Literature DB >> 22988072

Complexity of chromatin folding is captured by the strings and binders switch model.

Mariano Barbieri1, Mita Chotalia, James Fraser, Liron-Mark Lavitas, Josée Dostie, Ana Pombo, Mario Nicodemi.   

Abstract

Chromatin has a complex spatial organization in the cell nucleus that serves vital functional purposes. A variety of chromatin folding conformations has been detected by single-cell imaging and chromosome conformation capture-based approaches. However, a unified quantitative framework describing spatial chromatin organization is still lacking. Here, we explore the "strings and binders switch" model to explain the origin and variety of chromatin behaviors that coexist and dynamically change within living cells. This simple polymer model recapitulates the scaling properties of chromatin folding reported experimentally in different cellular systems, the fractal state of chromatin, the processes of domain formation, and looping out. Additionally, the strings and binders switch model reproduces the recently proposed "fractal-globule" model, but only as one of many possible transient conformations.

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Year:  2012        PMID: 22988072      PMCID: PMC3479593          DOI: 10.1073/pnas.1204799109

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  36 in total

1.  Radial arrangement of chromosome territories in human cell nuclei: a computer model approach based on gene density indicates a probabilistic global positioning code.

Authors:  G Kreth; J Finsterle; J von Hase; M Cremer; C Cremer
Journal:  Biophys J       Date:  2004-05       Impact factor: 4.033

Review 2.  Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions.

Authors:  Christian Lanctôt; Thierry Cheutin; Marion Cremer; Giacomo Cavalli; Thomas Cremer
Journal:  Nat Rev Genet       Date:  2007-02       Impact factor: 53.242

3.  Transcription factories and nuclear organization of the genome.

Authors:  C H Eskiw; N F Cope; I Clay; S Schoenfelder; T Nagano; P Fraser
Journal:  Cold Spring Harb Symp Quant Biol       Date:  2011-04-05

Review 4.  Polycomb group proteins: repression in 3D.

Authors:  Frédéric Bantignies; Giacomo Cavalli
Journal:  Trends Genet       Date:  2011-07-25       Impact factor: 11.639

5.  Critical DNA binding interactions of the insulator protein CTCF: a small number of zinc fingers mediate strong binding, and a single finger-DNA interaction controls binding at imprinted loci.

Authors:  Mario Renda; Ilaria Baglivo; Bonnie Burgess-Beusse; Sabrina Esposito; Roberto Fattorusso; Gary Felsenfeld; Paolo V Pedone
Journal:  J Biol Chem       Date:  2007-09-07       Impact factor: 5.157

6.  Global chromatin architecture reflects pluripotency and lineage commitment in the early mouse embryo.

Authors:  Kashif Ahmed; Hesam Dehghani; Peter Rugg-Gunn; Eden Fussner; Janet Rossant; David P Bazett-Jones
Journal:  PLoS One       Date:  2010-05-07       Impact factor: 3.240

7.  Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription.

Authors:  Séverine Chambeyron; Wendy A Bickmore
Journal:  Genes Dev       Date:  2004-05-15       Impact factor: 11.361

8.  Subchromosomal positioning of the epidermal differentiation complex (EDC) in keratinocyte and lymphoblast interphase nuclei.

Authors:  Ruth R E Williams; Simon Broad; Denise Sheer; Jiannis Ragoussis
Journal:  Exp Cell Res       Date:  2002-01-15       Impact factor: 3.905

9.  Topological domains in mammalian genomes identified by analysis of chromatin interactions.

Authors:  Jesse R Dixon; Siddarth Selvaraj; Feng Yue; Audrey Kim; Yan Li; Yin Shen; Ming Hu; Jun S Liu; Bing Ren
Journal:  Nature       Date:  2012-04-11       Impact factor: 49.962

10.  Folding and organization of a contiguous chromosome region according to the gene distribution pattern in primary genomic sequence.

Authors:  Lindsay S Shopland; Christopher R Lynch; Kevin A Peterson; Kathleen Thornton; Nick Kepper; Johann von Hase; Stefan Stein; Sarah Vincent; Kelly R Molloy; Gregor Kreth; Christoph Cremer; Carol J Bult; Timothy P O'Brien
Journal:  J Cell Biol       Date:  2006-07-03       Impact factor: 10.539

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  178 in total

Review 1.  Two major mechanisms of chromosome organization.

Authors:  Leonid A Mirny; Maxim Imakaev; Nezar Abdennur
Journal:  Curr Opin Cell Biol       Date:  2019-06-20       Impact factor: 8.382

2.  Structure-driven homology pairing of chromatin fibers: the role of electrostatics and protein-induced bridging.

Authors:  A G Cherstvy; V B Teif
Journal:  J Biol Phys       Date:  2013-01-17       Impact factor: 1.365

3.  DNA double-strand breaks: linking gene expression to chromosome morphology and mobility.

Authors:  Yang Zhang; Dieter W Heermann
Journal:  Chromosoma       Date:  2013-08-28       Impact factor: 4.316

Review 4.  Evolving methodologies and concepts in 4D nucleome research.

Authors:  Thomas M Sparks; Izabela Harabula; Ana Pombo
Journal:  Curr Opin Cell Biol       Date:  2020-05-27       Impact factor: 8.382

5.  Producing genome structure populations with the dynamic and automated PGS software.

Authors:  Nan Hua; Harianto Tjong; Hanjun Shin; Ke Gong; Xianghong Jasmine Zhou; Frank Alber
Journal:  Nat Protoc       Date:  2018-04-05       Impact factor: 13.491

Review 6.  Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data.

Authors:  Job Dekker; Marc A Marti-Renom; Leonid A Mirny
Journal:  Nat Rev Genet       Date:  2013-05-09       Impact factor: 53.242

Review 7.  Models of polymer physics for the architecture of the cell nucleus.

Authors:  Andrea Esposito; Carlo Annunziatella; Simona Bianco; Andrea M Chiariello; Luca Fiorillo; Mario Nicodemi
Journal:  Wiley Interdiscip Rev Syst Biol Med       Date:  2018-12-19

8.  Topology, structures, and energy landscapes of human chromosomes.

Authors:  Bin Zhang; Peter G Wolynes
Journal:  Proc Natl Acad Sci U S A       Date:  2015-04-27       Impact factor: 11.205

9.  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

10.  Bridging chromatin structure and function over a range of experimental spatial and temporal scales by molecular modeling.

Authors:  Stephanie Portillo-Ledesma; Tamar Schlick
Journal:  Wiley Interdiscip Rev Comput Mol Sci       Date:  2019-08-06
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