Widespread RNA binding by chromatin-associated proteins

Genome Biology
David G HendricksonJohn L Rinn

Abstract

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. 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. 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.

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Datasets Mentioned

BETA
GSE67963
GSE28865
GSE3554

Methods Mentioned

BETA
immunoprecipitation
cross-link IP
ChIP
fRIP-Seq
RNA-Seq
CLIP-Seq
pull down
fRIP-Seqs
RRBS
ChIP-Seq

Software Mentioned

GENCODE
fRIP
Cuffdiff
TopHat
R package PAM
FIRE
Database for Annotation , Visualization and Integrated Discove...
DAVID

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