title: Distinct distribution of ectopically expressed histone variants H2A.Bbd and MacroH2A in open and closed chromatin domains.
abstract: BACKGROUND
  It becomes increasingly evident that nuclesomes are far from being identical to each other. This nucleosome diversity is due partially to the existence of histone variants encoded by separate genes. Among the known histone variants the less characterized are H2A.Bbd and different forms of macroH2A. This is especially true in the case of H2A.Bbd as there are still no commercially available antibodies specific to H2A.Bbd that can be used for chromatin immunoprecipitation (ChIP).
  
  
  METHODS
  We have generated HeLa S3 cell lines stably expressing epitope-tagged versions of macroH2A1.1, H2A.Bbd or canonical H2A and analyzed genomic distribution of the tagged histones using ChIP-on-chip technique.
  
  
  RESULTS
  The presence of histone H2A variants macroH2A1.1 and H2A.Bbd has been analyzed in the chromatin of several segments of human chromosomes 11, 16 and X that have been chosen for their different gene densities and chromatin status. Chromatin immunoprecipitation (ChIP) followed by hybridization with custom NimbleGene genomic microarrays demonstrated that in open chromatin domains containing tissue-specific along with housekeeping genes, the H2A.Bbd variant was preferentially associated with the body of a subset of transcribed genes. The macroH2A1.1 variant was virtually absent from some genes and underrepresented in others. In contrast, in closed chromatin domains which contain only tissue-specific genes inactive in HeLa S3 cells, both macroH2A1.1 and H2A.Bbd histone variants were present and often colocalized.
  
  
  CONCLUSIONS
  Genomic distribution of macro H2A and H2A.Bbd does not follow any simple rule and is drastically different in open and closed genomic domains.
authors.affiliation: Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.
authors.forename: Elena S
authors.initials: ES
authors.lastname: Ioudinkova
authors.forename: Ana
authors.initials: A
authors.lastname: Barat
authors.forename: Andrey
authors.initials: A
authors.lastname: Pichugin
authors.forename: Elena
authors.initials: E
authors.lastname: Markova
authors.forename: Ilya
authors.initials: I
authors.lastname: Sklyar
authors.forename: Iryna
authors.initials: I
authors.lastname: Pirozhkova
authors.forename: Chloe
authors.initials: C
authors.lastname: Robin
authors.forename: Marc
authors.initials: M
authors.lastname: Lipinski
authors.forename: Vasily
authors.initials: V
authors.lastname: Ogryzko
authors.forename: Yegor S
authors.initials: YS
authors.lastname: Vassetzky
authors.forename: Sergey V
authors.initials: SV
authors.lastname: Razin
mesh_terms: D002843:Chromatin / Q000235:genetics / Q000378:metabolism; D047369:Chromatin Immunoprecipitation; D002880:Chromosomes, Human, Pair 11 / Q000235:genetics; D002885:Chromosomes, Human, Pair 16 / Q000235:genetics; D041321:Chromosomes, Human, X / Q000235:genetics; D015870:Gene Expression; D006367:HeLa Cells; D006657:Histones / Q000235:genetics / Q000378:metabolism; D006801:Humans; D009707:Nucleosomes
chemical_list: D002843:Chromatin; C468783:H2AX protein, human; D006657:Histones; D009707:Nucleosomes; C120756:macroH2A histone