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Emerging Evidence of Chromosome Folding by Loop Extrusion

View ORCID ProfileGeoffrey Fudenberg, View ORCID ProfileNezar Abdennur, View ORCID ProfileMaxim Imakaev, View ORCID ProfileAnton Goloborodko, View ORCID ProfileLeonid A. Mirny
doi: https://doi.org/10.1101/264648
Geoffrey Fudenberg
1Gladstone Institutes, University of California, San Francisco, California, USA.
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  • For correspondence: geoff.fudenberg@gmail.com leonid@mit.edu
Nezar Abdennur
2Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
3Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
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Maxim Imakaev
3Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
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Anton Goloborodko
4Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
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Leonid A. Mirny
3Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
4Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
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  • For correspondence: geoff.fudenberg@gmail.com leonid@mit.edu
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Abstract

Chromosome organization poses a remarkable physical problem with many biological consequences: how can molecular interactions between proteins at the nanometer scale organize micron-long chromatinized DNA molecules, insulating or facilitating interactions between specific genomic elements? The mechanism of active loop extrusion holds great promise for explaining interphase and mitotic chromosome folding, yet remains difficult to assay directly. We discuss predictions from our polymer models of loop extrusion with barrier elements, and review recent experimental studies that provide strong support for loop extrusion, focusing on perturbations to CTCF and cohesin assayed via Hi-C in interphase. Finally, we discuss a likely molecular mechanism of loop extrusion by SMC complexes.

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Posted February 16, 2018.
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Emerging Evidence of Chromosome Folding by Loop Extrusion
Geoffrey Fudenberg, Nezar Abdennur, Maxim Imakaev, Anton Goloborodko, Leonid A. Mirny
bioRxiv 264648; doi: https://doi.org/10.1101/264648
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Emerging Evidence of Chromosome Folding by Loop Extrusion
Geoffrey Fudenberg, Nezar Abdennur, Maxim Imakaev, Anton Goloborodko, Leonid A. Mirny
bioRxiv 264648; doi: https://doi.org/10.1101/264648

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