Widespread RNA binding by chromatin-associated proteins.

Genome Biol
Authors
Keywords
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
Journal
Genome Biol
Volume
17
Pages
28
Date Published
2016 Feb 16
ISSN
1474-760X
DOI
10.1186/s13059-016-0878-3
PubMed ID
26883116
PubMed Central ID
PMC4756407
Links
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