Higher-order chromatin structure: bridging physics and biology.
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TLDR
Polymer models provide a framework for the interpretation of experimental data as ensembles of conformations rather than collections of loops, and will be crucial for untangling functional implications of chromosomal organization as mentioned in this paper.About:
This article is published in Current Opinion in Genetics & Development.The article was published on 2012-04-01 and is currently open access. It has received 149 citations till now. The article focuses on the topics: Chromosome conformation capture & Higher Order Chromatin Structure.read more
Citations
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Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data
TL;DR: Several types of statistical and computational approaches that have recently been developed to analyse chromatin interaction data are described.
Journal ArticleDOI
Organization of the Mitotic Chromosome
Natalia Naumova,Maxim Imakaev,Geoffrey Fudenberg,Geoffrey Fudenberg,Ye Zhan,Bryan R. Lajoie,Leonid A. Mirny,Job Dekker +7 more
TL;DR: Using polymer simulations, it is found that metaphase Hi-C data are inconsistent with classic hierarchical models and are instead best described by a linearly organized longitudinally compressed array of consecutive chromatin loops.
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The Hierarchy of the 3D Genome
Johan H. Gibcus,Job Dekker +1 more
TL;DR: The experimental and theoretical data on this hierarchy of structures and a key role for the recently discovered topologically associating domains are reviewed and proposed.
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Single-Molecule Dynamics of Enhanceosome Assembly in Embryonic Stem Cells
Jiji Chen,Zhengjian Zhang,Li M. Li,Bi-Chang Chen,Andrey Revyakin,Bassam Hajj,Wesley R. Legant,Maxime Dahan,Maxime Dahan,Timothée Lionnet,Eric Betzig,Robert Tjian,Zhe Liu +12 more
TL;DR: In vivo and in vitro single-molecule imaging, transcription factor (TF) mutagenesis, and ChIP-exo mapping are combined to determine how TFs dynamically search for and assemble on their cognate DNA target sites and find that enhanceosome assembly is hierarchically ordered.
Journal ArticleDOI
Predictive Polymer Modeling Reveals Coupled Fluctuations in Chromosome Conformation and Transcription
Luca Giorgetti,Luca Giorgetti,Luca Giorgetti,Rafael Galupa,Rafael Galupa,Rafael Galupa,Elphège P. Nora,Tristan Piolot,Tristan Piolot,Tristan Piolot,Job Dekker,Guido Tiana,Edith Heard +12 more
TL;DR: It is demonstrated that contacts between potential regulatory elements occur in the context of fluctuating structures rather than stable loops and proposed that such fluctuations may contribute to asymmetric expression in the Xic during X inactivation.
References
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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.
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Stochastic Gene Expression in a Single Cell
TL;DR: This work constructed strains of Escherichia coli that enable detection of noise and discrimination between the two mechanisms by which it is generated and reveals how low intracellular copy numbers of molecules can fundamentally limit the precision of gene regulation.
Journal ArticleDOI
Capturing Chromosome Conformation
TL;DR: Using the yeast Saccharomyces cerevisiae, this work could confirm known qualitative features of chromosome organization within the nucleus and dynamic changes in that organization during meiosis and found that chromatin is highly flexible throughout.
Mediator and cohesin connect gene expression and chromatin architecture
Michael H. Kagey,Jamie J. Newman,Steve Bilodeau,Ye Zhan,David A. Orlando,Nynke L. van Berkum,Christopher C. Ebmeier,Jesse Goossens,Peter B. Rahl,Stuart S. Levine,Dylan J. Taatjes,Job Dekker,Richard A. Young +12 more
TL;DR: It is reported that mediator and cohesin physically and functionally connect the enhancers and core promoters of active genes in murine embryonic stem cells.
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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