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
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TLDR
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.About:
This article is published in Cell.The article was published on 2017-10-05 and is currently open access. It has received 1290 citations till now. The article focuses on the topics: Cohesin & CTCF.read more
Citations
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Coactivator condensation at super-enhancers links phase separation and gene control
Benjamin R. Sabari,Alessandra Dall’Agnese,Ann Boija,Isaac A. Klein,Isaac A. Klein,Eliot L. Coffey,Krishna Shrinivas,Brian J. Abraham,Nancy M. Hannett,Alicia V. Zamudio,John C. Manteiga,Charles H. Li,Yang Eric Guo,Daniel S. Day,Jurian Schuijers,Eliza Vasile,Sohail Malik,Denes Hnisz,Tong Ihn Lee,Ibrahim I Cisse,Robert G. Roeder,Phillip A. Sharp,Arup K. Chakraborty,Richard A. Young +23 more
TL;DR: It is postulated that super-enhancers are phase-separated multimolecular assemblies, also known as biomolecular condensates, which provide a means to compartmentalize and concentrate biochemical reactions within cells.
Journal ArticleDOI
Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells
Bogdan Bintu,Leslie J. Mateo,Jun-Han Su,Nicholas A Sinnott-Armstrong,Mirae Parker,Seon Kinrot,Kei Yamaya,Alistair N. Boettiger,Xiaowei Zhuang +8 more
TL;DR: A super-resolution chromatin tracing method that allows determination of both the structural features and their genomic coordinates with high resolution in single cells is reported, suggesting that cohesin is not required for the formation or maintenance of single-cell domain structures, but that their preferential boundary positions are influenced by cohes in-CTCF interaction.
Journal ArticleDOI
Long-range enhancer-promoter contacts in gene expression control.
TL;DR: The latest understanding of long-range enhancer–promoter crosstalk is discussed, including target-gene specificity, interaction dynamics, protein and RNA architects of interactions, roles of 3D genome organization and the pathological consequences of regulatory rewiring.
Journal ArticleDOI
Organization of Chromatin by Intrinsic and Regulated Phase Separation
Bryan A. Gibson,Lynda K. Doolittle,Maximillian W.G. Schneider,Liv E. Jensen,Nathan Gamarra,Lisa Henry,Daniel W. Gerlich,Sy Redding,Michael K. Rosen +8 more
TL;DR: It is demonstrated that reconstituted chromatin undergoes histone tail-driven liquid-liquid phase separation (LLPS) in physiologic salt and when microinjected into cell nuclei, producing dense and dynamic droplets.
Journal ArticleDOI
Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins
Gordana Wutz,Csilla Várnai,Kota Nagasaka,David A. Cisneros,Roman R. Stocsits,Wen Tang,Stefan Schoenfelder,Gregor Jessberger,Matthias Muhar,M. Julius Hossain,Nike Walther,Birgit Koch,Moritz Kueblbeck,Jan Ellenberg,Johannes Zuber,Peter Fraser,Peter Fraser,Jan-Michael Peters +17 more
TL;DR: It is shown that cohesin suppresses compartments but is required for TADs and loops, that CTCF defines their boundaries, and that the cohes in unloading factor WAPL and its PDS5 binding partners control the length of loops.
References
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Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
TL;DR: This work presents DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates, which enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression.
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