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Poly(ADP-ribosyl)ation regulates CTCF-dependent chromatin insulation

Nature Genetics volume 36, pages 1105–1110 (2004)Cite this article

Abstract

Chromatin insulators demarcate expression domains by blocking the cis effects of enhancers or silencers in a position-dependent manner1,2. We show that the chromatin insulator protein CTCF carries a post-translational modification: poly(ADP-ribosyl)ation. Chromatin immunoprecipitation analysis showed that a poly(ADP-ribosyl)ation mark, which exclusively segregates with the maternal allele of the insulator domain in the H19 imprinting control region, requires the bases that are essential for interaction with CTCF3. Chromatin immunoprecipitation–on–chip analysis documented that the link between CTCF and poly(ADP-ribosyl)ation extended to more than 140 mouse CTCF target sites. An insulator trap assay showed that the insulator function of most of these CTCF target sites is sensitive to 3-aminobenzamide, an inhibitor of poly(ADP-ribose) polymerase activity. We suggest that poly(ADP-ribosyl)ation imparts chromatin insulator properties to CTCF at both imprinted and nonimprinted loci, which has implications for the regulation of expression domains and their demise in pathological lesions.

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Figure 1: A PAR mark of the H19 ICR is allele-specific and depends on intact CTCF target sites.
Figure 2: CTCF is poly(ADP-ribosyl)ated.
Figure 3: Extensive overlap in the patterns of poly(ADP-ribosyl)ation marks and CTCF occupancy.
Figure 4: The insulator trap assay and 3-ABA sensitivity of chromatin insulator functions.

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Acknowledgements

We thank A. Mattsson for expert technical assistance, H. Smith and M. O'Farrell for help with the in vitro poly(ADP-ribosyl)ation assay, S. Shamsuddin for providing the domains of CTCF expressed in bacterial system, P. Hassa for helpful comments, A. Vostrov and W. Quitschke for the recombinant CTCF from Pichia and A. Isaksson and the Wallenberg microarray platform at the Rudbeck Laboratory for their assistance. This work was supported by the Swedish Science Research Council (V.R., R.O.), the Swedish Cancer Research Foundation (C.F., R.O.), the Swedish Pediatric Cancer Foundation (B.C.F., R.O.), the Lundberg Foundation (R.O.), the Wallenberg Foundation (R.O.), the Juvenile Diabetes Research Foundation International (R.O.), the Breast Cancer Campaign (F.D., E.K.), PhD Studentship from the University of Essex (D.F.), Research Promotion Fund from the University of Essex (I.C., F.D., E.K.) and the Association for International Cancer Research (I.C., E.K.).

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Author notes

  1. Wenqiang Yu, Vasudeva Ginjala, Vinod Pant, Igor Chernukhin and Joanne Whitehead: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Development & Genetics, Evolution Biology Centre, Uppsala University, Norbyvägen 18A, Uppsala, S-752 36, Sweden

    Wenqiang Yu, Vasudeva Ginjala, Vinod Pant, Joanne Whitehead, Gholamreza Tavoosidana, Rituparna Mukhopadhyay, Chandrasekhar Kanduri & Rolf Ohlsson

  2. Department of Biological Sciences, Central Campus, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, Essex, UK

    Igor Chernukhin, France Docquier, Dawn Farrar & Elena Klenova

  3. Department of Molecular and Cellular Biology, Tottori University, Tottori, Japan

    Mitsuo Oshimura

  4. Institute of Genetic Medicine, Johns Hopkins University School of Medicine, 1064 Ross, 720 Rutland Avenue, Baltimore, 21205, Maryland, USA

    Andrew P Feinberg

  5. Molecular Pathology Section, Laboratory of Immunopathology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, 20892, Maryland, USA

    Victor Lobanenkov

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Correspondence to Rolf Ohlsson.

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Yu, W., Ginjala, V., Pant, V. et al. Poly(ADP-ribosyl)ation regulates CTCF-dependent chromatin insulation. Nat Genet 36, 1105–1110 (2004). https://doi.org/10.1038/ng1426

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