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Large-scale identification of microRNA targets in murine Dgcr8-deficient embryonic stem cell lines.

Published version
Peer-reviewed

Type

Article

Change log

Authors

Davis, Matthew PA 
Abreu-Goodger, Cei 
van Dongen, Stijn 
Lu, Dong 
Tate, Peri H 

Abstract

Small RNAs such as microRNAs play important roles in embryonic stem cell maintenance and differentiation. A broad range of microRNAs is expressed in embryonic stem cells while only a fraction of their targets have been identified. We have performed large-scale identification of embryonic stem cell microRNA targets using a murine embryonic stem cell line deficient in the expression of Dgcr8. These cells are heavily depleted for microRNAs, allowing us to reintroduce specific microRNA duplexes and identify refined target sets. We used deep sequencing of small RNAs, mRNA expression profiling and bioinformatics analysis of microRNA seed matches in 3' UTRs to identify target transcripts. Consequently, we have identified a network of microRNAs that converge on the regulation of several important cellular pathways. Additionally, our experiments have revealed a novel candidate for Dgcr8-independent microRNA genesis and highlighted the challenges currently facing miRNA annotation.

Description

Keywords

Animals, Cell Line, Embryonic Stem Cells, Gene Expression Profiling, Mice, MicroRNAs, Oligonucleotide Array Sequence Analysis, Proteins, RNA, Messenger, RNA-Binding Proteins, Transcription Factors

Journal Title

PLoS One

Conference Name

Journal ISSN

1932-6203
1932-6203

Volume Title

7

Publisher

Public Library of Science (PLoS)