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Title: Transcription factor trapping by RNA in gene regulatory elements (ChIP-Seq)      
keywords:
Epigenomics
ID:
PRJNA282102
description:
Transcription factors (TFs) bind specific sequences in promoter-proximal and distal DNA elements in order to regulate gene transcription. RNA is transcribed from both promoter-proximal and distal DNA elements, and some DNA-binding TFs have also been shown to bind RNA. These obsevations led us to postulate that RNA transcribed from regulatory elements contributes to stable TF occupancy at these regulatory elements. We show here that the ubiquitously expressed TF YY1 binds to both proximal and distal regulatory elements and to the RNA species associated with these elements near active genes in embryonic stem cells. Inhibition of transcription from these elements reduces YY1 occupancy. In contrast, tethering of RNA species near YY1 DNA binding sites enhances YY1 occupancy. We propose that RNA acts as trap to maintain certain TFs at active enhancer and promoter-proximal regulatory elements. Thus, transcriptional control generally involves a positive feedback loop, where YY1 and other TFs stimulate local transcription, and newly transcribed nascent RNA reinforces local TF occupancy. This model helps explain why TFs occupy only the small fraction of their consensus motifs in the mammalian genome where transcription is detected. Overall design: Affinity purification (ChIP-Seq) for YY1 in mouse embryonic stem cells treated with transcription-affecting compounds
accesstypes:
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landingpage: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA282102
authentication:
none
authorization:
none
ID:
pmid:26516199
name:
Mus musculus
ncbiID:
ncbitax:10090
abbreviation:
NCBI
homePage: http://www.ncbi.nlm.nih.gov
ID:
SCR:006472
name:
National Center for Biotechnology Information
homePage: http://www.ncbi.nlm.nih.gov/bioproject
ID:
SCR:004801
name:
NCBI BioProject
  • P01 CA042063/CA/NCI NIH HHS/United States

  • P30 DK043351/DK/NIDDK NIH HHS/United States

  • R01 HG002668/HG/NHGRI NIH HHS/United States

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