• [Presentation] gEVE, genome-scale endogenous viral element database, and its applications (2017)
  • Author(s): So Nakagawa
  • Organizer: NIG International Symposium 2017 Commemorating the 30th Anniversary of DDBJ
  • Int'l Joint Research
• [Presentation] Genome-Wide Analyses of Endogenous Viral Elements in Mammalian Genomes Using the gEVE Database and Next-generation DNA Sequencing Data (2017)
  • Author(s): So Nakagawa
  • Organizer: 29th International Conference of the Korean Society for Molecular and Cellular Biology (KSMCB)
  • Int'l Joint Research / Invited
• [Presentation] 細胞融合にかかわる内在性レトロウイルス由来遺伝子の同定 (2017)
  • Author(s): 上田真保子、三橋里美、三橋弘明、今西規、中川草
  • Organizer: 2017年度生命科学系学会合同年次大会
• [Presentation] Transcriptome analysis to identify expressed sequences derived from endogeouns viral elements (2016)
  • Author(s): So Nakagawa, Mahoko Ueda Takahashi
  • Organizer: 28th International Workshop on Retroviral Pathogenesis
  • Place of Presentation: Bourbon Orleans Hotel (New Orleans, USA)
  • Year and Date: 2016-12-05
  • Int'l Joint Research
• [Presentation] 哺乳類ゲノムに内在化するウイルス由来の配列の比較トランスクリプトーム解析 (2016)
  • Author(s): 中川草、上田真保子
  • Organizer: 第39回日本分子生物学会年会
  • Place of Presentation: パシフィコ横浜（神奈川県横浜市）
  • Year and Date: 2016-11-30
• [Presentation] 合胞体栄養膜細胞分化モデルを用いた内在性レトロウイルスの網羅的発現解析 (2016)
  • Author(s): 森田一輝, 永松健, 中川草, 杉本潤, 川名敬, 大須賀穣, 藤井知行
  • Organizer: 第24回日本胎盤学会学術集会 第34回日本絨毛性疾患研究会
  • Place of Presentation: ホテルアバローム紀の国（和歌山県和歌山市）
  • Year and Date: 2016-11-25
• [Presentation] マウスサプレシン遺伝子の単離・同定 (2016)
  • Author(s): 杉本潤, Danny Schust, 中川草, 小田高也, 陣野吉廣
  • Organizer: 第24回日本胎盤学会学術集会 第34回日本絨毛性疾患研究会
  • Place of Presentation: ホテルアバローム紀の国（和歌山県和歌山市）
  • Year and Date: 2016-11-25
• [Presentation] 哺乳類ゲノムに内在化するウイルス由来の配列データベースgEVEとその活用方法 (2016)
  • Author(s): 中川草、上田真保子
  • Organizer: 日本遺伝学会 第８８回大会
  • Place of Presentation: 日本大学国際関係学部 三島駅北口校舎（静岡県三島市）
  • Year and Date: 2016-09-07
• [Presentation] 哺乳類ゲノムに内在化するウイルス由来の比較トランスクリプトーム解析 (2016)
  • Author(s): 中川草、上田真保子
  • Organizer: 日本進化学会 第１８回東京大会
  • Place of Presentation: 東京工業大学大岡山キャンパス（東京都目黒区）
  • Year and Date: 2016-08-25
• [Presentation] gEVE: a genome-based endogenous viral element database provides open reading frame sequences derived from viruses in 20 mammalian genomes (2016)
  • Author(s): So Nakagawa, Mahoko U Takahashi
  • Organizer: International Congress on Transposable Elements (ICTE) 2016
  • Place of Presentation: Saint-Malo’s Convention Center (San Malo, France)
  • Year and Date: 2016-04-16
  • Int'l Joint Research