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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Classes of fast and specific search mechanisms for proteins on DNA
TL;DR: This review focuses on the challenges posed by interactions between proteins, in particular transcription factors, and DNA and possible mechanisms which allow for fast and selective target location and introduces a new mechanism which is based on barrier discrimination.
Journal ArticleDOI
Transcription rate and transcript length drive formation of chromosomal interaction domain boundaries.
Tung B. K. Le,Michael T. Laub +1 more
TL;DR: It is found that in Caulobacter crescentus, both transcription rate and transcript length, independent of concurrent translation, drive the formation of domain boundaries, and this support a model in which long, active regions of transcription drive local decompaction of the chromosome.
Journal ArticleDOI
Chromatin Topology and the Regulation of Antigen Receptor Assembly
TL;DR: The epigenetic modifications that take place in the different antigen receptors loci, the chromatin structure adopted by the antigen receptor loci to allow recombination of elements separated by large genomic distances, and the relationship between epigenetics and Chromatin structure and how they relate to the generation of antigen receptor diversity are discussed.
Journal ArticleDOI
Epigenetic reprogramming at estrogen-receptor binding sites alters 3D chromatin landscape in endocrine-resistant breast cancer.
Joanna Achinger-Kawecka,Joanna Achinger-Kawecka,Fatima Valdes-Mora,Fatima Valdes-Mora,Phuc-Loi Luu,Phuc-Loi Luu,Katherine A. Giles,C. Elizabeth Caldon,Wenjia Qu,Shalima S. Nair,Sebastian Soto,Warwick J. Locke,Nicole S. Yeo-Teh,Cathryn M. Gould,Qian Du,Grady C. Smith,Irene Ramos,Kristine F Fernandez,Dave S.B. Hoon,Julia Margaret Wendy Gee,Clare Stirzaker,Clare Stirzaker,Susan J. Clark,Susan J. Clark +23 more
TL;DR: 3D epigenome remodelling at ER-bound enhancer-promoter interactions is a key mechanism underlying endocrine resistance in ER+ breast cancer.
Journal ArticleDOI
Promoter bivalency favors an open chromatin architecture in embryonic stem cells
Gloria Mas,Enrique Blanco,Cecilia Ballaré,Miriam Sansó,Yannick G. Spill,Deqing Hu,Yuki Aoi,François Le Dily,Ali Shilatifard,Marc A. Marti-Renom,Luciano Di Croce +10 more
TL;DR: It is shown that MLL2 plays a central role in ESC genome organization and it is posed that bivalency balances accessibility and long-range connectivity of promoters, allowing developmental gene expression to be properly modulated.
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
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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