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
CTCFBSDB 2.0: a database for CTCF-binding sites and genome organization
TL;DR: The updated database includes new features enabled by new CTCF-binding site data, including binding site occupancy and the ability to visualize overlapping CTCf-binding sites determined in separate experiments.
Journal ArticleDOI
Diffusion-Driven Looping Provides a Consistent Framework for Chromatin Organization
Manfred Bohn,Dieter W. Heermann +1 more
TL;DR: In this article, the formation of loops can be accomplished solely on the basis of diffusional motion and the probabilistic nature of temporary contacts mimics the effects of proteins in the solvent.
Posted ContentDOI
Cell cycle dynamics of chromosomal organisation at single-cell resolution
Takashi Nagano,Yaniv Lubling,Csilla Várnai,Carmel Dudley,Wing Leung,Yael Baran,Netta Mendelson Cohen,Steven W. Wingett,Peter Fraser,Amos Tanay +9 more
TL;DR: It is shown that chromosomal compartments, topological domains, contact insulation and long-range loops, all defined by ensemble Hi-C maps, are governed by distinct cell cycle dynamics, while DNA replication correlates with build-up of compartments and reduction in TAD insulation, while loops are generally stable from G1 through S and G2.
Journal ArticleDOI
HiCPlotter integrates genomic data with interaction matrices
Kadir C. Akdemir,Lynda Chin +1 more
TL;DR: An easy-to-use open-source visualization tool, HiCPlotter, is presented to facilitate juxtaposition of Hi-C matrices with diverse genomic assay outputs, as well as to compare interaction matrices between various conditions.
Journal ArticleDOI
Memories from the Polycomb Group Proteins
Chiara Lanzuolo,Valerio Orlando +1 more
TL;DR: This review focuses on the multiple modes of action of the PcG complexes and describes their biological roles.
References
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