title: Bipartite structure of the inactive mouse X chromosome.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Pathology, University of Washington, Seattle, Washington, USA.
authors.forename: Xinxian
authors.initials: X
authors.lastname: Deng
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
authors.forename: Wenxiu
authors.initials: W
authors.lastname: Ma
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
authors.forename: Vijay
authors.initials: V
authors.lastname: Ramani
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
authors.forename: Andrew
authors.initials: A
authors.lastname: Hill
authors.affiliation: Department of Pathology, University of Washington, Seattle, Washington, USA.
authors.forename: Fan
authors.initials: F
authors.lastname: Yang
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
authors.forename: Ferhat
authors.initials: F
authors.lastname: Ay
authors.affiliation: Department of Pathology, University of Washington, Seattle, Washington, USA.
authors.forename: Joel B
authors.initials: JB
authors.lastname: Berletch
authors.affiliation: Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA.|Division of Hematology, University of Washington, Seattle, Washington, USA.
authors.forename: Carl Anthony
authors.initials: CA
authors.lastname: Blau
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
authors.forename: Jay
authors.initials: J
authors.lastname: Shendure
authors.affiliation: Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA. zjduan@uw.edu.|Division of Hematology, University of Washington, Seattle, Washington, USA. zjduan@uw.edu.
authors.forename: Zhijun
authors.initials: Z
authors.lastname: Duan
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, USA. william-noble@uw.edu.|Department of Computer Science and Engineering, University of Washington, Seattle, Washington, USA. william-noble@uw.edu.
authors.forename: William S
authors.initials: WS
authors.lastname: Noble
authors.affiliation: Department of Pathology, University of Washington, Seattle, Washington, USA. cdistech@u.washington.edu.|Department of Medicine, University of Washington, Seattle, Washington, USA. cdistech@u.washington.edu.
authors.forename: Christine M
authors.initials: CM
authors.lastname: Disteche
mesh_terms: D000818:Animals; D000076246:CCCTC-Binding Factor; D002460:Cell Line; D002466:Cell Nucleolus / Q000378:metabolism; D002478:Cells, Cultured; D041321:Chromosomes, Human, X / Q000737:chemistry; D005260:Female; D018392:Genomic Imprinting; D006801:Humans; D008297:Male; D051379:Mice; D012319:RNA Polymerase II / Q000737:chemistry / Q000378:metabolism; D012097:Repressor Proteins / Q000737:chemistry / Q000378:metabolism; D014960:X Chromosome / Q000737:chemistry* / Q000378:metabolism; D049951:X Chromosome Inactivation
chemical_list: D000076246:CCCTC-Binding Factor; C000619697:CTCF protein, human; C000619698:Ctcf protein, mouse; D012097:Repressor Proteins; D012319:RNA Polymerase II