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
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Chromosome organization by one-sided and two-sided loop extrusion
TL;DR: This work simulates one-sided loop extrusion to investigate whether SMC complexes in vivo can compact mitotic chromosomes, organize interphase domains, and juxtapose bacterial chromosomal arms, as can be done by ‘two-sided’ loop extruders.
Journal ArticleDOI
Laying a solid foundation for Manhattan--'setting the functional basis for the post-GWAS era'.
TL;DR: Recent work annotating the non-coding regions of the genome has contributed to post-GWAS studies by facilitating the identification of the functional targets of risk-associated loci, and their importance to the interpretation of disease-associated mutations identified through whole-genome sequencing is related.
Journal ArticleDOI
Cohesin-Dependent and -Independent Mechanisms Mediate Chromosomal Contacts between Promoters and Enhancers
Michiel J. Thiecke,Gordana Wutz,Matthias Muhar,Wen Tang,Stephen Bevan,Valeriya Malysheva,Valeriya Malysheva,Roman R. Stocsits,Tobias Neumann,Johannes Zuber,Peter Fraser,Peter Fraser,Stefan Schoenfelder,Jan-Michael Peters,Mikhail Spivakov,Mikhail Spivakov +15 more
TL;DR: This work uses high-resolution Capture Hi-C to interrogate the dynamics of chromosomal contacts of all annotated human gene promoters upon degradation of cohesin and CTCF, and shows that a majority of promoter-anchored contacts are lost in these conditions, but many contacts with distinct properties are maintained, and some new ones are gained.
Journal ArticleDOI
Sub-nucleosomal Genome Structure Reveals Distinct Nucleosome Folding Motifs.
TL;DR: This work coupled nucleosome-resolved Hi-C technology with simulated annealing-molecular dynamics simulation to reveal 3D spatial distributions of nucleosomes and their genome-wide orientation in chromatin, and uncovered distinct nucleosom folding motifs across the yeast genome.
Journal ArticleDOI
Genome-wide Hi-C analysis reveals extensive hierarchical chromatin interactions in rice
Qianli Dong,Ning Li,Xiaochong Li,Zan Yuan,Dejian Xie,Xiaofei Wang,Jianing Li,Yanan Yu,Jinbin Wang,Baoxu Ding,Zhibin Zhang,Changping Li,Yao Bian,Ai Zhang,Ying Wu,Bao Liu,Lei Gong +16 more
TL;DR: It is concluded that genomic composition, epigenetic modification, and transcriptional activity could act in combination to shape global and local chromatin packing in rice.
References
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