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
TLDR
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.Abstract:
We describe Hi-C, a method that probes the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. We constructed spatial proximity maps of the human genome with Hi-C at a resolution of 1 megabase. These maps confirm the presence of chromosome territories and the spatial proximity of small, gene-rich chromosomes. We identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free, polymer conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. The fractal globule is distinct from the more commonly used globular equilibrium model. Our results demonstrate the power of Hi-C to map the dynamic conformations of whole genomes.read more
Citations
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Journal ArticleDOI
Ring Polymers in the Melt State: The Physics of Crumpling
Angelo Rosa,Ralf Everaers +1 more
TL;DR: It is shown that melts of rings of total contour length Lr can be quantitatively mapped onto melts of interacting lattice trees with gyration radii R(g)(2)(Lr)⟩ ∝ L(r)(2ν) and ν = 0.32 ± 0.01.
Journal ArticleDOI
Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms
Martial Marbouty,Axel Cournac,Axel Cournac,Jean-François Flot,Hervé Marie-Nelly,Hervé Marie-Nelly,Julien Mozziconacci,Romain Koszul,Romain Koszul +8 more
TL;DR: Using controlled mixes of bacterial and yeast species, meta3C is developed, a metagenomic chromosome conformation capture approach that allows characterizing individual genomes and their average organization within a mix of organisms.
Journal ArticleDOI
A predictive computational model of the dynamic 3D interphase yeast nucleus.
Hua Wong,Hervé Marie-Nelly,Sébastien Herbert,Pascal Carrivain,Hervé Blanc,Romain Koszul,Emmanuelle Fabre,Christophe Zimmer +7 more
TL;DR: The results suggest that large-scale yeast nuclear architecture can be largely understood as a consequence of generic properties of crowded polymers rather than of specific DNA-binding factors and that configurations of chromosomes and DNA contacts are dictated mainly by genomic location and chromosome lengths.
Journal ArticleDOI
Long Noncoding RNA in Hematopoiesis and Immunity
TL;DR: This work discusses recent advances, future prospects, and challenges in understanding the roles of lncRNAs in immunity and immune-mediated diseases.
Journal ArticleDOI
Systematic Mapping of RNA-Chromatin Interactions In Vivo
Bharat Sridhar,Bharat Sridhar,Marcelo Rivas-Astroza,Tri C. Nguyen,Weizhong Chen,Zhangming Yan,Xiaoyi Cao,Lucie Hebert,Sheng Zhong +8 more
TL;DR: Using MARGI (mapping RNA-genome interactions), a technology to massively reveal native RNA-chromatin interactions from unperturbed cells, hundreds of caRNAs were revealed, including previously known XIST, SNHG1, NEAT1, and MALAT1 as well as each caRNA's genomic interaction loci.
References
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Book
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