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
Evolutionary stability of topologically associating domains is associated with conserved gene regulation
TL;DR: This work hypothesizes that TADs represent essential functional units of genomes, which are stable against rearrangements during evolution, and investigates this using whole-genome alignments to identify evolutionary rearrangement breakpoints of different vertebrates.
Journal ArticleDOI
Characterization of Enhancer Function from Genome-Wide Analyses
TL;DR: There has been a recent surge in the use of genome-wide methodologies to identify and annotate the transcriptional regulatory elements in the human genome, and several aspects of enhancer function have been shown to be more widespread than was previously appreciated.
Journal ArticleDOI
The origins and evolution of chromosomes, dosage compensation, and mechanisms underlying venom regulation in snakes.
Drew R. Schield,Daren C. Card,Nicole R. Hales,Blair W. Perry,Giulia I M Pasquesi,Heath Blackmon,Richard Adams,Andrew B. Corbin,Cara F. Smith,Balan Ramesh,Jeffery P. Demuth,Esther Betrán,Marc Tollis,Jesse M. Meik,Stephen P. Mackessy,Todd A. Castoe +15 more
TL;DR: The rattlesnake Z Chromosome is identified, including the recombining pseudoautosomal region, and evidence for partial dosage compensation driven by an evolutionary accumulation of a female-biased up-regulation mechanism is found.
Journal ArticleDOI
Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products
Christopher Beitel,Lutz Froenicke,Jenna M. Lang,Ian F Korf,Richard W Michelmore,Jonathan A. Eisen,Aaron E. Darling +6 more
TL;DR: Hi-C sequencing data provide valuable information for metagenome analyses that are not currently obtainable by other methods, and it is demonstrated that Hi-C data provides a long-range signal of strain-specific genotypes, indicating such data may be useful for high-resolution genotyping of microbial populations.
Journal ArticleDOI
Cell-type-specific long-range looping interactions identify distant regulatory elements of the CFTR gene
Nele Gheldof,Emily M. Smith,Tomoko M. Tabuchi,Christoph M. Koch,Ian Dunham,John A. Stamatoyannopoulos,Job Dekker +6 more
TL;DR: Four elements in a 460-kb region around the locus that loop specifically to the CFTR promoter exclusively in CFTR expressing cells are identified and suggest that 3C-based approaches can be used for discovery of novel regulatory elements.
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