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
Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C
TL;DR: Investigation of chromosome folding in mutants confirms roles for RSC, "gene looping" factor Ssu72, Mediator, H3K56 acetyltransferase Rtt109, and the N-terminal tail of H4 in folding of the yeast genome, and findings provide insights into the machinery underlying chromosome compaction.
Journal ArticleDOI
Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues
Jiang Zhu,Mazhar Adli,James Zou,Griet Verstappen,Griet Verstappen,Michael Coyne,Xiaolan Zhang,Timothy Durham,Mohammad Miri,Vikram Deshpande,Philip L. De Jager,Philip L. De Jager,David A. Bennett,Joseph A. Houmard,Deborah M. Muoio,Tamer T. Onder,Raymond Camahort,Raymond Camahort,Chad A. Cowan,Chad A. Cowan,Alexander Meissner,Alexander Meissner,Charles B. Epstein,Noam Shoresh,Bradley E. Bernstein +24 more
TL;DR: The chromatin genome-wide in a large and diverse collection of human tissues and stem cells is mapped to yield unprecedented annotations of functional genomic elements and their regulation across developmental stages, lineages, and cellular environments.
Journal ArticleDOI
The nuclear pore complex: bridging nuclear transport and gene regulation
TL;DR: The nuclear pore complex is emerging as an important regulator of gene expression through its influence on the internal architectural organization of the nucleus and its apparently extensive involvement in coordinating the seamless delivery of genetic information to the cytoplasmic protein synthesis machinery.
Journal ArticleDOI
Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome
Derek M. Bickhart,Benjamin D. Rosen,Sergey Koren,B.L. Sayre,Alex Hastie,Saki Chan,Joyce Lee,Ernest T. Lam,Ivan Liachko,Shawn T. Sullivan,Joshua N. Burton,Heather J. Huson,John C Nystrom,Christy M. Kelley,J.L. Hutchison,Yang Zhou,Yang Zhou,Jiajie Sun,Alessandra Crisà,F. Abel Ponce de León,John C. Schwartz,John A. Hammond,Geoffrey C. Waldbieser,Steven G. Schroeder,George E. Liu,Maitreya J. Dunham,Jay Shendure,Jay Shendure,Tad S. Sonstegard,Adam M. Phillippy,Curtis P. Van Tassell,Timothy P L Smith +31 more
TL;DR: This assembly represents a ∼400-fold improvement in continuity due to properly assembled gaps, compared to the previously published C. hircus assembly, and better resolves repetitive structures longer than 1 kb, representing the largest repeat family and immune gene complex yet produced for an individual of a ruminant species.
The 3D Genome as Moderator of Chromosomal Communication
Job Dekker,Leonid A. Mirny +1 more
TL;DR: In this article, the authors present a view of the interphase 3D genome characterized by extensive physical compartmentalization and insulation on the one hand and facilitated long-range interactions on the other.
References
More filters
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
TL;DR: PfPMP1)与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作�ly.
Journal ArticleDOI
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
TL;DR: The application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells is reported and it is shown that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms.
Journal ArticleDOI
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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