Literature DB >> 26111025

Breaking TADs: insights into hierarchical genome organization.

Pedro P Rocha1, Ramya Raviram1, Richard Bonneau2,3,4, Jane A Skok1.   

Abstract

Entities:  

Keywords:  Hi-C; TADs; chromosome confirmation capture; gene regulation; nuclear organization

Mesh：

Year:  2015        PMID： 26111025      PMCID： PMC4624204          DOI： 10.2217/epi.15.25

Source DB:  PubMed          Journal:  Epigenomics        ISSN： 1750-192X            Impact factor:   4.778


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  20 in total

1.  A switch between topological domains underlies HoxD genes collinearity in mouse limbs.

Authors:  Guillaume Andrey; Thomas Montavon; Bénédicte Mascrez; Federico Gonzalez; Daan Noordermeer; Marion Leleu; Didier Trono; François Spitz; Denis Duboule
Journal:  Science       Date:  2013-06-07       Impact factor: 47.728

2.  Spatial partitioning of the regulatory landscape of the X-inactivation centre.

Authors:  Elphège P Nora; Bryan R Lajoie; Edda G Schulz; Luca Giorgetti; Ikuhiro Okamoto; Nicolas Servant; Tristan Piolot; Nynke L van Berkum; Johannes Meisig; John Sedat; Joost Gribnau; Emmanuel Barillot; Nils Blüthgen; Job Dekker; Edith Heard
Journal:  Nature       Date:  2012-04-11       Impact factor: 49.962

3.  Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription.

Authors:  Luca Giorgetti; Rafael Galupa; Elphège P Nora; Tristan Piolot; France Lam; Job Dekker; Guido Tiana; Edith Heard
Journal:  Cell       Date:  2014-05-08       Impact factor: 41.582

4.  A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.

Authors:  Suhas S P Rao; Miriam H Huntley; Neva C Durand; Elena K Stamenova; Ivan D Bochkov; James T Robinson; Adrian L Sanborn; Ido Machol; Arina D Omer; Eric S Lander; Erez Lieberman Aiden
Journal:  Cell       Date:  2014-12-11       Impact factor: 41.582

5.  Architectural protein subclasses shape 3D organization of genomes during lineage commitment.

Authors:  Jennifer E Phillips-Cremins; Michael E G Sauria; Amartya Sanyal; Tatiana I Gerasimova; Bryan R Lajoie; Joshua S K Bell; Chin-Tong Ong; Tracy A Hookway; Changying Guo; Yuhua Sun; Michael J Bland; William Wagstaff; Stephen Dalton; Todd C McDevitt; Ranjan Sen; Job Dekker; James Taylor; Victor G Corces
Journal:  Cell       Date:  2013-05-23       Impact factor: 41.582

6.  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

7.  The RAG2 C-terminus and ATM protect genome integrity by controlling antigen receptor gene cleavage.

Authors:  Julie Chaumeil; Mariann Micsinai; Panagiotis Ntziachristos; David B Roth; Iannis Aifantis; Yuval Kluger; Ludovic Deriano; Jane A Skok
Journal:  Nat Commun       Date:  2013       Impact factor: 14.919

8.  Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation.

Authors:  François Le Dily; Davide Baù; Andy Pohl; Guillermo P Vicent; François Serra; Daniel Soronellas; Giancarlo Castellano; Roni H G Wright; Cecilia Ballare; Guillaume Filion; Marc A Marti-Renom; Miguel Beato
Journal:  Genes Dev       Date:  2014-10-01       Impact factor: 11.361

9.  Insulator function and topological domain border strength scale with architectural protein occupancy.

Authors:  Kevin Van Bortle; Michael H Nichols; Li Li; Chin-Tong Ong; Naomi Takenaka; Zhaohui S Qin; Victor G Corces
Journal:  Genome Biol       Date:  2014-06-30       Impact factor: 13.583

10.  Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes.

Authors:  Jill M Dowen; Zi Peng Fan; Denes Hnisz; Gang Ren; Brian J Abraham; Lyndon N Zhang; Abraham S Weintraub; Jurian Schujiers; Tong Ihn Lee; Keji Zhao; Richard A Young
Journal:  Cell       Date:  2014-10-09       Impact factor: 41.582
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  20 in total

Review 1.  Epigenetic Regulation in Neurodegenerative Diseases.

Authors:  Amit Berson; Raffaella Nativio; Shelley L Berger; Nancy M Bonini
Journal:  Trends Neurosci       Date:  2018-06-07       Impact factor: 13.837

2.  Condensin Depletion Causes Genome Decompaction Without Altering the Level of Global Gene Expression in Saccharomyces cerevisiae.

Authors:  Matthew Robert Paul; Tovah Elise Markowitz; Andreas Hochwagen; Sevinç Ercan
Journal:  Genetics       Date:  2018-07-03       Impact factor: 4.562

Review 3.  Seeing the forest through the trees: prioritising potentially functional interactions from Hi-C.

Authors:  Ning Liu; Wai Yee Low; Hamid Alinejad-Rokny; Stephen Pederson; Timothy Sadlon; Simon Barry; James Breen
Journal:  Epigenetics Chromatin       Date:  2021-08-28       Impact factor: 4.954

4.  Restriction enzyme selection dictates detection range sensitivity in chromatin conformation capture-based variant-to-gene mapping approaches.

Authors:  Struan F A Grant; Andrew D Wells; Chun Su; Matthew C Pahl
Journal:  Hum Genet       Date:  2021-08-18       Impact factor: 5.881

5.  RAG Off-Target Activity Is in the Loop.

Authors:  Lili Blumenberg; Jane A Skok
Journal:  Trends Mol Med       Date:  2015-11-18       Impact factor: 11.951

6.  A critical assessment of topologically associating domain prediction tools.

Authors:  Rola Dali; Mathieu Blanchette
Journal:  Nucleic Acids Res       Date:  2017-04-07       Impact factor: 16.971

7.  Identification of multi-loci hubs from 4C-seq demonstrates the functional importance of simultaneous interactions.

Authors:  Tingting Jiang; Ramya Raviram; Valentina Snetkova; Pedro P Rocha; Charlotte Proudhon; Sana Badri; Richard Bonneau; Jane A Skok; Yuval Kluger
Journal:  Nucleic Acids Res       Date:  2016-07-20       Impact factor: 16.971

8.  CRISPR-dCas9 and sgRNA scaffolds enable dual-colour live imaging of satellite sequences and repeat-enriched individual loci.

Authors:  Yi Fu; Pedro P Rocha; Vincent M Luo; Ramya Raviram; Yan Deng; Esteban O Mazzoni; Jane A Skok
Journal:  Nat Commun       Date:  2016-05-25       Impact factor: 14.919

9.  Stratification of TAD boundaries reveals preferential insulation of super-enhancers by strong boundaries.

Authors:  Yixiao Gong; Charalampos Lazaris; Theodore Sakellaropoulos; Aurelie Lozano; Prabhanjan Kambadur; Panagiotis Ntziachristos; Iannis Aifantis; Aristotelis Tsirigos
Journal:  Nat Commun       Date:  2018-02-07       Impact factor: 14.919

10.  Genome-wide profiling of transcribed enhancers during macrophage activation.

Authors:  Elena Denisenko; Reto Guler; Musa M Mhlanga; Harukazu Suzuki; Frank Brombacher; Sebastian Schmeier
Journal:  Epigenetics Chromatin       Date:  2017-10-23       Impact factor: 4.954
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