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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Genome-wide Chromatin Interactions of the Nanog Locus in Pluripotency, Differentiation, and Reprogramming
Effie Apostolou,Francesco Ferrari,Ryan M. Walsh,Ryan M. Walsh,Ori Bar-Nur,Ori Bar-Nur,Matthias Stadtfeld,Matthias Stadtfeld,Sihem Cheloufi,Sihem Cheloufi,Hannah T. Stuart,Hannah T. Stuart,Jose M. Polo,Jose M. Polo,Toshiro K. Ohsumi,Mark L. Borowsky,Peter V. Kharchenko,Peter V. Kharchenko,Peter J. Park,Peter J. Park,Peter J. Park,Konrad Hochedlinger,Konrad Hochedlinger +22 more
TL;DR: A genome-wide, pluripotency-specific interaction network around the Nanog promoter is identified by adapting circular chromosome conformation capture sequencing and this network was rearranged during differentiation and restored in induced pluripotent stem cells.
Journal ArticleDOI
Living without 30nm chromatin fibers.
TL;DR: It is suggested that the organization of the genome based on 10nm chromatin fibers is sufficient to describe the complexities of nuclear organization and gene regulation.
Journal ArticleDOI
High order chromatin architecture shapes the landscape of chromosomal alterations in cancer.
TL;DR: Fudenberg et al. as mentioned in this paper found that copy number gain and loss is influenced by the three-dimensional organization of the genome in the nucleus, and they used statistical approaches to model different processes.
Journal ArticleDOI
CTCF-Mediated Enhancer-Promoter Interaction Is a Critical Regulator of Cell-to-Cell Variation of Gene Expression
Gang Ren,Wenfei Jin,Kairong Cui,Joseph Rodrigez,Gangqing Hu,Zhiying Zhang,Daniel R. Larson,Keji Zhao +7 more
TL;DR: It is reported that CTCF decreases cell-to-cell variation of expression by stabilizing enhancer-promoter interaction, and it is shown that C TCF binding sites are interwoven with enhancers within topologically associated domains (TADs) and a positive correlation is found between CTCf binding and the activity of the associated enhancers.
Journal ArticleDOI
Differential DNA Methylation Correlates with Differential Expression of Angiogenic Factors in Human Heart Failure
TL;DR: In this article, the role of DNA methylation, another well-characterized epigenetic mark, is unknown, and the authors examined whether human cardiomyopathy of different etiologies are connected by a unifying pattern of DNA epigenetic pattern, and identified 3 angiogenesis-related genes that were differentially methylated.
References
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