HCFC1 is a common component of active human CpG-island promoters and coincides with ZNF143, THAP11, YY1, and GABP transcription factor occupancy

Genome Res. 2013 Jun;23(6):907-16. doi: 10.1101/gr.150078.112. Epub 2013 Mar 28.

Abstract

In human transcriptional regulation, DNA-sequence-specific factors can associate with intermediaries that orchestrate interactions with a diverse set of chromatin-modifying enzymes. One such intermediary is HCFC1 (also known as HCF-1). HCFC1, first identified in herpes simplex virus transcription, has a poorly defined role in cellular transcriptional regulation. We show here that, in HeLa cells, HCFC1 is observed bound to 5400 generally active CpG-island promoters. Examination of the DNA sequences underlying the HCFC1-binding sites revealed three sequence motifs associated with the binding of (1) ZNF143 and THAP11 (also known as Ronin), (2) GABP, and (3) YY1 sequence-specific transcription factors. Subsequent analysis revealed colocalization of HCFC1 with these four transcription factors at ∼90% of the 5400 HCFC1-bound promoters. These studies suggest that a relatively small number of transcription factors play a major role in HeLa-cell transcriptional regulation in association with HCFC1.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Binding Sites
  • CpG Islands*
  • GA-Binding Protein Transcription Factor / metabolism*
  • Gene Expression Regulation
  • HeLa Cells
  • Host Cell Factor C1 / metabolism*
  • Humans
  • Nucleotide Motifs
  • Position-Specific Scoring Matrices
  • Promoter Regions, Genetic*
  • Protein Binding
  • RNA, Messenger / genetics
  • Repressor Proteins / metabolism*
  • Signal Transduction
  • Trans-Activators / metabolism*
  • Transcription Initiation Site
  • Transcriptional Activation
  • YY1 Transcription Factor / metabolism*

Substances

  • GA-Binding Protein Transcription Factor
  • HCFC1 protein, human
  • Host Cell Factor C1
  • RNA, Messenger
  • Repressor Proteins
  • THAP11 protein, human
  • Trans-Activators
  • YY1 Transcription Factor
  • ZNF143 protein, human