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 Article
Dynamics of gene silencing during X inactivation using allele-specific RNA-seq (vol 16, 149, 2015)
Hendrik Marks,Hindrik H. D. Kerstens,Tahsin Stefan Barakat,Erik Splinter,René A.M. Dirks,G. van Mierlo,Onkar Joshi,Shuang-Yin Wang,Tomas Babak,Cornelis A. Albers,T. Kalkan,Austin Smith,Alice Jouneau,W. de Laat,Joost Gribnau,Henk Stunnenberg +15 more
TL;DR: In this paper, the authors used mouse female embryonic stem cells (ESCs) with non-random X chromosome inactivation and polymorphic X chromosomes to study the dynamics of gene silencing over the inactive X chromosome by high-resolution allele-specific RNA-seq.
Journal ArticleDOI
Transcription-induced supercoiling as the driving force of chromatin loop extrusion during formation of TADs in interphase chromosomes.
Dušan Račko,Dušan Račko,Dušan Račko,Fabrizio Benedetti,Fabrizio Benedetti,Julien Dorier,Julien Dorier,Andrzej Stasiak,Andrzej Stasiak +8 more
TL;DR: It is shown here that growing plectonemes resulting from transcription-induced supercoiling have the ability to actively push cohesin rings along chromatin fibres, and the supercoiled-driven loop extrusion mechanism is consistent with earlier explanations proposing why TADs flanked by convergent CTCF binding sites form more stable chromatin loops than TADS flanked by divergent C TCF binding Sites.
Journal ArticleDOI
Three-dimensional chromatin packing and positioning of plant genomes
Ezgi Sueheyla Dogan,Chang Liu +1 more
TL;DR: This Review summarizes the understanding of plant chromatin organization and positioning beyond the nucleosomal level, advanced by up-to-date chromatin conformation capture methods and visualization techniques, as well as discusses future directions.
Journal ArticleDOI
4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments
Ramya Raviram,Pedro P. Rocha,Christian L. Müller,Christian L. Müller,Emily R. Miraldi,Emily R. Miraldi,Sana Badri,Yi Fu,Emily Swanzey,Charlotte Proudhon,Valentina Snetkova,Richard Bonneau,Richard Bonneau,Jane A. Skok +13 more
TL;DR: 4C-ker is described, a Hidden-Markov Model based pipeline that identifies regions throughout the genome that interact with the 4C bait locus that outperforms all existing 4C-Seq pipelines in its ability to reproducibly identify interaction domains at all genomic ranges with different resolution enzymes.
Journal ArticleDOI
Attenuated chromatin compartmentalization in meiosis and its maturation in sperm development.
Kris G. Alavattam,Kris G. Alavattam,So Maezawa,So Maezawa,So Maezawa,Akihiko Sakashita,Akihiko Sakashita,Haia Khoury,Artem Barski,Artem Barski,Noam Kaplan,Satoshi H. Namekawa,Satoshi H. Namekawa +12 more
TL;DR: It is proposed that male meiosis occurs amid global reprogramming of 3D chromatin organization and that strengthening of chromatin compartmentalization takes place in spermiogenesis to prepare the next generation of life.
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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