Abstract
BackgroundRecent 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.ResultsHere, 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.ConclusionFor 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-0878-3) contains supplementary material, which is available to authorized users.
Highlights
Recent evidence suggests that RNA interaction can regulate the activity and localization of chromatin-associated proteins
It has been suggested that a large class of newly discovered long noncoding RNAs have functional roles in binding and modulating the activity of proteins involved in chromatin modification [38, 45, 57, 70,71,72, 82, 84]
Results formaldehyde RNA immunoprecipitation (fRIP)-Seq: a method for capturing and identifying RNA–chromatin-associated proteins (CAPs) interactions To survey a broad panel of RNA–CAP interactions, we required an immunoprecipitation (IP) method optimized for maximal RNA and protein recovery that is specific, scalable, quantitative, reproducible, and similar to chromatin immunoprecipitation (ChIP) conditions known to readily isolate CAP complexes and recover DNA–CAP interactions
Summary
Recent evidence suggests that RNA interaction can regulate the activity and localization of chromatin-associated proteins. Recent advances in systematic profiling of nucleic acid–protein interactions have blurred these conventions, finding that many DNA binding proteins associate with RNA to modulate both transcriptional and post-transcriptional outcomes [1, 7, 15, 28, 39, 44, 60, 71, 89]. These studies suggest a more intertwined regulatory network than previously appreciated. If Xist and other examples are to be generalized, RNA may be an important missing component of these incomplete models of chromatin dynamics
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