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
Chromatin three-dimensional interactions mediate genetic effects on gene expression
Olivier Delaneau,Olivier Delaneau,Marianna Zazhytska,Christelle Borel,Giuliana Giannuzzi,Guillaume Rey,Guillaume Rey,Cédric Howald,Cédric Howald,Sunil Kumar,Sunil Kumar,Halit Ongen,Halit Ongen,Konstantin Popadin,Konstantin Popadin,Daniel Marbach,Daniel Marbach,Giovanna Ambrosini,Giovanna Ambrosini,Deborah Bielser,David L. Hacker,Luciana Romano,Pascale Ribaux,Michaël Wiederkehr,Emilie Falconnet,Philipp Bucher,Philipp Bucher,Sven Bergmann,Sven Bergmann,Stylianos E. Antonarakis,Alexandre Reymond,Emmanouil T. Dermitzakis,Emmanouil T. Dermitzakis +32 more
TL;DR: This work suggests that three-dimensional (3D) organization in cis can be broadly categorized into functionally linked and unlinked domains, with the most-linked ones corresponding to CRDs.
Journal ArticleDOI
RNA sequencing: new technologies and applications in cancer research
Mingye Hong,Shuang Tao,Ling Zhang,Li-Ting Diao,Xuanmei Huang,Shaohui Huang,Shu-Juan Xie,Zhen Dong Xiao,Hua Zhang +8 more
TL;DR: The latest studies on RNA sequencing technology and their applications in cancer are summarized, and future challenges and opportunities forRNA sequencing technology in cancer applications are discussed.
Journal ArticleDOI
Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling
TL;DR: A probabilistic model linking 5C/Hi-C data to physical distances is formulated and a Markov chain Monte Carlo (MCMC) approach called MCMC5C is described to generate a representative sample from the posterior distribution over structures from IF data to reliably interpret the result of their assay and contrast conformations under different conditions.
Posted ContentDOI
YaHS: yet another Hi-C scaffolding tool
TL;DR: Yahs as mentioned in this paper is a command-line tool for constructing chromosome-scale scaffolds from Hi-C data, which can be run with a single-line command and requires minimal input from users (an assembly file and an alignment file).
Journal ArticleDOI
Reprogramming to pluripotency: stepwise resetting of the epigenetic landscape
Bernadett Papp,Kathrin Plath +1 more
TL;DR: This review addresses the steps involved in resetting the epigenetic landscape during reprogramming, and explains why some cells start to divide faster and quickly begin to lose their differentiated cell characteristics with robust downregulation of somatic genes.
References
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