title: A new link between transcriptional initiation and pre-mRNA splicing: The RNA binding histone variant H2A.B.
abstract: The replacement of histone H2A with its variant forms is critical for regulating all aspects of genome organisation and function. The histone variant H2A.B appeared late in evolution and is most highly expressed in the testis followed by the brain in mammals. This raises the question of what new function(s) H2A.B might impart to chromatin in these important tissues. We have immunoprecipitated the mouse orthologue of H2A.B, H2A.B.3 (H2A.Lap1), from testis chromatin and found this variant to be associated with RNA processing factors and RNA Polymerase (Pol) II. Most interestingly, many of these interactions with H2A.B.3 (Sf3b155, Spt6, DDX39A and RNA Pol II) were inhibited by the presence of endogenous RNA. This histone variant can bind to RNA directly in vitro and in vivo, and associates with mRNA at intron-exon boundaries. This suggests that the ability of H2A.B to bind to RNA negatively regulates its capacity to bind to these factors (Sf3b155, Spt6, DDX39A and RNA Pol II). Unexpectedly, H2A.B.3 forms highly decompacted nuclear subdomains of active chromatin that co-localizes with splicing speckles in male germ cells. H2A.B.3 ChIP-Seq experiments revealed a unique chromatin organization at active genes being not only enriched at the transcription start site (TSS), but also at the beginning of the gene body (but being excluded from the +1 nucleosome) compared to the end of the gene. We also uncover a general histone variant replacement process whereby H2A.B.3 replaces H2A.Z at intron-exon boundaries in the testis and the brain, which positively correlates with expression and exon inclusion. Taken together, we propose that a special mechanism of splicing may occur in the testis and brain whereby H2A.B.3 recruits RNA processing factors from splicing speckles to active genes following its replacement of H2A.Z.
authors.affiliation: The John Curtin School of Medical Research, The Australian National University, Canberra, Australia.
authors.forename: Tatiana A
authors.initials: TA
authors.lastname: Soboleva
authors.affiliation: The John Curtin School of Medical Research, The Australian National University, Canberra, Australia.
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Parker
authors.affiliation: The John Curtin School of Medical Research, The Australian National University, Canberra, Australia.
authors.forename: Maxim
authors.initials: M
authors.lastname: Nekrasov
authors.affiliation: NSW Systems Biology Initiative, University of New South Wales, Sydney, Australia.
authors.forename: Gene
authors.initials: G
authors.lastname: Hart-Smith
authors.affiliation: The John Curtin School of Medical Research, The Australian National University, Canberra, Australia.
authors.forename: Ying Jin
authors.initials: YJ
authors.lastname: Tay
authors.affiliation: The John Curtin School of Medical Research, The Australian National University, Canberra, Australia.
authors.forename: Wei-Quan
authors.initials: WQ
authors.lastname: Tng
authors.affiliation: NSW Systems Biology Initiative, University of New South Wales, Sydney, Australia.
authors.forename: Marc
authors.initials: M
authors.lastname: Wilkins
authors.affiliation: The John Curtin School of Medical Research, The Australian National University, Canberra, Australia.
authors.forename: Daniel
authors.initials: D
authors.lastname: Ryan
authors.affiliation: The John Curtin School of Medical Research, The Australian National University, Canberra, Australia.
authors.forename: David J
authors.identifier: 0000-0001-5274-8078
authors.initials: DJ
authors.lastname: Tremethick
mesh_terms: D000818:Animals; D015153:Blotting, Western; D001921:Brain / Q000378:metabolism; D002843:Chromatin / Q000235:genetics / Q000378:metabolism; D005091:Exons / Q000235:genetics; D005455:Fluorescent Antibody Technique; D014644:Genetic Variation; D006657:Histones / Q000235:genetics* / Q000378:metabolism; D007438:Introns / Q000235:genetics; D008297:Male; D013058:Mass Spectrometry; D008807:Mice, Inbred BALB C; D011485:Protein Binding; D012313:RNA / Q000235:genetics / Q000378:metabolism; D012319:RNA Polymerase II / Q000378:metabolism; D012322:RNA Precursors / Q000235:genetics* / Q000378:metabolism; D022821:RNA Splice Sites / Q000235:genetics; D012326:RNA Splicing; D016601:RNA-Binding Proteins / Q000378:metabolism; D013737:Testis / Q000166:cytology / Q000378:metabolism; D024363:Transcription Initiation Site; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D002843:Chromatin; D006657:Histones; D012322:RNA Precursors; D022821:RNA Splice Sites; D016601:RNA-Binding Proteins; D012313:RNA; D012319:RNA Polymerase II