Literature DB >> 24472896

From a melt of rings to chromosome territories: the role of topological constraints in genome folding.

Jonathan D Halverson1, Jan Smrek, Kurt Kremer, Alexander Y Grosberg.   

Abstract

We review pro and contra of the hypothesis that generic polymer properties of topological constraints are behind many aspects of chromatin folding in eukaryotic cells. For that purpose, we review, first, recent theoretical and computational findings in polymer physics related to concentrated, topologically simple (unknotted and unlinked) chains or a system of chains. Second, we review recent experimental discoveries related to genome folding. Understanding in these fields is far from complete, but we show how looking at them in parallel sheds new light on both.

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Year:  2014        PMID: 24472896     DOI: 10.1088/0034-4885/77/2/022601

Source DB:  PubMed          Journal:  Rep Prog Phys        ISSN: 0034-4885


  57 in total

1.  Self-Similar Conformations and Dynamics in Entangled Melts and Solutions of Nonconcatenated Ring Polymers.

Authors:  Ting Ge; Sergey Panyukov; Michael Rubinstein
Journal:  Macromolecules       Date:  2016       Impact factor: 5.985

2.  Unexpected Stretching of Entangled Ring Macromolecules.

Authors:  Q Huang; J Ahn; D Parisi; T Chang; O Hassager; S Panyukov; M Rubinstein; D Vlassopoulos
Journal:  Phys Rev Lett       Date:  2019-05-24       Impact factor: 9.161

3.  Heterogeneous Loop Model to Infer 3D Chromosome Structures from Hi-C.

Authors:  Lei Liu; Min Hyeok Kim; Changbong Hyeon
Journal:  Biophys J       Date:  2019-07-04       Impact factor: 4.033

4.  Quantified effects of chromosome-nuclear envelope attachments on 3D organization of chromosomes.

Authors:  Nicholas Allen Kinney; Alexey V Onufriev; Igor V Sharakhov
Journal:  Nucleus       Date:  2015       Impact factor: 4.197

5.  TAD-free analysis of architectural proteins and insulators.

Authors:  Raphaël Mourad; Olivier Cuvier
Journal:  Nucleic Acids Res       Date:  2018-03-16       Impact factor: 16.971

6.  Contact Statistics Highlight Distinct Organizing Principles of Proteins and RNA.

Authors:  Lei Liu; Changbong Hyeon
Journal:  Biophys J       Date:  2016-06-07       Impact factor: 4.033

7.  Extruding Loops to Make Loopy Globules?

Authors:  Alexander Y Grosberg
Journal:  Biophys J       Date:  2016-05-24       Impact factor: 4.033

Review 8.  Ensemble View of RNAs and Proteins: Loops, Knots, Territories, and Evolution.

Authors:  Alexander Y Grosberg
Journal:  Biophys J       Date:  2016-06-07       Impact factor: 4.033

9.  Flory theory of randomly branched polymers.

Authors:  Ralf Everaers; Alexander Y Grosberg; Michael Rubinstein; Angelo Rosa
Journal:  Soft Matter       Date:  2017-02-08       Impact factor: 3.679

10.  Spatial organization of chromatin domains and compartments in single chromosomes.

Authors:  Siyuan Wang; Jun-Han Su; Brian J Beliveau; Bogdan Bintu; Jeffrey R Moffitt; Chao-ting Wu; Xiaowei Zhuang
Journal:  Science       Date:  2016-07-21       Impact factor: 47.728

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