CTCF interacts with and recruits the largest subunit of RNA polymerase II to CTCF target sites genome-wide

Igor Chernukhin, Shaharum Shamsuddin, Sung Yun Kang, Rosita Bergström, Yoo Wook Kwon, WenQiang Yu, Joanne Whitehead, Rituparna Mukhopadhyay, France Docquier, Dawn Farrar, Ian Morrison, Marc Vigneron, Shwu Yuan Wu, Cheng Ming Chiang, Dmitri Loukinov, Victor Lobanenkov, Rolf Ohlsson, Elena Klenova

Research output: Contribution to journalArticle

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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.

Original languageEnglish (US)
Pages (from-to)1631-1648
Number of pages18
JournalMolecular and Cellular Biology
Volume27
Issue number5
DOIs
StatePublished - Mar 2007

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Chromatin Immunoprecipitation
Globins
Genome
DNA Polymerase II
Proteins
RNA Polymerase II
DNA
Reporter Genes
Transcriptional Activation
Libraries
Transcription Factors
RNA polymerase II largest subunit
N-glycolylneuraminyllactosylceramide

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Cell Biology

Cite this

Chernukhin, I., Shamsuddin, S., Kang, S. Y., Bergström, R., Kwon, Y. W., Yu, W., ... Klenova, E. (2007). CTCF interacts with and recruits the largest subunit of RNA polymerase II to CTCF target sites genome-wide. Molecular and Cellular Biology, 27(5), 1631-1648. https://doi.org/10.1128/MCB.01993-06

CTCF interacts with and recruits the largest subunit of RNA polymerase II to CTCF target sites genome-wide. / Chernukhin, Igor; Shamsuddin, Shaharum; Kang, Sung Yun; Bergström, Rosita; Kwon, Yoo Wook; Yu, WenQiang; Whitehead, Joanne; Mukhopadhyay, Rituparna; Docquier, France; Farrar, Dawn; Morrison, Ian; Vigneron, Marc; Wu, Shwu Yuan; Chiang, Cheng Ming; Loukinov, Dmitri; Lobanenkov, Victor; Ohlsson, Rolf; Klenova, Elena.

In: Molecular and Cellular Biology, Vol. 27, No. 5, 03.2007, p. 1631-1648.

Research output: Contribution to journalArticle

Chernukhin, I, Shamsuddin, S, Kang, SY, Bergström, R, Kwon, YW, Yu, W, Whitehead, J, Mukhopadhyay, R, Docquier, F, Farrar, D, Morrison, I, Vigneron, M, Wu, SY, Chiang, CM, Loukinov, D, Lobanenkov, V, Ohlsson, R & Klenova, E 2007, 'CTCF interacts with and recruits the largest subunit of RNA polymerase II to CTCF target sites genome-wide', Molecular and Cellular Biology, vol. 27, no. 5, pp. 1631-1648. https://doi.org/10.1128/MCB.01993-06
Chernukhin, Igor ; Shamsuddin, Shaharum ; Kang, Sung Yun ; Bergström, Rosita ; Kwon, Yoo Wook ; Yu, WenQiang ; Whitehead, Joanne ; Mukhopadhyay, Rituparna ; Docquier, France ; Farrar, Dawn ; Morrison, Ian ; Vigneron, Marc ; Wu, Shwu Yuan ; Chiang, Cheng Ming ; Loukinov, Dmitri ; Lobanenkov, Victor ; Ohlsson, Rolf ; Klenova, Elena. / CTCF interacts with and recruits the largest subunit of RNA polymerase II to CTCF target sites genome-wide. In: Molecular and Cellular Biology. 2007 ; Vol. 27, No. 5. pp. 1631-1648.
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T1 - CTCF interacts with and recruits the largest subunit of RNA polymerase II to CTCF target sites genome-wide

AU - Chernukhin, Igor

AU - Shamsuddin, Shaharum

AU - Kang, Sung Yun

AU - Bergström, Rosita

AU - Kwon, Yoo Wook

AU - Yu, WenQiang

AU - Whitehead, Joanne

AU - Mukhopadhyay, Rituparna

AU - Docquier, France

AU - Farrar, Dawn

AU - Morrison, Ian

AU - Vigneron, Marc

AU - Wu, Shwu Yuan

AU - Chiang, Cheng Ming

AU - Loukinov, Dmitri

AU - Lobanenkov, Victor

AU - Ohlsson, Rolf

AU - Klenova, Elena

PY - 2007/3

Y1 - 2007/3

N2 - 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.

AB - 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.

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