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Genome-wide Mapping of DROSHA Cleavage Sites on Primary MicroRNAs and Noncanonical Substrates

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Title
Genome-wide Mapping of DROSHA Cleavage Sites on Primary MicroRNAs and Noncanonical Substrates
Author(s)
Baekgyu Kim; Kyowon Jeong; V. Narry Kim
Subject
CLIP-seq, ; DGCR8, ; DROSHA, ; formaldehyde crosslinking, ; microprocessor, ; microRNA, ; pri-miRNA, ; RNA, ; sequencing
Publication Date
2017-04
Journal
MOLECULAR CELL, v.66, no.2, pp.258 - 269
Publisher
CELL PRESS
Abstract
MicroRNA (miRNA) maturation is initiated by DROSHA, a double-stranded RNA (dsRNA)-specific RNase III enzyme. By cleaving primary miRNAs (pri-miRNAs) at specific positions, DROSHA serves as a main determinant of miRNA sequences and a highly selective gatekeeper for the canonical miRNA pathway. However, the sites of DROSHA-mediated processing have not been annotated, and it remains unclear to what extent DROSHA functions outside the miRNA pathway. Here, we establish a protocol termed “formaldehyde crosslinking, immunoprecipitation, and sequencing (fCLIP-seq),” which allows identification of DROSHA cleavage sites at single-nucleotide resolution. fCLIP identifies numerous processing sites, suggesting widespread end modifications during miRNA maturation. fCLIP also finds many pri-miRNAs that undergo alternative processing, yielding multiple miRNA isoforms. Moreover, we discovered dozens of DROSHA substrates on non-miRNA loci, which may serve as cis-elements for DROSHA-mediated gene regulation. We anticipate that fCLIP-seq could be a general tool for investigating interactions between dsRNA-binding proteins and structured RNAs. © 2017 Elsevier Inc
URI
https://pr.ibs.re.kr/handle/8788114/3744
DOI
10.1016/j.molcel.2017.03.013
ISSN
1097-2765
Appears in Collections:
Center for RNA Research(RNA 연구단) > 1. Journal Papers (저널논문)
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PIIS1097276517302034.pdfDownload

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