CTCF Interacts with and Recruits the Largest Subunit of RNA Polymerase II to CTCF Target Sites Genome-Wide

Abstract

CTCF is a transcription factor with highly versatile functions ranging from gene activation and repression to the regulation of insulator function and imprinting. Although many of these functions rely on CTCF-DNA interactions, it is an emerging realization that CTCF-dependent molecular processes involve CTCF interactions with other proteins. In this study, we report the association of a subpopulation of CTCF with the RNA polymerase II (Pol II) protein complex. We identified the largest subunit of Pol II (LS Pol II) as a protein significantly colocalizing with CTCF in the nucleus and specifically interacting with CTCF in vivo and in vitro. The role of CTCF as a link between DNA and LS Pol II has been reinforced by the observation that the association of LS Pol II with CTCF target sites in vivo depends on intact CTCF binding sequences. “Serial” chromatin immunoprecipitation (ChIP) analysis revealed that both CTCF and LS Pol II were present at the β-globin insulator in proliferating HD3 cells but not in differentiated globin synthesizing HD3 cells. Further, a single wild-type CTCF target site (N-Myc-CTCF), but not the mutant site deficient for CTCF binding, was sufficient to activate the transcription from the promoterless reporter gene in stably transfected cells. Finally, a ChIP-on-ChIP hybridization assay using microarrays of a library of CTCF target sites revealed that many intergenic CTCF target sequences interacted with both CTCF and LS Pol II. We discuss the possible implications of our observations with respect to plausible mechanisms of transcriptional regulation via a CTCF-mediated direct link of LS Pol II to the DNA.

We thank S. Muller and J. Dadoune for anti-histone H2A and histone H3 antibodies. We are also grateful to M. Metodiev, A. Harrison, A. Akoulitchev, and A. Ramadass for helpful discussions and P. O'Toole for assistance with confocal microscopy. We gratefully acknowledge the assistance of A. Isaksson and the Wallenberg microarray platform at the Rudbeck laboratory.

This research was supported by the Association for International Cancer Research (I.C. and E.K.), the Breast Cancer Campaign (F.D. and E.K.), the Medical Research Council (D.F. and E.K.), the Research Promotion Fund from University of Essex (E.K.), the National Institutes of Health grant CA103867 (C.-M.C.), a scholarship from the Malaysian Government and Fundamental Research Grant Scheme from the Malaysian Government (S.S.), the Swedish Science Research Council (R.O.), the Juvenile Diabetes Research Foundation International (R.O.), the Swedish Cancer Research Foundation (R.O.), the Swedish Pediatric Cancer Foundation (R.O.), the Wallenberg and Lundberg Foundations (R.O.), Stiftelsen Wenner-Grenska Samfundet (R.O.), and the Intramural Research Program of the NIH, NIAID (V.L., D.L., and Y.-W.K.).