Widespread RNA binding by chromatin-associated proteins.
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Abstract | BACKGROUND: Recent evidence suggests that RNA interaction can regulate the activity and localization of chromatin-associated proteins. However, it is unknown if these observations are specialized instances for a few key RNAs and chromatin factors in specific contexts, or a general mechanism underlying the establishment of chromatin state and regulation of gene expression. RESULTS: Here, we perform formaldehyde RNA immunoprecipitation (fRIP-Seq) to survey the RNA associated with a panel of 24 chromatin regulators and traditional RNA binding proteins. For each protein that reproducibly bound measurable quantities of bulk RNA (90% of the panel), we detect enrichment for hundreds to thousands of both noncoding and mRNA transcripts. CONCLUSION: For each protein, we find that the enriched sets of RNAs share distinct biochemical, functional, and chromatin properties. Thus, these data provide evidence for widespread specific and relevant RNA association across diverse classes of chromatin-modifying complexes. |
Year of Publication | 2016
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Journal | Genome Biol
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Volume | 17
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Pages | 28
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Date Published | 2016 Feb 16
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ISSN | 1474-760X
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DOI | 10.1186/s13059-016-0878-3
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PubMed ID | 26883116
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PubMed Central ID | PMC4756407
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Grant list | U54 HG006991 / HG / NHGRI NIH HHS / United States
DP2 OD006670 / OD / NIH HHS / United States
HG006991 / HG / NHGRI NIH HHS / United States
R01 ES020260 / ES / NIEHS NIH HHS / United States
DP2OD006670 / OD / NIH HHS / United States
K25 ES022984 / ES / NIEHS NIH HHS / United States
R01ES020260 / ES / NIEHS NIH HHS / United States
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