title: Widespread RNA binding by chromatin-associated proteins.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA. david.gillis.hendrickson@gmail.com.|Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA. david.gillis.hendrickson@gmail.com.
authors.forename: David
authors.initials: D
authors.lastname: G Hendrickson
authors.affiliation: Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA. dkelley@fas.harvard.edu.|Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA. dkelley@fas.harvard.edu.
authors.forename: David R
authors.initials: DR
authors.lastname: Kelley
authors.affiliation: Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA. dtenen@broadinstitute.org.|Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA. dtenen@broadinstitute.org.
authors.forename: Danielle
authors.initials: D
authors.lastname: Tenen
authors.affiliation: Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA. Bernstein.Bradley@mgh.harvard.edu.
authors.forename: Bradley
authors.initials: B
authors.lastname: Bernstein
authors.affiliation: Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA. john_rinn@harvard.edu.|Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA. john_rinn@harvard.edu.|Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA. john_rinn@harvard.edu.
authors.forename: John L
authors.initials: JL
authors.lastname: Rinn
mesh_terms: D002843:Chromatin / Q000235:genetics* / Q000378:metabolism; D006801:Humans; D012313:RNA / Q000235:genetics* / Q000378:metabolism; D062085:RNA, Long Noncoding / Q000096:biosynthesis; D012333:RNA, Messenger / Q000096:biosynthesis / Q000235:genetics; D016601:RNA-Binding Proteins / Q000096:biosynthesis / Q000235:genetics* / Q000378:metabolism
chemical_list: D002843:Chromatin; D062085:RNA, Long Noncoding; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; D012313:RNA