Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs
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Sharp_Genome-wide.pdf
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Author(s)
Leung, Anthony
Young, Amanda G.
Bhutkar, Arjun (AJ)
Zheng, Grace X.
Bosson, Andrew David
Nielsen, Cydney B.
Sharp, Phillip A.
Date Issued
January 2011
Journal
Nature Structural and Molecular Biology
Publisher
Nature Publishing Group
Citation
Leung, Anthony K L et al. “Genome-wide Identification of Ago2 Binding Sites from Mouse Embryonic Stem Cells with and Without Mature microRNAs.” Nature Structural & Molecular Biology 18.2 (2011): 237–244.
Version
Author's final manuscript
Abstract
MicroRNAs (miRNAs) are 19–22-nucleotide noncoding RNAs that post-transcriptionally regulate mRNA targets. We have identified endogenous miRNA binding sites in mouse embryonic stem cells (mESCs), by performing photo-cross-linking immunoprecipitation using antibodies to Argonaute (Ago2) followed by deep sequencing of RNAs (CLIP-seq). We also performed CLIP-seq in Dicer[superscript −/−] mESCs that lack mature miRNAs, allowing us to define whether the association of Ago2 with the identified sites was miRNA dependent. A significantly enriched motif, GCACUU, was identified only in wild-type mESCs in 3′ untranslated and coding regions. This motif matches the seed of a miRNA family that constitutes ~68% of the mESC miRNA population. Unexpectedly, a G-rich motif was enriched in sequences cross-linked to Ago2 in both the presence and absence of miRNAs. Expression analysis and reporter assays confirmed that the seed-related motif confers miRNA-directed regulation on host mRNAs and that the G-rich motif can modulate this regulation.
MIT Department
Massachusetts Institute of Technology. Computational and Systems Biology Program
Massachusetts Institute of Technology. Department of Biology
Koch Institute for Integrative Cancer Research at MIT
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Creative Commons Attribution-Noncommercial-Share Alike 3.0
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DOI of Published Version
https://doi.org/10.1038/nsmb.1991
