The evolution and functional divergence of the histone H2B family in plants

Abstract

Chromatin regulation of eukaryotic genomes depends on the formation of nucleosome complexes between histone proteins and DNA. Histone variants, which are diversified by sequence or expression pattern, can profoundly alter chromatin properties. While variants in histone H2A and H3 families are well characterized, the extent of diversification of histone H2B proteins is less understood. Here, we report a systematic analysis of the histone H2B family in plants, which have undergone substantial divergence during the evolution of each major group in the plant kingdom. By characterising Arabidopsis H2Bs, we substantiate this diversification and reveal potential functional specialization that parallels the phylogenetic structure of emergent clades in eudicots. In addition, we identify a new class of highly divergent H2B variants, H2B.S, that specifically accumulate during chromatin compaction of dry seed embryos in multiple species of flowering plants. Our findings thus identify unsuspected diverse properties among histone H2B proteins in plants that has manifested into potentially novel groups of histone variants.

The Histone Chaperone HIRA Is a Positive Regulator of Seed Germination

“…As a result, chromatin in the embryo shows a low H3.1/H3.3 ratio. This is not the only peculiarity of the histone variant repertoire in dry seed embryos, as recent reports revealed enrichment of seed chromatin in a particular H2B variant, termed H2B.8 [ 58 , 59 ]. It is interesting to speculate that these different features of seed chromatin contribute to the highly condensed chromatin state and the small nuclei that characterize the dry seed [ 60 ].…”

Histone variants at a glance

“…In Arabidopsis, ten H2Bs differ mostly in the lysinerich N-terminal tails and in tissue-specific expression (Bergmuller et al, 2007). Although most appear to be RC H2Bs, H2B.3 is enriched in mature leaves and in nucleosomes containing H3.3 and/or H2A.Z, consistent with it being a RI variant, and H2B.8 is enriched in dry seed (Jiang et al, 2020) (see poster). A similar heterogeneity of RC H2B and H2A proteins is found in humans, mice and sea urchins (Marzluff et al, 2002(Marzluff et al, , 2006.…”

MS Amanda 2.0: Advancements in the standalone implementation

“…In addition, users have reported great results achieved using MS Amanda on phosphorylated data sets and it has frequently been used to identify modified peptides [23]- [25]. We therefore analyzed four phospho-enriched HeLa cell lysates from the Chorus Project [26] (https://chorusproject.org/, identifier 1374, DDA files only) and compared results of MS Amanda 2.0 with a search engine thoroughly accepted by the community: X!Tandem [27] (v. 5.0.1).…”