Mechanistic modeling of chromatin folding to understand function

doi:10.1038/s41592-020-0852-6

Review

. 2020 Aug;17(8):767-775.

doi: 10.1038/s41592-020-0852-6. Epub 2020 Jun 8.

Mechanistic modeling of chromatin folding to understand function

Chris A Brackey¹, Davide Marenduzzo², Nick Gilbert³

Affiliations

¹ SUPA School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK.
² SUPA School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK. Davide.Marenduzzo@ed.ac.uk.
³ MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK. Nick.Gilbert@ed.ac.uk.

PMID: 32514111
DOI: 10.1038/s41592-020-0852-6

Free article

Review

Mechanistic modeling of chromatin folding to understand function

Chris A Brackey et al. Nat Methods. 2020 Aug.

Free article

. 2020 Aug;17(8):767-775.

doi: 10.1038/s41592-020-0852-6. Epub 2020 Jun 8.

Authors

Chris A Brackey¹, Davide Marenduzzo², Nick Gilbert³

Affiliations

¹ SUPA School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK.
² SUPA School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK. Davide.Marenduzzo@ed.ac.uk.
³ MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK. Nick.Gilbert@ed.ac.uk.

PMID: 32514111
DOI: 10.1038/s41592-020-0852-6

Abstract

Experimental approaches have been applied to address questions in understanding three-dimensional chromatin organization and function. As datasets increase in size and complexity, it becomes a challenge to reach a mechanistic interpretation of experimental results. Polymer simulations and mechanistic modeling have been applied to explain experimental observations and their links to different aspects of genome function. Here we provide a guide for biologists, explaining different simulation approaches and the contexts in which they have been used.

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References

1. Han, J., Zhang, Z. & Wang, K. 3C and 3C-based techniques: the powerful tools for spatial genome organization deciphering. Mol. Cytogenet. 11, 21 (2018). - PubMed - PMC
1. Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289–293 (2009). - PubMed - PMC
1. Dixon, J. R. et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485, 376–380 (2012). - PubMed - PMC
1. Rao, S. S. P. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665–1680 (2014). - PubMed - PMC
1. Schmitt, A. D. et al. A compendium of chromatin contact maps reveals spatially active regions in the human genome. Cell Rep. 17, 2042–2059 (2016). - PubMed - PMC

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[1] Han, J., Zhang, Z. & Wang, K. 3C and 3C-based techniques: the powerful tools for spatial genome organization deciphering. Mol. Cytogenet. 11, 21 (2018). - PubMed - PMC

[2] Han, J., Zhang, Z. & Wang, K. 3C and 3C-based techniques: the powerful tools for spatial genome organization deciphering. Mol. Cytogenet. 11, 21 (2018). - PubMed - PMC

[3] Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289–293 (2009). - PubMed - PMC

[4] Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289–293 (2009). - PubMed - PMC

[5] Dixon, J. R. et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485, 376–380 (2012). - PubMed - PMC

[6] Dixon, J. R. et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485, 376–380 (2012). - PubMed - PMC

[7] Rao, S. S. P. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665–1680 (2014). - PubMed - PMC

[8] Rao, S. S. P. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665–1680 (2014). - PubMed - PMC

[9] Schmitt, A. D. et al. A compendium of chromatin contact maps reveals spatially active regions in the human genome. Cell Rep. 17, 2042–2059 (2016). - PubMed - PMC

[10] Schmitt, A. D. et al. A compendium of chromatin contact maps reveals spatially active regions in the human genome. Cell Rep. 17, 2042–2059 (2016). - PubMed - PMC

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Mechanistic modeling of chromatin folding to understand function

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Mechanistic modeling of chromatin folding to understand function

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