title: The lncRNA Firre anchors the inactive X chromosome to the nucleolus by binding CTCF and maintains H3K27me3 methylation.
abstract: BACKGROUND
  In mammals, X chromosome genes are present in one copy in males and two in females. To balance the dosage of X-linked gene expression between the sexes, one of the X chromosomes in females is silenced. X inactivation is initiated by upregulation of the lncRNA (long non-coding RNA) Xist and recruitment of specific chromatin modifiers. The inactivated X chromosome becomes heterochromatic and visits a specific nuclear compartment adjacent to the nucleolus.
  
  
  RESULTS
  Here, we show a novel role for the lncRNA Firre in anchoring the inactive mouse X chromosome and preserving one of its main epigenetic features, H3K27me3. Similar to Dxz4, Firre is X-linked and expressed from a macrosatellite repeat locus associated with a cluster of CTCF and cohesin binding sites, and is preferentially located adjacent to the nucleolus. CTCF binding present initially in both male and female mouse embryonic stem cells is lost from the active X during development. Knockdown of Firre disrupts perinucleolar targeting and H3K27me3 levels in mouse fibroblasts, demonstrating a role in maintenance of an important epigenetic feature of the inactive X chromosome. No X-linked gene reactivation is seen after Firre knockdown; however, a compensatory increase in the expression of chromatin modifier genes implicated in X silencing is observed. Further experiments in female embryonic stem cells suggest that Firre does not play a role in X inactivation onset.
  
  
  CONCLUSIONS
  The X-linked lncRNA Firre helps to position the inactive X chromosome near the nucleolus and to preserve one of its main epigenetic features.
authors.affiliation: Department of Pathology, University of Washington, Seattle, Washington, 98195, USA. fyang8191@gmail.com.
authors.forename: Fan
authors.initials: F
authors.lastname: Yang
authors.affiliation: Department of Pathology, University of Washington, Seattle, Washington, 98195, USA. dengx2@uw.edu.
authors.forename: Xinxian
authors.initials: X
authors.lastname: Deng
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, 98195, USA. wenxiu@uw.edu.
authors.forename: Wenxiu
authors.initials: W
authors.lastname: Ma
authors.affiliation: Department of Pathology, University of Washington, Seattle, Washington, 98195, USA. joelb07@u.washington.edu.
authors.forename: Joel B
authors.initials: JB
authors.lastname: Berletch
authors.affiliation: Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA. nrabaia@fhcrc.org.
authors.forename: Natalia
authors.initials: N
authors.lastname: Rabaia
authors.affiliation: Department of Integrative Physiology and Neuroscience, Washington State University, Pullman, Washington, 99164, USA. weigengze@vetmed.wsu.edu.
authors.forename: Gengze
authors.initials: G
authors.lastname: Wei
authors.affiliation: Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA. jmmoore@fhcrc.org.
authors.forename: James M
authors.initials: JM
authors.lastname: Moore
authors.affiliation: Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA. gfilippo@fhcrc.org.
authors.forename: Galina N
authors.initials: GN
authors.lastname: Filippova
authors.affiliation: Department of Integrative Physiology and Neuroscience, Washington State University, Pullman, Washington, 99164, USA. junxu@vetmed.wsu.edu.
authors.forename: Jun
authors.initials: J
authors.lastname: Xu
authors.affiliation: Department of Pathology, University of Washington, Seattle, Washington, 98195, USA. yajuan@uw.edu.
authors.forename: Yajuan
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, 98195, USA. wnoble@uw.edu.|Department of Computer Science and Engineering, University of Washington, Seattle, Washington, 98155, USA. wnoble@uw.edu.
authors.forename: William S
authors.initials: WS
authors.lastname: Noble
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, 98195, USA. shendure@uw.edu.
authors.forename: Jay
authors.initials: J
authors.lastname: Shendure
authors.affiliation: Department of Pathology, University of Washington, Seattle, Washington, 98195, USA. cdistech@u.washington.edu.|Department of Medicine, University of Washington, Seattle, Washington, 98195, USA. cdistech@u.washington.edu.
authors.forename: Christine M
authors.initials: CM
authors.lastname: Disteche
mesh_terms: D000818:Animals; D001665:Binding Sites; D000076246:CCCTC-Binding Factor; D019175:DNA Methylation / Q000235:genetics; D005260:Female; D056484:Jumonji Domain-Containing Histone Demethylases / Q000235:genetics*; D008297:Male; D051379:Mice; D011401:Promoter Regions, Genetic; D062085:RNA, Long Noncoding / Q000235:genetics*; D012097:Repressor Proteins / Q000235:genetics* / Q000378:metabolism; D014960:X Chromosome / Q000235:genetics; D049951:X Chromosome Inactivation / Q000235:genetics*
chemical_list: D000076246:CCCTC-Binding Factor; C000619698:Ctcf protein, mouse; C000603211:Firre long non coding RNA, mouse; D062085:RNA, Long Noncoding; D012097:Repressor Proteins; D056484:Jumonji Domain-Containing Histone Demethylases; C523761:Kdm6b protein, mouse