Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival
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Conway-2016-Enhanced CLIP Uncove.pdf
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Author(s)
Conway, Anne E.
Van Nostrand, Eric L.
Pratt, Gabriel A.
Aigner, Stefan
Wilbert, Melissa L.
Sundararaman, Balaji
Lambert, Nicole J.
Sathe, Shashank
Liang, Tiffany Y.
Essex, Anthony
Date Issued
April 2016
Journal
Cell Reports
Publisher
Elsevier
Citation
Conway, Anne E., Eric L. Van Nostrand, Gabriel A. Pratt, Stefan Aigner, Melissa L. Wilbert, Balaji Sundararaman, Peter Freese, et al. “Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival.” Cell Reports 15, no. 3 (April 2016): 666–679.
Version
Final published version
Abstract
Human pluripotent stem cells (hPSCs) require precise control of post-transcriptional RNA networks to maintain proliferation and survival. Using enhanced UV crosslinking and immunoprecipitation (eCLIP), we identify RNA targets of the IMP/IGF2BP family of RNA-binding proteins in hPSCs. At the broad region and binding site levels, IMP1 and IMP2 show reproducible binding to a large and overlapping set of 3′ UTR-enriched targets. RNA Bind-N-seq applied to recombinant full-length IMP1 and IMP2 reveals CA-rich motifs that are enriched in eCLIP-defined binding sites. We observe that IMP1 loss in hPSCs recapitulates IMP1 phenotypes, including a reduction in cell adhesion and increase in cell death. For cell adhesion, we find IMP1 maintains levels of integrin mRNA specifically regulating RNA stability of ITGB5 in hPSCs. Additionally, we show that IMP1 can be linked to hPSC survival via direct target BCL2. Thus, transcriptome-wide binding profiles identify hPSC targets modulating well-characterized IMP1 roles.
MIT Department
Massachusetts Institute of Technology. Computational and Systems Biology Program
Massachusetts Institute of Technology. Department of Biology
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DOI of Published Version
https://doi.org/10.1016/j.celrep.2016.03.052
