The specificity of H2A.Z occupancy in the yeast genome and its relationship to transcription
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MINI-REVIEW
The specificity of H2A.Z occupancy in the yeast genome and its relationship to transcription Vishwanath R. Iyer1 Received: 26 April 2020 / Revised: 8 June 2020 / Accepted: 9 June 2020 © Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract The incorporation of histone variants into nucleosomes has important functional consequences in all aspects of eukaryotic chromatin biology. H2A.Z is a conserved histone variant found in all eukaryotes from yeast to mammals. Recent studies in yeast have shed light on the questions of where and how nucleosomes containing this variant are situated at promoters and in relation to genes, and what its specificity implies with regard to transcription. In yeast, H2A.Z appears to be primarily incorporated into the first nucleosome in the direction of transcription initiation, either of an mRNA transcript or a divergently transcribed upstream antisense non-coding RNA. This specificity of H2A.Z is due in part to the localization at promoters of SWR1, the ATP-dependent chromatin remodeler that incorporates H2A.Z into nucleosomes. Replacement of H2A.Z with canonical H2A is dependent on the function of the transcription pre-initiation complex. The recent studies summarized in this review reveal that the directionality of H2A.Z occupancy in relation to transcription thus reflects a balance of incorporation and eviction activities, which likely have varying contributions at distinct sets of genes across the genome. Keywords H2A.Z · Histone variant · Nucleosome · SWR1 · INO80
Introduction The long and linear genomic DNA in eukaryotic chromosomes has to be systematically compacted to fit within the confines of the nucleus. The first level of compaction of the eukaryotic genome occurs by the wrapping of DNA in a left-handed superhelix around a histone octamer to form nucleosomes. Incorporation of histone variants, post-translational modifications of histones, and the positioning of nucleosomes along the DNA influence all processes that the genomic DNA participates in, including transcription, DNA replication, repair, and higher order chromosomal organization. The canonical histones H2A, H2B, H3, and H4 constitute the standard nucleosome octamer, which comprises an H3–H4 tetramer and two H2A–H2B dimers. The Communicated by M. Kupiec. * Vishwanath R. Iyer [email protected] 1
Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Livestrong Cancer Institutes, Dell Medical School, University of Texas, Austin, TX 78712, USA
incorporation of non-allelic alternative versions of certain histones, or histone variants, is one mechanism by which the uniform nucleosomal structure of chromatin is altered, with important functional consequences. Many histone variants have been identified, but the centromere-specific H3 variants (CenH3) (Ichikawa and Kaufman 2019) and the H2A variant H2A.Z are considered to be universal histone variants given their presence in all domains of eukaryotes. The variant H2A.Z is found in virtually all eukaryotes from yeas
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