title: Setdb1-mediated H3K9 methylation is enriched on the inactive X and plays a role in its epigenetic silencing.
abstract: BACKGROUND
  The presence of histone 3 lysine 9 (H3K9) methylation on the mouse inactive X chromosome has been controversial over the last 15 years, and the functional role of H3K9 methylation in X chromosome inactivation in any species has remained largely unexplored.
  
  
  RESULTS
  Here we report the first genomic analysis of H3K9 di- and tri-methylation on the inactive X: we find they are enriched at the intergenic, gene poor regions of the inactive X, interspersed between H3K27 tri-methylation domains found in the gene dense regions. Although H3K9 methylation is predominantly non-genic, we find that depletion of H3K9 methylation via depletion of H3K9 methyltransferase Set domain bifurcated 1 (Setdb1) during the establishment of X inactivation, results in failure of silencing for around 150 genes on the inactive X. By contrast, we find a very minor role for Setdb1-mediated H3K9 methylation once X inactivation is fully established. In addition to failed gene silencing, we observed a specific failure to silence X-linked long-terminal repeat class repetitive elements.
  
  
  CONCLUSIONS
  Here we have shown that H3K9 methylation clearly marks the murine inactive X chromosome. The role of this mark is most apparent during the establishment phase of gene silencing, with a more muted effect on maintenance of the silent state. Based on our data, we hypothesise that Setdb1-mediated H3K9 methylation plays a role in epigenetic silencing of the inactive X via silencing of the repeats, which itself facilitates gene silencing through alterations to the conformation of the whole inactive X chromosome.
authors.affiliation: The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.|Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia.
authors.forename: Andrew
authors.initials: A
authors.lastname: Keniry
authors.affiliation: The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.|Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia.
authors.forename: Linden J
authors.initials: LJ
authors.lastname: Gearing
authors.affiliation: The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.|Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia.
authors.forename: Natasha
authors.initials: N
authors.lastname: Jansz
authors.affiliation: The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.
authors.forename: Joy
authors.initials: J
authors.lastname: Liu
authors.affiliation: The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.|Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia.
authors.forename: Aliaksei Z
authors.initials: AZ
authors.lastname: Holik
authors.affiliation: The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.|Department of Mathematics and Statistics, University of Melbourne, Melbourne, VIC 3010 Australia.
authors.forename: Peter F
authors.initials: PF
authors.lastname: Hickey
authors.affiliation: The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.|Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia.
authors.forename: Sarah A
authors.initials: SA
authors.lastname: Kinkel
authors.affiliation: The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.|Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia.
authors.forename: Darcy L
authors.initials: DL
authors.lastname: Moore
authors.affiliation: The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.
authors.forename: Kelsey
authors.initials: K
authors.lastname: Breslin
authors.affiliation: The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.|Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia.
authors.forename: Kelan
authors.initials: K
authors.lastname: Chen
authors.affiliation: The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.
authors.forename: Ruijie
authors.initials: R
authors.lastname: Liu
authors.affiliation: The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.
authors.forename: Catherine
authors.initials: C
authors.lastname: Phillips
authors.affiliation: The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.
authors.forename: Miha
authors.initials: M
authors.lastname: Pakusch
authors.affiliation: The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.|Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia.
authors.forename: Christine
authors.initials: C
authors.lastname: Biben
authors.affiliation: The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.|Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia.
authors.forename: Julie M
authors.initials: JM
authors.lastname: Sheridan
authors.affiliation: The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.|Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia.
authors.forename: Benjamin T
authors.initials: BT
authors.lastname: Kile
authors.affiliation: The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.|Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia.
authors.forename: Catherine
authors.initials: C
authors.lastname: Carmichael
authors.affiliation: The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.|Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia.|Department of Mathematics and Statistics, University of Melbourne, Melbourne, VIC 3010 Australia.
authors.forename: Matthew E
authors.initials: ME
authors.lastname: Ritchie
authors.affiliation: The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.|Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia.
authors.forename: Douglas J
authors.initials: DJ
authors.lastname: Hilton
authors.affiliation: The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.|Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia.|Department of Genetics, University of Melbourne, Melbourne, VIC 3010 Australia.
authors.forename: Marnie E
authors.initials: ME
authors.lastname: Blewitt
keywords: Epigenetic silencing; H3K9 methylation; Setdb1; X inactivation