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Bioinformatics. 2013 Jun 15;29(12):1485-7. doi: 10.1093/bioinformatics/bts596. Epub 2012 Oct 9.

Promoter-proximal CCCTC-factor binding is associated with an increase in the transcriptional pausing index.

Author information

1
Curriculum in Bioinformatics and Computational Biology, Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

Abstract

MOTIVATION:

It has been known for more than 2 decades that after RNA polymerase II (RNAPII) initiates transcription, it can enter into a paused or stalled state immediately downstream of the transcription start site before productive elongation. Recent advances in high-throughput genomic technologies facilitated the discovery that RNAPII pausing at promoters is a widespread physiologically regulated phenomenon. The molecular underpinnings of pausing are incompletely understood. The CCCTC-factor (CTCF) is a ubiquitous nuclear factor that has diverse regulatory functions, including a recently discovered role in promoting RNAPII pausing at splice sites.

RESULTS:

In this study, we analyzed CTCF binding sites and nascent transcriptomic data from three different cell types, and found that promoter-proximal CTCF binding is significantly associated with RNAPII pausing.

PMID:
23047559
PMCID:
PMC3673211
DOI:
10.1093/bioinformatics/bts596
[Indexed for MEDLINE]
Free PMC Article

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