Literature DB >> 22207201

Discovering genome regulation with 3C and 3C-related technologies.

Sylvain D Ethier1, Hisashi Miura, Josée Dostie.   

Abstract

It has been known for some time that eukaryotic genomic DNA is packaged in the form of highly organized chromatin in vivo. This organization is important not only to reduce the length of chromosomes during interphase but also because it represents a type of higher-order genome regulation mechanism. Indeed, spatial chromatin architecture is known to be important for transcription, DNA replication and repair. Chromosome structure can be observed at different scales and studied with a variety of complementary techniques. For example, microscopy can provide single cell information while technologies such as the chromosome conformation capture (3C) method and its derivatives can yield higher-resolution data from cell populations. In this review, we report on the biological questions addressed with 3C and 3C-related techniques and what has been uncovered to date. We also explore what these methods may further reveal about the regulation of genomic DNA activities.
Copyright © 2011 Elsevier B.V. All rights reserved.

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Year:  2011        PMID: 22207201     DOI: 10.1016/j.bbagrm.2011.12.004

Source DB:  PubMed          Journal:  Biochim Biophys Acta        ISSN: 0006-3002


  16 in total

1.  Single-cell Hi-C for genome-wide detection of chromatin interactions that occur simultaneously in a single cell.

Authors:  Takashi Nagano; Yaniv Lubling; Eitan Yaffe; Steven W Wingett; Wendy Dean; Amos Tanay; Peter Fraser
Journal:  Nat Protoc       Date:  2015-11-05       Impact factor: 13.491

Review 2.  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

3.  Spatial Organization of Epigenomes.

Authors:  Jonathan Christopher Dubé; Xue Qing David Wang; Josée Dostie
Journal:  Curr Mol Biol Rep       Date:  2016-02-04

Review 4.  Chromatin loop formation in the β-globin locus and its role in globin gene transcription.

Authors:  Aeri Kim; Ann Dean
Journal:  Mol Cells       Date:  2012-05-18       Impact factor: 5.034

Review 5.  Disentangling the many layers of eukaryotic transcriptional regulation.

Authors:  Katherine M Lelli; Matthew Slattery; Richard S Mann
Journal:  Annu Rev Genet       Date:  2012-08-28       Impact factor: 16.830

6.  Genome-wide association study identifies eight risk loci and implicates metabo-psychiatric origins for anorexia nervosa.

Authors:  Hunna J Watson; Zeynep Yilmaz; Laura M Thornton; Christopher Hübel; Jonathan R I Coleman; Héléna A Gaspar; Julien Bryois; Anke Hinney; Virpi M Leppä; Manuel Mattheisen; Sarah E Medland; Stephan Ripke; Shuyang Yao; Paola Giusti-Rodríguez; Ken B Hanscombe; Kirstin L Purves; Roger A H Adan; Lars Alfredsson; Tetsuya Ando; Ole A Andreassen; Jessica H Baker; Wade H Berrettini; Ilka Boehm; Claudette Boni; Vesna Boraska Perica; Katharina Buehren; Roland Burghardt; Matteo Cassina; Sven Cichon; Maurizio Clementi; Roger D Cone; Philippe Courtet; Scott Crow; James J Crowley; Unna N Danner; Oliver S P Davis; Martina de Zwaan; George Dedoussis; Daniela Degortes; Janiece E DeSocio; Danielle M Dick; Dimitris Dikeos; Christian Dina; Monika Dmitrzak-Weglarz; Elisa Docampo; Laramie E Duncan; Karin Egberts; Stefan Ehrlich; Geòrgia Escaramís; Tõnu Esko; Xavier Estivill; Anne Farmer; Angela Favaro; Fernando Fernández-Aranda; Manfred M Fichter; Krista Fischer; Manuel Föcker; Lenka Foretova; Andreas J Forstner; Monica Forzan; Christopher S Franklin; Steven Gallinger; Ina Giegling; Johanna Giuranna; Fragiskos Gonidakis; Philip Gorwood; Monica Gratacos Mayora; Sébastien Guillaume; Yiran Guo; Hakon Hakonarson; Konstantinos Hatzikotoulas; Joanna Hauser; Johannes Hebebrand; Sietske G Helder; Stefan Herms; Beate Herpertz-Dahlmann; Wolfgang Herzog; Laura M Huckins; James I Hudson; Hartmut Imgart; Hidetoshi Inoko; Vladimir Janout; Susana Jiménez-Murcia; Antonio Julià; Gursharan Kalsi; Deborah Kaminská; Jaakko Kaprio; Leila Karhunen; Andreas Karwautz; Martien J H Kas; James L Kennedy; Anna Keski-Rahkonen; Kirsty Kiezebrink; Youl-Ri Kim; Lars Klareskog; Kelly L Klump; Gun Peggy S Knudsen; Maria C La Via; Stephanie Le Hellard; Robert D Levitan; Dong Li; Lisa Lilenfeld; Bochao Danae Lin; Jolanta Lissowska; Jurjen Luykx; Pierre J Magistretti; Mario Maj; Katrin Mannik; Sara Marsal; Christian R Marshall; Morten Mattingsdal; Sara McDevitt; Peter McGuffin; Andres Metspalu; Ingrid Meulenbelt; Nadia Micali; Karen Mitchell; Alessio Maria Monteleone; Palmiero Monteleone; Melissa A Munn-Chernoff; Benedetta Nacmias; Marie Navratilova; Ioanna Ntalla; Julie K O'Toole; Roel A Ophoff; Leonid Padyukov; Aarno Palotie; Jacques Pantel; Hana Papezova; Dalila Pinto; Raquel Rabionet; Anu Raevuori; Nicolas Ramoz; Ted Reichborn-Kjennerud; Valdo Ricca; Samuli Ripatti; Franziska Ritschel; Marion Roberts; Alessandro Rotondo; Dan Rujescu; Filip Rybakowski; Paolo Santonastaso; André Scherag; Stephen W Scherer; Ulrike Schmidt; Nicholas J Schork; Alexandra Schosser; Jochen Seitz; Lenka Slachtova; P Eline Slagboom; Margarita C T Slof-Op 't Landt; Agnieszka Slopien; Sandro Sorbi; Beata Świątkowska; Jin P Szatkiewicz; Ioanna Tachmazidou; Elena Tenconi; Alfonso Tortorella; Federica Tozzi; Janet Treasure; Artemis Tsitsika; Marta Tyszkiewicz-Nwafor; Konstantinos Tziouvas; Annemarie A van Elburg; Eric F van Furth; Gudrun Wagner; Esther Walton; Elisabeth Widen; Eleftheria Zeggini; Stephanie Zerwas; Stephan Zipfel; Andrew W Bergen; Joseph M Boden; Harry Brandt; Steven Crawford; Katherine A Halmi; L John Horwood; Craig Johnson; Allan S Kaplan; Walter H Kaye; James E Mitchell; Catherine M Olsen; John F Pearson; Nancy L Pedersen; Michael Strober; Thomas Werge; David C Whiteman; D Blake Woodside; Garret D Stuber; Scott Gordon; Jakob Grove; Anjali K Henders; Anders Juréus; Katherine M Kirk; Janne T Larsen; Richard Parker; Liselotte Petersen; Jennifer Jordan; Martin Kennedy; Grant W Montgomery; Tracey D Wade; Andreas Birgegård; Paul Lichtenstein; Claes Norring; Mikael Landén; Nicholas G Martin; Preben Bo Mortensen; Patrick F Sullivan; Gerome Breen; Cynthia M Bulik
Journal:  Nat Genet       Date:  2019-07-15       Impact factor: 38.330

7.  TNFα signals through specialized factories where responsive coding and miRNA genes are transcribed.

Authors:  Argyris Papantonis; Takahide Kohro; Sabyasachi Baboo; Joshua D Larkin; Binwei Deng; Patrick Short; Shuichi Tsutsumi; Stephen Taylor; Yasuharu Kanki; Mika Kobayashi; Guoliang Li; Huay-Mei Poh; Xiaoan Ruan; Hiroyuki Aburatani; Yijun Ruan; Tatsuhiko Kodama; Youichiro Wada; Peter R Cook
Journal:  EMBO J       Date:  2012-10-26       Impact factor: 11.598

Review 8.  An Overview of Genome Organization and How We Got There: from FISH to Hi-C.

Authors:  James Fraser; Iain Williamson; Wendy A Bickmore; Josée Dostie
Journal:  Microbiol Mol Biol Rev       Date:  2015-09       Impact factor: 11.056

Review 9.  Three-dimensional genome architecture: players and mechanisms.

Authors:  Ana Pombo; Niall Dillon
Journal:  Nat Rev Mol Cell Biol       Date:  2015-03-11       Impact factor: 94.444

10.  Disclosure of a structural milieu for the proximity ligation reveals the elusive nature of an active chromatin hub.

Authors:  Alexey A Gavrilov; Ekaterina S Gushchanskaya; Olga Strelkova; Oksana Zhironkina; Igor I Kireev; Olga V Iarovaia; Sergey V Razin
Journal:  Nucleic Acids Res       Date:  2013-02-08       Impact factor: 16.971

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