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
More filters
Journal ArticleDOI
Replication timing and transcriptional control: beyond cause and effect-part III.
TL;DR: Mounting evidence supports a model in which replication timing is both cause and consequence of chromatin structure by providing a means to inherit chromatin states that, in turn, regulate replication timing in the subsequent cell cycle.
Journal ArticleDOI
RaGOO: fast and accurate reference-guided scaffolding of draft genomes
Michael Alonge,Sebastian Soyk,Srividya Ramakrishnan,Xingang Wang,Sara Goodwin,Fritz J. Sedlazeck,Zachary B. Lippman,Zachary B. Lippman,Michael C. Schatz,Michael C. Schatz +9 more
TL;DR: This work presents RaGOO, a reference-guided contig ordering and orienting tool that leverages the speed and sensitivity of Minimap2 to accurately achieve chromosome-scale assemblies in minutes and demonstrates the scalability and utility of the tool.
Journal ArticleDOI
The Spatial Organization of the Human Genome
TL;DR: Established light microscopy-based approaches and more recent molecular chromosome conformation capture methods are now combining to give us unprecedented insight into this fascinating aspect of human genomics.
Journal ArticleDOI
Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus.
Jiaming Song,Zhilin Guan,Jianlin Hu,Chaocheng Guo,Zhiquan Yang,Shuo Wang,Dongxu Liu,Bo Wang,Shaoping Lu,Run Zhou,Wen-Zhao Xie,Yuanfang Cheng,Yuting Zhang,Kede Liu,Qingyong Yang,Ling-Ling Chen,Liang Guo +16 more
TL;DR: PAV-based genome-wide association analysis uncovered causal variations for agronomic traits and ecotype differentiation in rapeseed and showed that PAVs in three FLOWERING LOCUS C genes were closely related to flowering time and ecotypes differentiation.
Journal ArticleDOI
Robust 4C-seq data analysis to screen for regulatory DNA interactions
Harmen J.G. van de Werken,Gilad Landan,Sjoerd J B Holwerda,Sjoerd J B Holwerda,Michael Hoichman,Petra Klous,Petra Klous,Ran Chachik,Erik Splinter,Erik Splinter,Christian Valdes-Quezada,Yuva Oz,Yuva Oz,Britta A M Bouwman,Britta A M Bouwman,Marjon J.A.M. Verstegen,Marjon J.A.M. Verstegen,Elzo de Wit,Elzo de Wit,Amos Tanay,Wouter de Laat,Wouter de Laat +21 more
TL;DR: This work presents a cost-effective methodology and computational analysis pipeline for robust characterization of the physical organization around selected promoters and other functional elements using chromosome conformation capture combined with high-throughput sequencing (4C-seq).
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.
Related Papers (5)
Spatial partitioning of the regulatory landscape of the X-inactivation centre
Elphège P. Nora,Bryan R. Lajoie,Edda G. Schulz,Luca Giorgetti,Luca Giorgetti,Luca Giorgetti,Ikuhiro Okamoto,Ikuhiro Okamoto,Ikuhiro Okamoto,Nicolas Servant,Nicolas Servant,Nicolas Servant,Tristan Piolot,Tristan Piolot,Tristan Piolot,Nynke L. van Berkum,Johannes Meisig,John W. Sedat,Joost Gribnau,Emmanuel Barillot,Emmanuel Barillot,Emmanuel Barillot,Nils Blüthgen,Job Dekker,Edith Heard,Edith Heard,Edith Heard +26 more