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
The Chromatin Fingerprint of Gene Enhancer Elements
TL;DR: The current understanding of the chromatin landscape at enhancers is reviewed and how these chromatin features enable robust identification of tissue-specific enhancers.
Journal ArticleDOI
Fractal dimension of chromatin is an independent prognostic factor for survival in melanoma
TL;DR: There is strong evidence that the fractal dimension of the nuclear chromatin texture is a new and promising variable in prognostic models of malignant melanomas.
Journal ArticleDOI
Regulatory Variation Within and Between Species
TL;DR: In this article, a review of differential gene regulation focusing on evolutionary-developmental biology, global comparison of genomic sequences, whole-genome gene expression, and transcription factor (TF) binding profiles is presented.
Journal ArticleDOI
Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions.
Stefan Schoenfelder,Biola-Maria Javierre,Mayra Furlan-Magaril,Steven W. Wingett,Peter Fraser +4 more
TL;DR: Promoter Capture Hi-C (PCHi-C) is developed to enable the genome-wide detection of distal promoter-interacting regions (PIRs), for all promoters in a single experiment, and an atlas of long-range promoter interactions in dozens of human and mouse cell types is generated.
Journal ArticleDOI
Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms.
Alexej Abyzov,Shantao Li,Daniel Rhee Kim,Marghoob Mohiyuddin,Adrian M. Stütz,Nicholas F. Parrish,Xinmeng Jasmine Mu,Wyatt T. Clark,Ken Chen,Matthew E. Hurles,Jan O. Korbel,Hugo Y. K. Lam,Charles Kai-Wu Lee,Mark Gerstein +13 more
TL;DR: The identification, classification and analysis of a large database of variants giving an insight into mechanisms generating them are presented, and a major source of complexity in the human genome is identified.
References
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