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Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures

Nature Structural & Molecular Biology volume 20, pages 387–395 (2013)Cite this article

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Abstract

DNA supercoiling is an inherent consequence of twisting DNA and is critical for regulating gene expression and DNA replication. However, DNA supercoiling at a genomic scale in human cells is uncharacterized. To map supercoiling, we used biotinylated trimethylpsoralen as a DNA structure probe to show that the human genome is organized into supercoiling domains. Domains are formed and remodeled by RNA polymerase and topoisomerase activities and are flanked by GC-AT boundaries and CTCF insulator protein–binding sites. Underwound domains are transcriptionally active and enriched in topoisomerase I, 'open' chromatin fibers and DNase I sites, but they are depleted of topoisomerase II. Furthermore, DNA supercoiling affects additional levels of chromatin compaction as underwound domains are cytologically decondensed, topologically constrained and decompacted by transcription of short RNAs. We suggest that supercoiling domains create a topological environment that facilitates gene activation, providing an evolutionary purpose for clustering genes along chromosomes.

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Figure 1: High-resolution mapping of DNA supercoiling.
Figure 2: Organization and boundaries of supercoiling domains.
Figure 3: Transcription- and topoisomerase-dependent remodeling of DNA supercoiling.
Figure 4: RNA polymerase and topoisomerases define supercoiling domains.
Figure 5: DNA supercoiling around TSSs and regulatory elements.
Figure 6: Underwound domains are cytologically decondensed and torsionally constrained.
Figure 7: Transcription and topoisomerase dependence of large-scale chromatin structures.
Figure 8: Relationship among transcription, DNA supercoiling and large-scale chromatin structures.

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Acknowledgements

We thank J. Reek for help with bioinformatic analysis, F. Rustenburg and D. Israeli for microarray hybridizations and B. Ramsahoye, J. Allan, W. Bickmore, J. Caceres and N. Hastie for helpful discussions. This work was funded by the Wellcome Trust 078219/Z/05/Z (N.G.) and Breakthrough Breast Cancer (N.G.). N.G. is a recipient of a UK Medical Research Council senior fellowship (MR/J00913X/1).

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Authors and Affiliations

  1. Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK

    Catherine Naughton, Samuel Corless, James G Prendergast & Nick Gilbert

  2. Breakthrough Breast Cancer Research Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK

    Catherine Naughton & Nick Gilbert

  3. School of Chemistry, University of Edinburgh, Edinburgh, UK

    Nicolaos Avlonitis, Ioulia K Mati, Scott L Cockroft & Mark Bradley

  4. Micro Array Facility, VU Medical Centre, Amsterdam, The Netherlands

    Paul P Eijk & Bauke Ylstra

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Contributions

C.N., S.L.C., M.B., B.Y. and N.G. conceived, designed and interpreted experiments. C.N., S.C. and N.G. did biological experiments. N.A., I.K.M. and N.G. carried out chemical synthesis, and P.P.E. did microarray experiments. J.G.P., S.C. and N.G. did all bioinformatic analysis. N.G. supervised the project and all authors wrote the manuscript.

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Correspondence to Nick Gilbert.

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Naughton, C., Avlonitis, N., Corless, S. et al. Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures. Nat Struct Mol Biol 20, 387–395 (2013). https://doi.org/10.1038/nsmb.2509

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