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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Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory
Alessandro Bertero,Paul A. Fields,Vijay Ramani,Giancarlo Bonora,Galip Gürkan Yardımcı,Hans Reinecke,Lil Pabon,William Stafford Noble,Jay Shendure,Jay Shendure,Charles E. Murry +10 more
TL;DR: A comprehensive profile of nuclear dynamics during human cardiogenesis from pluripotent stem cells is reported by integrating Hi-C, RNA-seq and ATAC-seq data and an RBM20-dependent splicing factory assembling the TTN locus with other R BM20 targets is described.
Journal ArticleDOI
Polycomb Group Proteins Regulate Chromatin Architecture in Mouse Oocytes and Early Embryos
Zhenhai Du,Hui Zheng,Yumiko K Kawamura,Ke Zhang,Johanna Gassler,Sean Powell,Qianhua Xu,Zili Lin,Kai Xu,Qian Zhou,Evgeniy A. Ozonov,Nathalie Véron,Bo Huang,Lijia Li,Guang Yu,Ling Liu,Wan Kin Au Yeung,Peizhe Wang,Lei Chang,Qiujun Wang,Aibin He,Yujie Sun,Jie Na,Qing-Yuan Sun,Hiroyuki Sasaki,Kikuë Tachibana,Kikuë Tachibana,Antoine H.F.M. Peters,Antoine H.F.M. Peters,Wei Xie +29 more
TL;DR: A critical role of Polycomb is revealed in regulating chromatin architecture during mammalian oocyte growth and early development using low-input Hi-C (genome-wide chromatin conformation capture) data.
Journal ArticleDOI
Transcription-induced DNA double strand breaks: both oncogenic force and potential therapeutic target?
Michael C. Haffner,Angelo M. De Marzo,Alan K. Meeker,William G. Nelson,Srinivasan Yegnasubramanian +4 more
TL;DR: It is proposed that, in hormone-dependent tumors like breast and prostate cancers, a hormone-cycling therapy, in combination with topoisomerase II poisons or inhibitors of the DNA repair components PARP1 and DNA-PK, could overwhelm cancer cells with transcription-associated DSBs.
Journal ArticleDOI
Disclosure of a structural milieu for the proximity ligation reveals the elusive nature of an active chromatin hub
Alexey A. Gavrilov,E. S. Gushchanskaya,Olga Strelkova,Oksana Zhironkina,Igor I. Kireev,Olga V. Iarovaia,Sergey V. Razin +6 more
TL;DR: It is shown that a substantial, and in some cases the major, part of DNA is not solubilized from cross-linked nuclei treated with restriction endonuclease(s) and sodium dodecyl sulphate and that this treatment neither causes lysis of the nucleus nor drastically affects its internal organization.
Journal ArticleDOI
Standardizing chromatin research: a simple and universal method for ChIP-seq
Laura Arrigoni,Andreas S. Richter,Emily Betancourt,Kerstin Bruder,Sarah Diehl,Thomas Manke,Ulrike Bönisch +6 more
TL;DR: This work established an ultrasound-based nuclei extraction method (NEXSON: Nuclei EXtraction by SONication) that is highly effective across various organisms, cell types and cell numbers and provides the basis for a fully standardized ChIP-seq and yields highly reproducible transcription factor and histone modifications maps for a wide range of different cell types.
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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