Bipartite structure of the inactive mouse X chromosome.
Xinxian Deng,Wenxiu Ma,Vijay Ramani,Andrew J. Hill,Fan Yang,Ferhat Ay,Joel B. Berletch,Carl Anthony Blau,Jay Shendure,Zhijun Duan,William Stafford Noble,Christine M. Disteche +11 more
TLDR
A novel Hi-C method is applied to map allelic chromatin contacts of the mouse inactive X chromosome to discover a specific bipartite organization that probably plays an important role in maintenance of gene silencing.Abstract:
In mammals, one of the female X chromosomes and all imprinted genes are expressed exclusively from a single allele in somatic cells. To evaluate structural changes associated with allelic silencing, we have applied a recently developed Hi-C assay that uses DNase I for chromatin fragmentation to mouse F1 hybrid systems. We find radically different conformations for the two female mouse X chromosomes. The inactive X has two superdomains of frequent intrachromosomal contacts separated by a boundary region. Comparison with the recently reported two-superdomain structure of the human inactive X shows that the genomic content of the superdomains differs between species, but part of the boundary region is conserved and located near the Dxz4/DXZ4 locus. In mouse, the boundary region also contains a minisatellite, Ds-TR, and both Dxz4 and Ds-TR appear to be anchored to the nucleolus. Genes that escape X inactivation do not cluster but are located near the periphery of the 3D structure, as are regions enriched in CTCF or RNA polymerase. Fewer short-range intrachromosomal contacts are detected for the inactive alleles of genes subject to X inactivation compared with the active alleles and with genes that escape X inactivation. This pattern is also evident for imprinted genes, in which more chromatin contacts are detected for the expressed allele. By applying a novel Hi-C method to map allelic chromatin contacts, we discover a specific bipartite organization of the mouse inactive X chromosome that probably plays an important role in maintenance of gene silencing.read more
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HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
Nicolas Servant,Nelle Varoquaux,Nelle Varoquaux,Nelle Varoquaux,Bryan R. Lajoie,Eric Viara,Chong-Jian Chen,Jean-Philippe Vert,Jean-Philippe Vert,Jean-Philippe Vert,Edith Heard,Edith Heard,Edith Heard,Job Dekker,Emmanuel Barillot,Emmanuel Barillot,Emmanuel Barillot +16 more
TL;DR: This work applied HiC-Pro to different Hi-C datasets, demonstrating its ability to easily process large data in a reasonable time and its fast implementation of the iterative correction method.
Journal ArticleDOI
Organization and function of the 3D genome.
TL;DR: The insights into chromatin architecture that have been gained through recent technological developments in quantitative biology, genomics and cell and molecular biology approaches are discussed and how these new concepts have been used to address important biological questions in development and disease are explained.
Control of Cell Identity Genes Occurs in Insulated Neighborhoods in Mammalian Chromosomes
Jill M. Dowen,Zi Peng Fan,Denes Hnisz,Gang Ren,Brian J. Abraham,Abraham S. Weintraub,Jurian Schuijers,Tong Ihn Lee,Keji Zhao,Lyndon Nuoxi Zhang,Richard A. Young +10 more
TL;DR: In this article, the authors used ESC cohesin ChIA-PET data to identify the local chromosomal structures at both active and repressed genes across the genome and reveal that super-enhancer-driven genes generally occur within chromosome structures that are formed by the looping of two interacting CTCF sites co-occupied by co-hesin.
Journal ArticleDOI
Spatial organization of chromatin domains and compartments in single chromosomes
Siyuan Wang,Jun-Han Su,Brian J. Beliveau,Bogdan Bintu,Jeffrey R. Moffitt,Chao-ting Wu,Xiaowei Zhuang +6 more
TL;DR: An imaging method for mapping the spatial positions of numerous genomic regions along individual chromosomes is developed and it is observed that chromosome folding deviates from the ideal fractal-globule model at large length scales and that TADs are largely organized into two compartments spatially arranged in a polarized manner in individual chromosomes.
Journal ArticleDOI
Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression
TL;DR: Emerging mechanistic insights into how lncRNAs can regulate gene expression by coordinating regulatory proteins, localizing to target loci and shaping three-dimensional (3D) nuclear organization are discussed.
References
More filters
Journal ArticleDOI
Maximum likelihood from incomplete data via the EM algorithm
Journal ArticleDOI
Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li,Richard Durbin +1 more
TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.
Journal ArticleDOI
The Human Genome Browser at UCSC
W. James Kent,Charles W. Sugnet,Terrence S. Furey,Krishna M. Roskin,Tom H. Pringle,Alan M. Zahler,and David Haussler +6 more
TL;DR: A mature web tool for rapid and reliable display of any requested portion of the genome at any scale, together with several dozen aligned annotation tracks, is provided at http://genome.ucsc.edu.
Journal ArticleDOI
On the implementation of an interior-point filter line-search algorithm for large-scale nonlinear programming
TL;DR: A comprehensive description of the primal-dual interior-point algorithm with a filter line-search method for nonlinear programming is provided, including the feasibility restoration phase for the filter method, second-order corrections, and inertia correction of the KKT matrix.
Journal ArticleDOI
A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
Suhas S.P. Rao,Miriam H. Huntley,Neva C. Durand,Elena K. Stamenova,Ivan D. Bochkov,James T. Robinson,James T. Robinson,Adrian L. Sanborn,Ido Machol,Ido Machol,Arina D. Omer,Arina D. Omer,Eric S. Lander,Eric S. Lander,Eric S. Lander,Erez Lieberman Aiden +15 more
TL;DR: In situ Hi-C is used to probe the 3D architecture of genomes, constructing haploid and diploid maps of nine cell types, identifying ∼10,000 loops that frequently link promoters and enhancers, correlate with gene activation, and show conservation across cell types and species.
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