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Genome Biol. 2016 Feb 16;17:28. doi: 10.1186/s13059-016-0878-3.

Widespread RNA binding by chromatin-associated proteins.

Author information

1
Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA. david.gillis.hendrickson@gmail.com.
2
Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA. david.gillis.hendrickson@gmail.com.
3
Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA. dkelley@fas.harvard.edu.
4
Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA. dkelley@fas.harvard.edu.
5
Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA. dtenen@broadinstitute.org.
6
Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA. dtenen@broadinstitute.org.
7
Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA. Bernstein.Bradley@mgh.harvard.edu.
8
Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA. john_rinn@harvard.edu.
9
Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA. john_rinn@harvard.edu.
10
Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA. john_rinn@harvard.edu.

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.

PMID:
26883116
PMCID:
PMC4756407
DOI:
10.1186/s13059-016-0878-3
[Indexed for MEDLINE]
Free PMC Article

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