Genomic binding of Pol III transcription machinery and relationship with TFIIS transcription factor distribution in mouse embryonic stem cells

Nucleic Acids Res. 2012 Jan;40(1):270-83. doi: 10.1093/nar/gkr737. Epub 2011 Sep 12.


RNA polymerase (Pol) III synthesizes the tRNAs, the 5S ribosomal RNA and a small number of untranslated RNAs. In vitro, it also transcribes short interspersed nuclear elements (SINEs). We investigated the distribution of Pol III and its associated transcription factors on the genome of mouse embryonic stem cells using a highly specific tandem ChIP-Seq method. Only a subset of the annotated class III genes was bound and thus transcribed. A few hundred SINEs were associated with the Pol III transcription machinery. We observed that Pol III and its transcription factors were present at 30 unannotated sites on the mouse genome, only one of which was conserved in human. An RNA was associated with >80% of these regions. More than 2200 regions bound by TFIIIC transcription factor were devoid of Pol III. These sites were associated with cohesins and often located close to CTCF-binding sites, suggesting that TFIIIC might cooperate with these factors to organize the chromatin. We also investigated the genome-wide distribution of the ubiquitous TFIIS variant, TCEA1. We found that, as in Saccharomyces cerevisiae, TFIIS is associated with class III genes and also with SINEs suggesting that TFIIS is a Pol III transcription factor in mammals.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Binding Sites
  • Butyrate Response Factor 1
  • Cell Line
  • Chromatin / metabolism
  • Chromatin Immunoprecipitation / methods
  • Embryonic Stem Cells / metabolism*
  • Genome
  • Mice
  • Nuclear Proteins / metabolism
  • RNA Polymerase II / metabolism
  • RNA Polymerase III / metabolism*
  • RNA, Small Nuclear / genetics
  • RNA, Transfer / genetics
  • RNA-Binding Proteins / metabolism
  • Sequence Analysis, DNA
  • Short Interspersed Nucleotide Elements
  • Transcription Factor TFIIIB / metabolism
  • Transcription Factors, TFIII / metabolism
  • Transcription, Genetic*
  • Transcriptional Elongation Factors / metabolism*


  • Butyrate Response Factor 1
  • Chromatin
  • Nuclear Proteins
  • RNA, Small Nuclear
  • RNA-Binding Proteins
  • Transcription Factor TFIIIB
  • Transcription Factors, TFIII
  • Transcriptional Elongation Factors
  • Zfp36l1 protein, mouse
  • transcription factor S-II
  • transcription factor TFIIIC
  • RNA, Transfer
  • RNA Polymerase II
  • RNA Polymerase III