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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Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions.
Diego I. Cattoni,Andrés M. Cardozo Gizzi,Mariya Georgieva,Marco Di Stefano,Marco Di Stefano,Alessandro Valeri,Delphine Chamousset,Christophe Houbron,Stephanie Dejardin,Jean-Bernard Fiche,Inma González,Jia-Ming Chang,Tom Sexton,Marc A. Marti-Renom,Marc A. Marti-Renom,Frédéric Bantignies,Giacomo Cavalli,Marcelo Nollmann +17 more
TL;DR: It is proposed that TADs and compartments are organized by multiple, small-frequency, yet specific interactions that are regulated by epigenetics and transcriptional state and is able to visualize nanometer-sized epigenetic domains at the single-cell level.
Journal ArticleDOI
Simulation Analysis of the Temperature Dependence of Lignin Structure and Dynamics
TL;DR: The detailed characterization obtained here provides insight at atomic detail into processes relevant to biomass pretreatment for cellulosic ethanol production and general polymer coil-globule transition phenomena.
Journal ArticleDOI
How best to identify chromosomal interactions: a comparison of approaches
TL;DR: This Review describes and compares the different available 3C-based approaches, with a focus on the analysis of mammalian genomes, and discusses the strengths and weaknesses of each technique.
Journal ArticleDOI
Genomic signatures of mitonuclear coevolution across populations of Tigriopus californicus
Felipe S. Barreto,Felipe S. Barreto,E. Watson,Thiago G. Lima,Thiago G. Lima,Christopher S. Willett,Suzanne Edmands,Weizhong Li,Ronald S. Burton +8 more
TL;DR: Comparative genomics of eight populations of the copepod Tigriopus californicus reveals extreme mtDNA divergence and rapid protein evolution as well as positive selection in genes predicted to interact with mtDNA, which suggests mitonuclear coevolution.
Journal ArticleDOI
Harnessing cloud computing with Galaxy Cloud.
Enis Afgan,Dannon Baker,Nate Coraor,Hiroki Goto,Ian M. Paul,Kateryna D. Makova,Anton Nekrutenko,James Taylor +7 more
TL;DR: Galaxy Cloud provides a solution that retains user control and privacy, makes complex analysis accessible and enables the use of practically limitless on-demand computing resources.
References
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Book
The Fractal Geometry of Nature
TL;DR: This book is a blend of erudition, popularization, and exposition, and the illustrations include many superb examples of computer graphics that are works of art in their own right.
疟原虫var基因转换速率变化导致抗原变异[英]/Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A
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Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
Tarjei S. Mikkelsen,Manching Ku,Manching Ku,David B. Jaffe,Biju Issac,Biju Issac,Erez Lieberman Aiden,Erez Lieberman Aiden,Georgia Giannoukos,Pablo Alvarez,William Brockman,Tae Kyung Kim,Richard Koche,Richard Koche,Richard Koche,William Lee,Eric M. Mendenhall,Eric M. Mendenhall,Aisling O'Donovan,Aviva Presser,Carsten Russ,Xiaohui Xie,Alexander Meissner,Marius Wernig,Rudolf Jaenisch,Chad Nusbaum,Eric S. Lander,Eric S. Lander,Bradley E. Bernstein,Bradley E. Bernstein +29 more
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Capturing Chromosome Conformation
TL;DR: Using the yeast Saccharomyces cerevisiae, this work could confirm known qualitative features of chromosome organization within the nucleus and dynamic changes in that organization during meiosis and found that chromatin is highly flexible throughout.
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