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
Wheat chromatin architecture is organized in genome territories and transcription factories
Lorenzo Concia,Alaguraj Veluchamy,Juan S. Ramirez-Prado,Azahara Martin-Ramirez,Ying Huang,Magali Perez,Séverine Domenichini,Natalia Y. Rodriguez Granados,Soon-Kap Kim,Thomas Blein,Susan Duncan,Clement Pichot,Deborah Manza-Mianza,Caroline Juery,Etienne Paux,Graham Moore,Heribert Hirt,Heribert Hirt,Catherine Bergounioux,Martin Crespi,Magdy M. Mahfouz,Abdelhafid Bendahmane,Chang Liu,Anthony Hall,Cécile Raynaud,David Latrasse,Moussa Benhamed,Moussa Benhamed +27 more
TL;DR: The results provide new insights into the physical chromosome organization of a polyploid genome, as well as on the relationship between epigenetic marks and chromosome conformation to determine a 3D spatial organization of gene expression, a key factor governing gene transcription in polyploids.
Journal ArticleDOI
p63 and Brg1 control developmentally regulated higher-order chromatin remodelling at the epidermal differentiation complex locus in epidermal progenitor cells
Andrei N. Mardaryev,Michal R. Gdula,Michal R. Gdula,Joanne L. Yarker,Vladimir N. Emelianov,Krzysztof Poterlowicz,Andrey A. Sharov,Tatyana Y. Sharova,Julie A. Scarpa,Pierre Chambon,Vladimir A. Botchkarev,Vladimir A. Botchkarev,Michael Y. Fessing +12 more
TL;DR: It is shown that p63 and its direct target Brg1 play an essential role in remodelling the higher-order chromatin structure of the EDC and in the specific positioning of this locus within the landscape of the 3D nuclear space, as required for the efficient expression of EDC genes in epidermal progenitor cells during skin development.
Journal ArticleDOI
Multi-species annotation of transcriptome and chromatin structure in domesticated animals.
Sylvain Foissac,Sarah Djebali,Kylie Munyard,Nathalie Vialaneix,Andrea Rau,Kévin Muret,Diane Esquerre,Diane Esquerre,Matthias Zytnicki,Thomas Derrien,Philippe Bardou,Fany Blanc,Cédric Cabau,Elisa Crisci,Elisa Crisci,Sophie Dhorne-Pollet,Françoise Drouet,Thomas Faraut,Ignacio González,Adeline Goubil,Sonia Lacroix-Lamandé,Fabrice Laurent,Sylvain Marthey,Maria Marti-Marimon,Raphaelle Momal-Leisenring,Florence Mompart,Pascale Quéré,David Robelin,Magali San Cristobal,Gwenola Tosser-Klopp,Silvia Vincent-Naulleau,Stéphane Fabre,Marie-Helene Pinard van der Laan,Christophe Klopp,Michèle Tixier-Boichard,Hervé Acloque,Hervé Acloque,Sandrine Lagarrigue,Elisabetta Giuffra +38 more
TL;DR: First multi-species and multi-assay genome annotation results obtained by a FAANG project are reported, showing that conserved TAD boundaries had stronger insulation properties than species-specific ones and that the genomic distribution of orthologous genes in A/B compartments was significantly conserved across species.
Journal ArticleDOI
The ChAHP Complex Counteracts Chromatin Looping at CTCF Sites that Emerged from SINE Expansions in Mouse
TL;DR: It is demonstrated that the ChAHP complex (CHD4, ADNP, HP1) competes with CTCF for a common set of binding motifs, and data reveal that CTCf-mediated loop formation is modulated by a distinct zinc-finger protein complex.
Journal ArticleDOI
Short-term memory of danger signals and environmental stimuli in immune cells
TL;DR: It is suggested that this transient phenomenon represents 'short-term memory' of environmental exposure and the evidence that this is mediated by the persistence of long-lived regulatory molecules, notably a subset of newly deposited chromatin modifications and inducible noncoding RNAs.
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