Transcriptomics

Dataset Information

62

Transcription factor trapping by RNA in gene regulatory elements (CLIP-Seq)


ABSTRACT: 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. CLIP-Seq for YY1 in mouse embryonic stem cells

ORGANISM(S): Mus musculus  

SUBMITTER: Brian J Abraham  Xiong Ji   Alla Sigova   Nancy M Hannett   Yang E Guo   Benoit Molinie   Cosmas C Giallourakis   Phillip A Sharp   Mohini Jangi   Richard A Young    

PROVIDER: E-GEOD-68196 | ArrayExpress | 2015-12-08

SECONDARY ACCESSION(S): SRP057597GSE68196PRJNA282101

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications


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 o  ...[more]

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