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

Joëlle Michaud; Viviane Praz; Nicole James Faresse; Courtney K. JnBaptiste; Shweta Tyagi; Frédéric Schütz; Winship Herr

doi:10.1101/gr.150078.112

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

¹Center for Integrative Genomics, University of Lausanne, Génopode, 1015 Lausanne, Switzerland;
²Bioinformatics Core Facility, SIB Swiss Institute of Bioinformatics, Génopode, 1015 Lausanne, Switzerland

↵Present addresses: ³Gene Predictis SA, Site EPFL, PSE-B, CP 128, 1015 Lausanne, Switzerland;
↵4 Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA;
↵5 Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Nampally, Hyderabad 500001, India.

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.

Footnotes

↵6 Corresponding author

E-mail winship.herr{at}unil.ch
[Supplemental material is available for this article.]
Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.150078.112.

Received September 28, 2012.
Accepted March 27, 2013.

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