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UPA-seq : prediction of functional lncRNAs using differential sensitivity to UV crosslinking

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タイトル: UPA-seq : prediction of functional lncRNAs using differential sensitivity to UV crosslinking
著者: Komatsu, Taiwa 著作を一覧する
Yokoi, Saori 著作を一覧する
Fujii, Koichi 著作を一覧する
Mito, Mari 著作を一覧する
Kimura, Yusuke 著作を一覧する
Iwasaki, Shintaro 著作を一覧する
Nakagawa, Shinichi 著作を一覧する
キーワード: noncoding RNAs
lncRNAs
RNA-binding proteins
UV crosslinking
eCLIP
RNA-seq
phenol-chloroform extraction
発行日: 2018年12月
出版者: Cold Spring Harbor Laboratory Press
誌名: RNA
巻: 24
号: 12
開始ページ: 1785
終了ページ: 1802
出版社 DOI: 10.1261/rna.067611.118
抄録: While a large number of long noncoding RNAs (lncRNAs) are transcribed from the genome of higher eukaryotes, systematic prediction of their functionality has been challenging due to the lack of conserved sequence motifs or structures. Assuming that some lncRNAs function as large ribonucleoprotein complexes and thus are easily crosslinked to proteins upon UV irradiation, we performed RNA-seq analyses of RNAs recovered from the aqueous phase after UV irradiation and phenol-chloroform extraction (UPA-seq). As expected, the numbers of UPA-seq reads mapped to known functional lncRNAs were remarkably reduced upon UV irradiation. Comparison with ENCODE eCLIP data revealed that lncRNAs that exhibited greater decreases upon UV irradiation preferentially associated with proteins containing prion-like domains (PrLDs). Fluorescent in situ hybridization (FISH) analyses revealed the nuclear localization of novel functional lncRNA candidates, including one that accumulated at the site of transcription. We propose that UPA-seq provides a useful tool for the selection of lncRNA candidates to be analyzed in depth in subsequent functional studies.
資料タイプ: article
URI: http://hdl.handle.net/2115/72220
出現コレクション:雑誌発表論文等 (Peer-reviewed Journal Articles, etc)

提供者: 中川 真一

 

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