Literature DB >> 28040646

Coupling 1D modifications and 3D nuclear organization: data, models and function.

Daniel Jost1, Cédric Vaillant2, Peter Meister3.   

Abstract

Over the past decade, advances in molecular methods have strikingly improved the resolution at which nuclear genome folding can be analyzed. This revealed a wealth of conserved features organizing the one dimensional DNA molecule into tridimensional nuclear domains. In this review, we briefly summarize the main findings and highlight how models based on polymer physics shed light on the principles underlying the formation of these domains. Finally, we discuss the mechanistic similarities allowing self-organization of these structures and the functional importance of these in the maintenance of transcriptional programs.
Copyright © 2016 Elsevier Ltd. All rights reserved.

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Year:  2016        PMID: 28040646     DOI: 10.1016/j.ceb.2016.12.001

Source DB:  PubMed          Journal:  Curr Opin Cell Biol        ISSN: 0955-0674            Impact factor:   8.382


  14 in total

1.  Epigenomics in 3D: importance of long-range spreading and specific interactions in epigenomic maintenance.

Authors:  Daniel Jost; Cédric Vaillant
Journal:  Nucleic Acids Res       Date:  2018-03-16       Impact factor: 16.971

2.  Nonequilibrium Biophysical Processes Influence the Large-Scale Architecture of the Cell Nucleus.

Authors:  Ankit Agrawal; Nirmalendu Ganai; Surajit Sengupta; Gautam I Menon
Journal:  Biophys J       Date:  2019-11-22       Impact factor: 4.033

3.  IC-Finder: inferring robustly the hierarchical organization of chromatin folding.

Authors:  Noelle Haddad; Cédric Vaillant; Daniel Jost
Journal:  Nucleic Acids Res       Date:  2017-06-02       Impact factor: 16.971

Review 4.  Caenorhabditis elegans Dosage Compensation: Insights into Condensin-Mediated Gene Regulation.

Authors:  Sarah Elizabeth Albritton; Sevinç Ercan
Journal:  Trends Genet       Date:  2017-10-13       Impact factor: 11.639

5.  Polymer Modeling of 3D Epigenome Folding: Application to Drosophila.

Authors:  Daniel Jost
Journal:  Methods Mol Biol       Date:  2022

6.  Modeling the 3D genome of plants.

Authors:  Marco Di Stefano; Hans-Wilhelm Nützmann
Journal:  Nucleus       Date:  2021-12       Impact factor: 4.197

7.  FISH-ing for captured contacts: towards reconciling FISH and 3C.

Authors:  Geoffrey Fudenberg; Maxim Imakaev
Journal:  Nat Methods       Date:  2017-06-12       Impact factor: 28.547

Review 8.  Integrating ChIP-seq with other functional genomics data.

Authors:  Shan Jiang; Ali Mortazavi
Journal:  Brief Funct Genomics       Date:  2018-03-01       Impact factor: 4.241

9.  Genome-Wide Chromatin Structure Changes During Adipogenesis and Myogenesis.

Authors:  Mengnan He; Yan Li; Qianzi Tang; Diyan Li; Long Jin; Shilin Tian; Tiandong Che; Shen He; Lamei Deng; Guangliang Gao; Yiren Gu; Zhi Jiang; Xuewei Li; Mingzhou Li
Journal:  Int J Biol Sci       Date:  2018-09-07       Impact factor: 6.580

10.  Chromatin organization by an interplay of loop extrusion and compartmental segregation.

Authors:  Johannes Nuebler; Geoffrey Fudenberg; Maxim Imakaev; Nezar Abdennur; Leonid A Mirny
Journal:  Proc Natl Acad Sci U S A       Date:  2018-07-02       Impact factor: 11.205

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