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
Emerging Principles of Gene Expression Programs and Their Regulation.
Scott D. Pope,Ruslan Medzhitov +1 more
TL;DR: The structure of transcription programs is discussed and a basic framework to categorize gene expression programs based on characteristics related to their control mechanisms is suggested.
Journal ArticleDOI
Cohesin promotes stochastic domain intermingling to ensure proper regulation of boundary-proximal genes.
Jennifer M. Luppino,Danny S. Park,Son C. Nguyen,Yemin Lan,Zhuxuan Xu,Rebecca Yunker,Eric F. Joyce +6 more
TL;DR: It is proposed that cohesin occasionally bypasses boundaries to promote incorporation of boundary-proximal genes into neighboring domains and a combination of super-resolution microscopy and Oligopaint technology shows that TAD boundaries are variable at the single-cell level.
Journal ArticleDOI
Mitotic Chromosome Mechanics: How Cells Segregate Their Genome.
Paul Batty,Daniel W. Gerlich +1 more
TL;DR: The requirements for mitotic chromosomes to successfully transmit genetic information to daughter cells and the biophysical principles that underpin such requirements are reviewed.
Journal ArticleDOI
New Approaches for Genome Assembly and Scaffolding
Edward S. Rice,Richard E. Green +1 more
TL;DR: An overview of the problem of chromosome-scale assembly and traditional methods for tackling this problem is given and new technologies for chromosome- scale assembly and recent genome projects that used these technologies to create highly contiguous genome assemblies at low cost are reviewed.
Journal ArticleDOI
Identification and Regulation of c-Myb Target Genes in MCF-7 Cells
TL;DR: It is suggested that estradiol stimulation leads to large-scale, genome-wide changes in c-Myb activity and subsequent changes in gene expression in human breast cancer cells.
References
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The Fractal Geometry of Nature
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Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
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