※ をクリックすると外部の論文のサイトが開きます。
論文
- タイトル
- タイトル（英）
- Predicting cell-type-specific non-coding RNA transcription from genome sequence
- 参照URL
- https://researchmap.jp/hkawaji/published_papers/37947820
- 著者
- 著者（英）
- Masaru Koido,Chung-Chau Hon,Satoshi Koyama,Hideya Kawaji,Yasuhiro Murakawa,Kazuyoshi Ishigaki,Kaoru Ito,Jun Sese,Yoichiro Kamatani,Piero Carninci,Chikashi Terao
- 担当区分
- 概要
- 概要（英）
- SUMMARY Transcription is regulated through complex mechanisms involving non-coding RNAs (ncRNAs). However, because transcription of ncRNAs, especially enhancer RNAs, is often low and cell type-specific, its dependency on genotype remains largely unexplored. Here, we developed mutation effect prediction on ncRNA transcription (MENTR), a quantitative machine learning framework reliably connecting genetic associations with expression of ncRNAs, resolved to the level of cell type. MENTR-predicted mutation effects on ncRNA transcription were concordant with estimates from previous genetic studies in a cell type-dependent manner. We inferred reliable causal variants from 41,223 GWAS variants, and proposed 7,775 enhancers and 3,548 long-ncRNAs as complex trait-associated ncRNAs in 348 major human primary cells and tissues, including plausible enhancer-mediated functional alterations in single-variant resolution in Crohn’s disease. In summary, we present new resources for discovering causal variants, the biological mechanisms driving complex traits, and the sequence-dependency of ncRNA regulation in relevant cell types.
- 出版者・発行元
- 出版者・発行元（英）
- Cold Spring Harbor Laboratory
- 誌名
- 誌名（英）
- 巻
- 号
- 開始ページ
- 終了ページ
- 出版年月
- 2020年3月30日
- 査読の有無
- 招待の有無
- 掲載種別
- ISSN
- DOI URL
- https://doi.org/10.1101/2020.03.29.011205
- 共同研究・競争的資金等の研究課題
研究者
川路 英哉
( )