Literature DB >> 27739532

Organization and function of the 3D genome.

Boyan Bonev1, Giacomo Cavalli1.   

Abstract

Understanding how chromatin is organized within the nucleus and how this 3D architecture influences gene regulation, cell fate decisions and evolution are major questions in cell biology. Despite spectacular progress in this field, we still know remarkably little about the mechanisms underlying chromatin structure and how it can be established, reset and maintained. In this Review, we discuss the insights into chromatin architecture that have been gained through recent technological developments in quantitative biology, genomics and cell and molecular biology approaches and explain how these new concepts have been used to address important biological questions in development and disease.

Mesh:

Substances:

Year:  2016        PMID: 27739532     DOI: 10.1038/nrg.2016.112

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  142 in total

1.  DNA-binding factors shape the mouse methylome at distal regulatory regions.

Authors:  Michael B Stadler; Rabih Murr; Lukas Burger; Robert Ivanek; Florian Lienert; Anne Schöler; Erik van Nimwegen; Christiane Wirbelauer; Edward J Oakeley; Dimos Gaidatzis; Vijay K Tiwari; Dirk Schübeler
Journal:  Nature       Date:  2011-12-14       Impact factor: 49.962

2.  Nanoscale spatial organization of the HoxD gene cluster in distinct transcriptional states.

Authors:  Pierre J Fabre; Alexander Benke; Elisabeth Joye; Thi Hanh Nguyen Huynh; Suliana Manley; Denis Duboule
Journal:  Proc Natl Acad Sci U S A       Date:  2015-10-26       Impact factor: 11.205

3.  Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps.

Authors:  William J Murphy; Denis M Larkin; Annelie Everts-van der Wind; Guillaume Bourque; Glenn Tesler; Loretta Auvil; Jonathan E Beever; Bhanu P Chowdhary; Francis Galibert; Lisa Gatzke; Christophe Hitte; Stacey N Meyers; Denis Milan; Elaine A Ostrander; Greg Pape; Heidi G Parker; Terje Raudsepp; Margarita B Rogatcheva; Lawrence B Schook; Loren C Skow; Michael Welge; James E Womack; Stephen J O'brien; Pavel A Pevzner; Harris A Lewin
Journal:  Science       Date:  2005-07-22       Impact factor: 47.728

4.  Crystal structure of the nucleosome core particle at 2.8 A resolution.

Authors:  K Luger; A W Mäder; R K Richmond; D F Sargent; T J Richmond
Journal:  Nature       Date:  1997-09-18       Impact factor: 49.962

5.  The 3D organization of chromatin explains evolutionary fragile genomic regions.

Authors:  Camille Berthelot; Matthieu Muffato; Judith Abecassis; Hugues Roest Crollius
Journal:  Cell Rep       Date:  2015-03-24       Impact factor: 9.423

6.  CTCF Binding Polarity Determines Chromatin Looping.

Authors:  Elzo de Wit; Erica S M Vos; Sjoerd J B Holwerda; Christian Valdes-Quezada; Marjon J A M Verstegen; Hans Teunissen; Erik Splinter; Patrick J Wijchers; Peter H L Krijger; Wouter de Laat
Journal:  Mol Cell       Date:  2015-10-29       Impact factor: 17.970

7.  Cooperativity, specificity, and evolutionary stability of Polycomb targeting in Drosophila.

Authors:  Bernd Schuettengruber; Noa Oded Elkayam; Tom Sexton; Marianne Entrevan; Shani Stern; Aubin Thomas; Eitan Yaffe; Hugues Parrinello; Amos Tanay; Giacomo Cavalli
Journal:  Cell Rep       Date:  2014-10-02       Impact factor: 9.423

8.  Stable Chromosome Condensation Revealed by Chromosome Conformation Capture.

Authors:  Kyle P Eagen; Tom A Hartl; Roger D Kornberg
Journal:  Cell       Date:  2015-11-05       Impact factor: 41.582

9.  Formation of Chromosomal Domains by Loop Extrusion.

Authors:  Geoffrey Fudenberg; Maxim Imakaev; Carolyn Lu; Anton Goloborodko; Nezar Abdennur; Leonid A Mirny
Journal:  Cell Rep       Date:  2016-05-19       Impact factor: 9.423

10.  Global reorganization of the nuclear landscape in senescent cells.

Authors:  Tamir Chandra; Philip Andrew Ewels; Stefan Schoenfelder; Mayra Furlan-Magaril; Steven William Wingett; Kristina Kirschner; Jean-Yves Thuret; Simon Andrews; Peter Fraser; Wolf Reik
Journal:  Cell Rep       Date:  2015-01-29       Impact factor: 9.423

View more
  272 in total

1.  MATCHA: Probing multi-way chromatin interaction with hypergraph representation learning.

Authors:  Ruochi Zhang; Jian Ma
Journal:  Cell Syst       Date:  2020-05-20       Impact factor: 10.304

2.  Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF.

Authors:  Yang Yang; Yang Zhang; Bing Ren; Jesse R Dixon; Jian Ma
Journal:  Cell Syst       Date:  2019-06-26       Impact factor: 10.304

Review 3.  Diverse Genome Topologies Characterize Dosage Compensation across Species.

Authors:  William Jordan; Leila E Rieder; Erica Larschan
Journal:  Trends Genet       Date:  2019-02-23       Impact factor: 11.639

4.  Genome-Wide Characterization of DNase I-Hypersensitive Sites and Cold Response Regulatory Landscapes in Grasses.

Authors:  Jinlei Han; Pengxi Wang; Qiongli Wang; Qingfang Lin; Zhiyong Chen; Guangrun Yu; Chenyong Miao; Yihang Dao; Ruoxi Wu; James C Schnable; Haibao Tang; Kai Wang
Journal:  Plant Cell       Date:  2020-05-29       Impact factor: 11.277

Review 5.  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

Review 6.  Mechanisms regulating zygotic genome activation.

Authors:  Katharine N Schulz; Melissa M Harrison
Journal:  Nat Rev Genet       Date:  2019-04       Impact factor: 53.242

7.  Computational Prediction of Position Effects of Apparently Balanced Human Chromosomal Rearrangements.

Authors:  Cinthya J Zepeda-Mendoza; Jonas Ibn-Salem; Tammy Kammin; David J Harris; Debra Rita; Karen W Gripp; Jennifer J MacKenzie; Andrea Gropman; Brett Graham; Ranad Shaheen; Fowzan S Alkuraya; Campbell K Brasington; Edward J Spence; Diane Masser-Frye; Lynne M Bird; Erica Spiegel; Rebecca L Sparkes; Zehra Ordulu; Michael E Talkowski; Miguel A Andrade-Navarro; Peter N Robinson; Cynthia C Morton
Journal:  Am J Hum Genet       Date:  2017-07-20       Impact factor: 11.025

Review 8.  Understanding 3D genome organization by multidisciplinary methods.

Authors:  Ivana Jerkovic; Giacomo Cavalli
Journal:  Nat Rev Mol Cell Biol       Date:  2021-05-05       Impact factor: 94.444

9.  A base-pair view of interactions between genes and their enhancers.

Authors:  Anne van Schoonhoven; Ralph Stadhouders
Journal:  Nature       Date:  2021-07       Impact factor: 49.962

Review 10.  Advances in targeting 'undruggable' transcription factors with small molecules.

Authors:  Matthew J Henley; Angela N Koehler
Journal:  Nat Rev Drug Discov       Date:  2021-05-18       Impact factor: 84.694

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.