Formation of Chromosomal Domains by Loop Extrusion
Geoffrey Fudenberg,Maxim Imakaev,Carolyn Lu,Anton Goloborodko,Nezar Abdennur,Leonid A. Mirny,Leonid A. Mirny +6 more
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TLDR
This model produces TADs and finer-scale features of Hi-C data because each TAD emerges from multiple loops dynamically formed through extrusion, contrary to typical illustrations of single static loops.About:
This article is published in Cell Reports.The article was published on 2016-05-31 and is currently open access. It has received 1479 citations till now. The article focuses on the topics: CTCF & Chromatin Loop.read more
Citations
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疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A
TL;DR: PfPMP1）与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作�ly.
Journal ArticleDOI
Cohesin Loss Eliminates All Loop Domains
Suhas S.P. Rao,Suhas S.P. Rao,Su Chen Huang,Brian Glenn St Hilaire,Brian Glenn St Hilaire,Jesse M. Engreitz,Elizabeth M. Perez,Kyong-Rim Kieffer-Kwon,Adrian L. Sanborn,Adrian L. Sanborn,Adrian L. Sanborn,Sarah E. Johnstone,Sarah E. Johnstone,Gavin D. Bascom,Ivan D. Bochkov,Xingfan Huang,Xingfan Huang,Muhammad S. Shamim,Muhammad S. Shamim,Jaeweon Shin,Jaeweon Shin,Douglass Turner,Douglass Turner,Ziyi Ye,Ziyi Ye,Arina D. Omer,James T. Robinson,James T. Robinson,James T. Robinson,Tamar Schlick,Tamar Schlick,Tamar Schlick,Bradley E. Bernstein,Bradley E. Bernstein,Rafael Casellas,Eric S. Lander,Eric S. Lander,Eric S. Lander,Erez Lieberman Aiden +38 more
TL;DR: In this paper, the effects of degrading cohesin were explored, showing that loop domains can be eliminated and re-formed in under an hour, consistent with a model where loop extrusion is rapid.
Journal ArticleDOI
Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization.
Elphège P. Nora,Anton Goloborodko,Anne-Laure Valton,Johan H. Gibcus,Alec Uebersohn,Nezar Abdennur,Job Dekker,Leonid A. Mirny,Benoit G. Bruneau +8 more
TL;DR: The data support that CTCF mediates transcriptional insulator function through enhancer blocking but not as a direct barrier to heterochromatin spreading, and provides new fundamental insights into the rules governing mammalian genome organization.
Journal ArticleDOI
Multiscale 3D Genome Rewiring during Mouse Neural Development
Boyan B. Bonev,Netta Mendelson Cohen,Quentin Szabo,Lauriane Fritsch,Giorgio L. Papadopoulos,Yaniv Lubling,Xiaole Xu,Xiaodan Lv,Jean-Philippe Hugnot,Amos Tanay,Giacomo Cavalli +10 more
TL;DR: This work comprehensively mapped 3D chromatin organization during mouse neural differentiation in vitro and in vivo, generating the highest-resolution Hi-C maps available to date and shows that multiple factors influence the dynamics of chromatin interactions in development.
Journal Article
Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes
Adrian L. Sanborn,Suhas S.P. Rao,Su-Chen Huang,Neva C. Durand,Miriam H. Huntley,Andrew I. Jewett,Ivan D. Bochkov,Dharmaraj Chinnappan,Ashok Cutkosky,Jian Li,Kristopher Geeting,Doug McKenna,Elena K. Stamenova,Andreas Gnirke,Alexandre Melnikov,Eric S. Lander,Erez Lieberman Aiden +16 more
TL;DR: In this article, high-resolution spatial proximity maps are consistent with a model in which a complex, including the proteins CCCTC-binding factor (CTCF) and cohesin, mediates the formation of loops by a process of extrusion.
References
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疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A
TL;DR: PfPMP1）与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作�ly.
Journal ArticleDOI
BEDTools: a flexible suite of utilities for comparing genomic features
Aaron R. Quinlan,Ira M. Hall +1 more
TL;DR: A new software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format, which allows the user to compare large datasets (e.g. next-generation sequencing data) with both public and custom genome annotation tracks.
Journal ArticleDOI
Comprehensive mapping of long-range interactions reveals folding principles of the human genome.
Erez Lieberman Aiden,Nynke L. van Berkum,Louise Williams,Maxim Imakaev,Tobias Ragoczy,Tobias Ragoczy,Agnes Telling,Agnes Telling,Ido Amit,Bryan R. Lajoie,Peter J. Sabo,Michael O. Dorschner,Richard Sandstrom,Bradley E. Bernstein,Bradley E. Bernstein,Michaël Bender,Mark Groudine,Mark Groudine,Andreas Gnirke,John A. Stamatoyannopoulos,Leonid A. Mirny,Eric S. Lander,Eric S. Lander,Job Dekker +23 more
TL;DR: Hi-C is described, a method that probes the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing and demonstrates the power of Hi-C to map the dynamic conformations of entire genomes.
Journal ArticleDOI
A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
Suhas S.P. Rao,Miriam H. Huntley,Neva C. Durand,Elena K. Stamenova,Ivan D. Bochkov,James T. Robinson,James T. Robinson,Adrian L. Sanborn,Ido Machol,Ido Machol,Arina D. Omer,Arina D. Omer,Eric S. Lander,Eric S. Lander,Eric S. Lander,Erez Lieberman Aiden +15 more
TL;DR: In situ Hi-C is used to probe the 3D architecture of genomes, constructing haploid and diploid maps of nine cell types, identifying ∼10,000 loops that frequently link promoters and enhancers, correlate with gene activation, and show conservation across cell types and species.
Journal ArticleDOI
Topological domains in mammalian genomes identified by analysis of chromatin interactions
Jesse R. Dixon,Siddarth Selvaraj,Siddarth Selvaraj,Feng Yue,Audrey Kim,Yan-Yan Li,Yin-Zhong Shen,Ming Hu,Jun Liu,Bing Ren,Bing Ren +10 more
TL;DR: It is found that the boundaries of topological domains are enriched for the insulator binding protein CTCF, housekeeping genes, transfer RNAs and short interspersed element (SINE) retrotransposons, indicating that these factors may have a role in establishing the topological domain structure of the genome.
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