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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GRID-seq reveals the global RNA-chromatin interactome.
TL;DR: A method to capture in situ global RNA interactions with DNA by deep sequencing (GRID-seq) is reported, which enables the comprehensive identification of the entire repertoire of chromatin-interacting RNAs and their respective binding sites.
Journal ArticleDOI
Genome organization in and around the nucleolus
Attila Németh,Gernot Längst +1 more
TL;DR: Current views on the structural organization of nucleolar DNA and on the targeting and anchoring of chromatin domains to this subnuclear compartment are summarized.
Journal ArticleDOI
Detection and replication of epistasis influencing transcription in humans
Gibran Hemani,Konstantin Shakhbazov,Harm-Jan Westra,Tõnu Esko,Anjali K. Henders,Allan F. McRae,Jian Yang,Greg Gibson,Nicholas G. Martin,Andres Metspalu,Lude Franke,Grant W. Montgomery,Peter M. Visscher,Joseph E. Powell +13 more
TL;DR: This study presents the first evidence, to the knowledge, for many instances of segregating common polymorphisms interacting to influence human traits.
Journal ArticleDOI
Genomic approaches towards finding cis-regulatory modules in animals.
Ross C. Hardison,James Taylor +1 more
TL;DR: The validation rates for predictions indicate that identifying diagnostic biochemical marks is the most reliable method, and understanding is enhanced by the analysis of motifs and conservation patterns within those predicted CRMs.
Journal ArticleDOI
Identification of alternative topological domains in chromatin
TL;DR: A new and efficient algorithm is introduced that is able to capture persistent domains across various resolutions by adjusting a single scale parameter and reveals a pronounced hierarchical structure in which larger stable domains tend to completely contain smaller domains.
References
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Book
The Fractal Geometry of Nature
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