Genomic study of RNA polymerase II and III SNAPc-bound promoters reveals a gene transcribed by both enzymes and a broad use of common activators

PLoS Genet. 2012;8(11):e1003028. doi: 10.1371/journal.pgen.1003028. Epub 2012 Nov 15.

Abstract

SNAP(c) is one of a few basal transcription factors used by both RNA polymerase (pol) II and pol III. To define the set of active SNAP(c)-dependent promoters in human cells, we have localized genome-wide four SNAP(c) subunits, GTF2B (TFIIB), BRF2, pol II, and pol III. Among some seventy loci occupied by SNAP(c) and other factors, including pol II snRNA genes, pol III genes with type 3 promoters, and a few un-annotated loci, most are primarily occupied by either pol II and GTF2B, or pol III and BRF2. A notable exception is the RPPH1 gene, which is occupied by significant amounts of both polymerases. We show that the large majority of SNAP(c)-dependent promoters recruit POU2F1 and/or ZNF143 on their enhancer region, and a subset also recruits GABP, a factor newly implicated in SNAP(c)-dependent transcription. These activators associate with pol II and III promoters in G1 slightly before the polymerase, and ZNF143 is required for efficient transcription initiation complex assembly. The results characterize a set of genes with unique properties and establish that polymerase specificity is not absolute in vivo.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA-Binding Proteins / genetics
  • Genome, Human
  • Humans
  • Promoter Regions, Genetic*
  • RNA Polymerase II* / genetics
  • RNA Polymerase II* / metabolism
  • RNA Polymerase III* / genetics
  • RNA Polymerase III* / metabolism
  • RNA, Small Nuclear / genetics
  • Regulatory Sequences, Nucleic Acid
  • Transcription Factor TFIIB / genetics
  • Transcription Factor TFIIB / metabolism
  • Transcription Factor TFIIIB / genetics
  • Transcription Factor TFIIIB / metabolism
  • Transcription Factors* / genetics
  • Transcription Factors* / metabolism

Substances

  • BRF2 protein, human
  • DNA-Binding Proteins
  • RNA, Small Nuclear
  • SNAPC protein complex, human
  • Transcription Factor TFIIB
  • Transcription Factor TFIIIB
  • Transcription Factors
  • RNA Polymerase II
  • RNA Polymerase III

Associated data

  • GEO/GSE38303

Grants and funding

This work was financed by the University of Lausanne and SNSF grants CRSI33_125230 and 31003A_132958. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.