Studying the Evolution of Histone Variants Using Phylogeny

Molaro, Antoine; Drinnenberg, Ines A.

doi:10.1007/978-1-4939-8663-7_15

Cited by 7 publications

(6 citation statements)

References 57 publications

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“…To identify variants of histone H2B in mammals, we interrogated genome assemblies from 18 representative mammals. We performed comprehensive and iterative homology-based searches using both previously identified histone variants and new histone variants identified during our analyses ( Molaro and Drinnenberg 2018 ) (see Materials and Methods). We further determined shared synteny (conserved genomic neighborhood) to identify orthologs.…”

Section: Resultsmentioning

confidence: 99%

Novel Classes and Evolutionary Turnover of Histone H2B Variants in the Mammalian Germline

Raman

Rominger

Young

et al. 2022

Molecular Biology and Evolution

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Histones and their post-translational modifications facilitate diverse chromatin functions in eukaryotes. Core histones (H2A, H2B, H3, and H4) package genomes after DNA replication. In contrast, variant histones promote specialized chromatin functions, including DNA repair, genome stability, and epigenetic inheritance. Previous studies have identified only a few H2B variants in animals; their roles and evolutionary origins remain largely unknown. Here, using phylogenomic analyses, we reveal the presence of five H2B variants broadly present in mammalian genomes. Three of these variants have been previously described: H2B.1, H2B.L (also called subH2B), and H2B.W. In addition, we identify and describe two new variants: H2B.K and H2B.N. Four of these variants originated in mammals, whereas H2B.K arose prior to the last common ancestor of bony vertebrates. We find that though H2B variants are subject to high gene turnover, most are broadly retained in mammals, including humans. Despite an overall signature of purifying selection, H2B variants evolve more rapidly than core H2B with considerable divergence in sequence and length. All five H2B variants are expressed in the germline. H2B.K and H2B.N are predominantly expressed in oocytes, an atypical expression site for mammalian histone variants. Our findings suggest that H2B variants likely encode potentially redundant but vital functions via unusual chromatin packaging or non-chromatin functions in mammalian germline cells. Our discovery of novel histone variants highlights the advantages of comprehensive phylogenomic analyses and provides unique opportunities to study how innovations in chromatin function evolve.

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Section: Resultsmentioning

confidence: 99%

Novel Classes and Evolutionary Turnover of Histone H2B Variants in the Mammalian Germline

Raman

Rominger

Young

et al. 2022

Molecular Biology and Evolution

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“…Phylogenetic analyses of plant H2A was carried out following recommendation in. 45 Plant H2A sequences were identified through BLASTP 46 searches of published genomes [12][13][14][15][46][47][48][49][50][51] as indicated in Data S1 using Arabidopsis thaliana H2A sequences. Full-length sequences were aligned with MAFFT v7.427 52 using the default settings.…”

Section: Reportmentioning

confidence: 99%

A Synthetic Approach to Reconstruct the Evolutionary and Functional Innovations of the Plant Histone Variant H2A.W

et al. 2021

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“…To identify variants of histone H2B in mammals, we interrogated genome assemblies from eighteen representative mammals. We performed comprehensive and iterative homology-based searches using both previously identified histone variants and new histone variants identified during our analyses (Molaro and Drinnenberg 2018) (see Methods). We further determined shared synteny (conserved genomic neighborhood) to identify orthologs.…”

Section: Resultsmentioning

confidence: 99%

Novel classes and evolutionary turnover of histone H2B variants in the mammalian germline

Raman

Rominger

Young

et al. 2021

Preprint

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Histones and their post-translational modifications facilitate diverse chromatin functions in eukaryotes. Core histones (H2A, H2B, H3, and H4) package genomes after DNA replication. In contrast, variant histones promote specialized chromatin functions, including DNA repair, genome stability, and epigenetic inheritance. Previous studies have identified only a few H2B variants in animals; their roles and evolutionary origins remain largely unknown. Here, using phylogenomic analyses, we reveal the presence of five H2B variants broadly present in mammalian genomes. In addition to three previously described variants (H2B.1, subH2B, and H2B.W), we identify and describe two new variants: H2B.L and H2B.N. Four of these five H2B variants originated in mammals, whereas H2B.L arose prior to the last common ancestor of bony vertebrates. We find that though mammalian H2B variants are subject to high gene turnover, most are broadly retained in mammals, including humans. Despite an overall signature of purifying selection, H2B variants evolve more rapidly than core H2B with considerable divergence in sequence and length. All five H2B variants are expressed in the germline. H2B.L and H2B.N are predominantly expressed in oocytes, an atypical expression site for mammalian histone variants. Our findings suggest that H2B variants likely encode potentially redundant but vital functions via unusual chromatin packaging or non-chromatin functions in mammalian germline cells. Our discovery of novel histone variants highlights the advantages of comprehensive phylogenomic analyses and provides unique opportunities to study how innovations in chromatin function evolve.

show abstract

Studying the Evolution of Histone Variants Using Phylogeny

Cited by 7 publications

References 57 publications

Novel Classes and Evolutionary Turnover of Histone H2B Variants in the Mammalian Germline

Novel Classes and Evolutionary Turnover of Histone H2B Variants in the Mammalian Germline

A Synthetic Approach to Reconstruct the Evolutionary and Functional Innovations of the Plant Histone Variant H2A.W

Novel classes and evolutionary turnover of histone H2B variants in the mammalian germline

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