Identification of novel H2A histone variants across diverse clades of algae

Histones are among the most conserved proteins in eukaryotes. They not only ensure DNA compaction in the nucleus but also participate in epigenetic regulation of gene expression. These key epigenetic players are divided into replication-coupled histones, expressed during the S-phase, and replication-independent variants, expressed throughout the cell cycle. Compared with other core histones, H2A proteins exhibit a high level of variability but the characterization of algal H2A variants remains very limited.

In this study, we exploit genome and transcriptome data from 22 species to identify H2A variants in brown seaweeds. Combined analyses of phylogenetic data, synteny and protein motifs enable us to reveal the presence of new H2A variants as well as their evolutionary history. We identify three new H2A variants: H2A.N, H2A.O and H2A.E. In brown seaweeds, the H2A.E and H2A.O variants arose from the same monophyletic clade while the H2A.N variant emerged independently. Moreover, the H2A.E variant seems to have a shared ancestry with RC H2A while the H2A.O variant has an H2A.X-characteristic signature without being orthologous to this variant. Based on mass spectrometry, we identify distinct epigenetic marks on these H2A variants. Finally, the H2A.Z, H2A.N and H2A.O from brown seaweeds are ubiquitously expressed while expression of H2A.E has tissue-specific patterns, especially in reproductive tissues.

We thus hypothesize that H2A.O and H2A.X might have convergent functions while H2A.E might fulfil some functions of replication-coupled H2As and/or compensate for the absence of repressive histone marks along with H2A.N.