Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival.
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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. |
Year of Publication | 2016
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Journal | Cell Rep
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Volume | 15
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Issue | 3
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Pages | 666-79
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Date Published | 2016 Apr 19
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ISSN | 2211-1247
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URL | |
DOI | 10.1016/j.celrep.2016.03.052
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PubMed ID | 27068461
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PubMed Central ID | PMC4839292
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Grant list | HG004659 / HG / NHGRI NIH HHS / United States
U54HG007005 / HG / NHGRI NIH HHS / United States
NS075449 / NS / NINDS NIH HHS / United States
U54 HG007005 / HG / NHGRI NIH HHS / United States
HG007005 / HG / NHGRI NIH HHS / United States
T32 GM087237 / GM / NIGMS NIH HHS / United States
R01 HG004659 / HG / NHGRI NIH HHS / United States
P30 CA023100 / CA / NCI NIH HHS / United States
T32 GM008666 / GM / NIGMS NIH HHS / United States
R01 NS075449 / NS / NINDS NIH HHS / United States
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