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Exhaustive detection of condition-specific splicing variants in non-model organisms

Research Project

Project/Area Number 17K00419
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Life / Health / Medical informatics
Research InstitutionNagahama Institute of Bio-Science and Technology

Principal Investigator

Kouki Yonezawa  長浜バイオ大学, バイオサイエンス学部, 助教 (00374744)

Project Period (FY) 2017-04-01 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
Fiscal Year 2019: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2018: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2017: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
Keywords選択的スプライシング / 条件依存的 / バイオインフォマティクス / スプライシングバリアント / 非モデル生物 / 生体生命情報学 / アルゴリズム
Outline of Final Research Achievements

Alternative splicing is a mechanism to generate more than one mRNA isoforms from a single locus, and it increases the genetic diversity during post-ranscriptional gene regulation. Furthermore, alternative splicing is often differentially regulated across tissues and during development. It suggests that each splicing isoform may have specific spatial and temporal roles in life system.
We have developed the differential alternative splicing variants estimation method. To assess applicability of our method using RNA-sequence data for estimation of conditional-specific alternative events, we used several RNA-seq datasets. We confirmed that the newest version of our method could extract many candidates of condition-specific alternative splicing variants.

Academic Significance and Societal Importance of the Research Achievements

非モデル生物の条件依存型選択的スプライシングについては研究がそれほど進んでいない.これはモデル生物におけるリファレンスゲノムが無いことが一因であるが,これにより非モデル生物の特殊性についてのさらなる知見が得られることが予想される.またマリアナイトエラゴカイの温度耐性のように,ヒトの反応メカニズムを解明するための手掛かりを得ることも可能となる.
また本手法では,従来の解析手法では困難だった巨大なRNA-seqに対して適用すること,さらに3つ以上の異なる条件下のRNA-seqデータをまとめて取り扱うことを可能にしている.

Report

(4 results)
  • 2019 Annual Research Report   Final Research Report ( PDF )
  • 2018 Research-status Report
  • 2017 Research-status Report
  • Research Products

    (3 results)

All 2019 2017

All Journal Article (1 results) (of which Peer Reviewed: 1 results) Presentation (2 results) (of which Int'l Joint Research: 1 results)

  • [Journal Article] DASE2: differential alternative splicing variants estimation method without reference genome, and comparison with mapping strategy2017

    • Author(s)
      Kouki Yonezawa, Keisuke Nakata, Ryuhei Minei, Atsushi Ogura
    • Journal Title

      Int. J. Data Mining and Bioinformatics

      Volume: 18 Issue: 1 Pages: 56-73

    • DOI

      10.1504/ijdmb.2017.086101

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Presentation] DASE-AG: conditional-specific differential alternative splicing events estimation method for around-gap regions2019

    • Author(s)
      Kouki Yonezawa and Atsushi Ogura
    • Organizer
      Bioinformatics: from Algorithms to Applications (BiATA 2019)
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 非モデル生物における条件依存的選択的スプライシングの網羅的発見手法の改良 -発現量に関する"外れ度"の定量化による精度向上-2017

    • Author(s)
      米澤 弘毅,嶺井 隆平,小倉 淳
    • Organizer
      第50回バイオ情報学研究会
    • Related Report
      2017 Research-status Report

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Published: 2017-04-28   Modified: 2021-02-19  

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