title: Transcription factor trapping by RNA in gene regulatory elements.
abstract: Transcription factors (TFs) bind specific sequences in promoter-proximal and -distal DNA elements to regulate gene transcription. RNA is transcribed from both of these DNA elements, and some DNA binding TFs bind RNA. Hence, RNA transcribed from regulatory elements may contribute to stable TF occupancy at these sites. We show that the ubiquitously expressed TF Yin-Yang 1 (YY1) binds to both gene regulatory elements and their associated RNA species across the entire genome. Reduced transcription of regulatory elements diminishes YY1 occupancy, whereas artificial tethering of RNA enhances YY1 occupancy at these elements. We propose that RNA makes a modest but important contribution to the maintenance of certain TFs at gene regulatory elements and suggest that transcription of regulatory elements produces a positive-feedback loop that contributes to the stability of gene expression programs.
authors.affiliation: Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
authors.forename: Alla A
authors.initials: AA
authors.lastname: Sigova
authors.affiliation: Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Abraham
authors.affiliation: Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
authors.forename: Xiong
authors.initials: X
authors.lastname: Ji
authors.affiliation: Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
authors.forename: Benoit
authors.initials: B
authors.lastname: Molinie
authors.affiliation: Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
authors.forename: Nancy M
authors.initials: NM
authors.lastname: Hannett
authors.affiliation: Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
authors.forename: Yang Eric
authors.initials: YE
authors.lastname: Guo
authors.affiliation: Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA. David H. Koch Institute for Integrative Cancer Research, Cambridge, MA 02140, USA.
authors.forename: Mohini
authors.initials: M
authors.lastname: Jangi
authors.affiliation: Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
authors.forename: Cosmas C
authors.initials: CC
authors.lastname: Giallourakis
authors.affiliation: Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA. David H. Koch Institute for Integrative Cancer Research, Cambridge, MA 02140, USA.
authors.forename: Phillip A
authors.initials: PA
authors.lastname: Sharp
authors.affiliation: Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA. young@wi.mit.edu.
authors.forename: Richard A
authors.initials: RA
authors.lastname: Young
mesh_terms: D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D002460:Cell Line; D016384:Consensus Sequence; D004247:DNA / Q000378:metabolism; D053595:Embryonic Stem Cells / Q000378:metabolism; D004742:Enhancer Elements, Genetic; D005786:Gene Expression Regulation; D051379:Mice; D011401:Promoter Regions, Genetic; D012333:RNA, Messenger / Q000378:metabolism*; D014158:Transcription, Genetic; D050986:YY1 Transcription Factor / Q000378:metabolism*
chemical_list: D012333:RNA, Messenger; D050986:YY1 Transcription Factor; D004247:DNA