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Complementary chromosome folding by transcription factors and cohesin

M. C. F. Pereira, C. A. Brackley, D. Michieletto, C. Annunziatella, S. Bianco, A. M. Chiariello, M. Nicodemi, D. Marenduzzo
doi: https://doi.org/10.1101/305359
M. C. F. Pereira
1SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, Edinburgh, UK
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C. A. Brackley
1SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, Edinburgh, UK
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D. Michieletto
1SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, Edinburgh, UK
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C. Annunziatella
2Dipartimento di Fisica, Università degli Studi di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo - 80126 Naples, Italy
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S. Bianco
2Dipartimento di Fisica, Università degli Studi di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo - 80126 Naples, Italy
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A. M. Chiariello
2Dipartimento di Fisica, Università degli Studi di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo - 80126 Naples, Italy
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M. Nicodemi
2Dipartimento di Fisica, Università degli Studi di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo - 80126 Naples, Italy
3Berlin Institute of Health (BIH), and Berlin Institute for Medical Systems Biology at the Max Delbruck Center for Molecular Medicine - 13125 Berlin, Germany
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D. Marenduzzo
1SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, Edinburgh, UK
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Abstract

The spatial organisation of interphase chromosomes is known to affect genomic function, yet the principles behind such organisation remain elusive. Here, we first compare and then combine two well-known biophysical models, the transcription factor (TF) and loop extrusion (LE) models, and dissect their respective roles in organising the genome. Our results suggest that extrusion and transcription factors play complementary roles in folding the genome: the former are necessary to compact gene deserts or “inert chromatin” regions, the latter are sufficient to explain most of the structure found in transcriptionally active or repressed domains. Finally, we find that to reproduce interaction patterns found in HiC experiments we do not need to postulate an explicit motor activity of cohesin (or other extruding factors): a model where co-hesin molecules behave as molecular slip-links sliding diffusively along chromatin works equally well.

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Posted April 23, 2018.
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Complementary chromosome folding by transcription factors and cohesin
M. C. F. Pereira, C. A. Brackley, D. Michieletto, C. Annunziatella, S. Bianco, A. M. Chiariello, M. Nicodemi, D. Marenduzzo
bioRxiv 305359; doi: https://doi.org/10.1101/305359
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Complementary chromosome folding by transcription factors and cohesin
M. C. F. Pereira, C. A. Brackley, D. Michieletto, C. Annunziatella, S. Bianco, A. M. Chiariello, M. Nicodemi, D. Marenduzzo
bioRxiv 305359; doi: https://doi.org/10.1101/305359

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