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Cohesin mediates transcriptional insulation by CCCTC-binding factor

Abstract

Cohesin complexes mediate sister-chromatid cohesion in dividing cells but may also contribute to gene regulation in postmitotic cells. How cohesin regulates gene expression is not known. Here we describe cohesin-binding sites in the human genome and show that most of these are associated with the CCCTC-binding factor (CTCF), a zinc-finger protein required for transcriptional insulation. CTCF is dispensable for cohesin loading onto DNA, but is needed to enrich cohesin at specific binding sites. Cohesin enables CTCF to insulate promoters from distant enhancers and controls transcription at the H19/IGF2 (insulin-like growth factor 2) locus. This role of cohesin seems to be independent of its role in cohesion. We propose that cohesin functions as a transcriptional insulator, and speculate that subtle deficiencies in this function contribute to ‘cohesinopathies’ such as Cornelia de Lange syndrome.

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Figure 1: Cohesin is expressed in postmitotic cells.
Figure 2: Identification of cohesin- and CTCF-binding sites in the human genome.
Figure 3: Cohesin is required for the insulator function of the H19 ICR.
Figure 4: Cohesin co-localizes with CTCF on the maternal allele of the H19 ICR.
Figure 5: Cohesin controls transcription at the H19/IGF2 locus.

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Gene Expression Omnibus

Data deposits

Microarray data presented in this article have been deposited in the Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo) under the accession number GSE9613.

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Acknowledgements

We thank K. Nakagawa, A. Watanabe and Y. Hayakawa for assistance, M. Oshimura for providing cell lines, and D. Barlow, B. Dickson, N. Galjart, A. Lander, M. Merkenschlager, C. Meyer, T. Taniguchi and members of the Peters and Shirahige laboratories for discussions. K.S.W. was supported by a research fellowship of the German Research Foundation (DFG). K.S. and H.A. were supported by a grant of the Genome Network Project and Grant-in-Aid for Scientific Research (S) from the MEXT, Japan. F.I. was supported in by Invitrogen Corporation and Grant-in-Aid for Scientific Research from the Ministry of Economy, Trade and Industry, Japan. K.M. and N.I. were supported by a MEXT grant-in-aid and RIKEN institute program of Bioarchitect. Research in the laboratory of J.-M.P. is supported by Boehringer Ingelheim, the 6th Framework Program of the European Union via the Integrated Project MitoCheck, the Austrian Research Promotion Agency, and the Austrian Science Fund via the EuroDYNA Program of the European Science Foundation.

Author Contributions Experiments were designed and data interpreted by K.S.W., K. Yoshida., T.I., K.S. and J.-M.P. K.S.W. performed SMC3 and SA2 ChIP-chip and ChIP-qPCR, and analysed the role of cohesin at the H19 ICR. K. Yoshida performed SCC1 and CTCF ChIP-qPCR, ChIP-chip on ENCODE and whole-genome arrays, and re-ChIP. T.I. carried out bioinformatic analyses. M.B. performed RNAi, chromatin fractionation and transcriptome experiments. B.K. analysed cohesin expression in mouse tissues, carried out CTCF localization by IFM and performed cohesin/CTCF RNAi-qIFM experiments. E.S. characterized mouse–human hybrid cell lines and the binding of CTCF to mitotic chromatin. K.M. and N.I. analysed the effect of cohesin RNAi on chicken HS4 function using constructs provided by F.I. and K. Yahata. S.T., G.N., H.A., K.I., T.M. and M.N. prepared the initial genome-wide CTCF map. J.-M.P., K.S.W. and K.S. wrote the manuscript.

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Correspondence to Katsuhiko Shirahige or Jan-Michael Peters.

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Wendt, K., Yoshida, K., Itoh, T. et al. Cohesin mediates transcriptional insulation by CCCTC-binding factor. Nature 451, 796–801 (2008). https://doi.org/10.1038/nature06634

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