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Keywords {🔍}

genes, pubmed, mouse, contacts, chromosome, hic, article, contact, google, scholar, structure, region, dnase, ctcf, cells, regions, cas, brain, genome, superdomains, human, dxz, reads, fig, escape, patski, imprinted, expressed, chromosomes, chromatin, binding, hinge, central, dstr, allele, maps, resolution, allelic, allelespecific, xist, additional, situ, intrachromosomal, located, gene, cell, dna, data, file, superdomain,

Topics {✒️}

}_{\otimes }}\sim gamma\kern0 $$ \frac{\frac{{\displaystyle {\sum}_{ active-x-chromosome state accompanies carl anthony blau allelic 3d view bac clone rp23-299l1 da-tailed dna-beads mixture high-quality uniquely mapped occupy specific locations poly-lysine-coated coverslips mof-mediated h4k16 acetylation accurate long-read alignment article download pdf large-scale nonlinear programming overline{\uplambda_{i_{\odot } }_{\otimes }}\sim poisson\left rna-directed chromosome conformation redundant paired-end reads allele-specific contact maps ^2}+\frac{{\displaystyle {\sum}_{ }^2}}{2\frac{{\displaystyle {\sum}_{ assign allele-uncertain reads gamma prior hyper-parameters allele-specific contact counts dxz4/dxz4 macrosatellite locus capture genomic regions allele-specific contact map air-dried bead-nuclei mixture sided kolmogorov-smirnov test control x-linked genes dxz4/ds-tr region represents {\lambda}_{i_{\odot } $$ {\lambda}_{i_{\odot } hypoxanthine-aminopterin-thymidine l1 detect long-range contacts {\uplambda}_{i_{\odot } allele-specific polii peaks gamma minisatellite ds-tr full size image chromatin end-repair ferhat ay frequent long-range contacts related subjects transcription start site obtain allele-specific maps x-linked genes determined resulting bead-dna pellet solid agarose gel maintains h3k27me3 methylation restrict enhancer access

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         headline:Bipartite structure of the inactive mouse X chromosome
         description: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.
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            Hinge Region
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            Animal Genetics and Genomics
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      headline:Bipartite structure of the inactive mouse X chromosome
      description: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.
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         Hinge Region
         CTCF Binding
         Escape Gene
         CTCF Site
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         Human Genetics
         Plant Genetics and Genomics
         Microbial Genetics and Genomics
         Bioinformatics
         Evolutionary Biology
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      name:Division of Hematology, University of Washington, Seattle, USA
      name:Department of Genome Sciences, University of Washington, Seattle, USA
      name:Department of Computer Science and Engineering, University of Washington, Seattle, USA
      name:Department of Pathology, University of Washington, Seattle, USA
      name:Department of Medicine, University of Washington, Seattle, USA

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