Lorkovic, Z. | bioRxiv Science

bioRxiv2022

Transcriptional activity is shaped by the chromatin landscapes in Arabidopsis

SummaryHow histone variants and histone modifications shape nucleosome-mediated transcriptional repression, and how transcriptional activity shapes the enrichment of histone modifications and variants remain unclear. To clarify these relationships, we examined chromatin organization in the Arabidopsis thaliana genome, identifying a limited number of chromatin landscapes that distinguish transposon families and distinct groups of genes based on their transcriptional regulation. Unexpectedly, H2A variants are strong determinants of the landscape architecture. Combinations of H2A.W and four histone modifications define six domains that are occupied by specific transposon families and organized concentrically around the centromere. Moreover, H2A.Z defines transcriptional gene repression in specific domains. Expressed genes occupy four chromatin landscapes with specific RNA Polymerase II profiles. Although the composition of each chromatin landscape is invariant, they cover genes with a wide range of expression levels. Therefore, chromatin landscapes control the range of transcriptional activity, but transcriptional activity has little effect on chromatin composition. One Sentence SummaryHistone variants and histone modifications build a limited number of distinct chromatin landscapes that instruct the transcriptional regulation of genes and transposons in Arabidopsis.

genomics↗

bioRxiv2021

Crosstalk between H2A variant-specific modifications impacts vital cell functions

Histone variants are distinguished by specific substitutions and motifs that might be subject to post-translational modifications (PTMs). Compared with the high conservation of H3 variants, the N- and C-terminal tails of H2A variants are more divergent and are potential substrates for a more complex array of PTMs, which have remained largely unexplored. We used mass spectrometry to inventory the PTMs of the two heterochromatin-enriched variants H2A.W.6 and H2A.W.7 of Arabidopsis, which harbor the C-terminal motif KSPK. This motif is also found in macroH2A variants in animals and confers specific properties to the nucleosome. We showed that H2A.W.6 is phosphorylated by the cell cycle-dependent kinase CDKA specifically at KSPK. In contrast, this modification is absent on H2A.W.7, which also harbors the SQ motif associated with the variant H2A.X. Phosphorylation of the SQ motif is critical for the DNA damage response but is suppressed in H2A.W.7 by phosphorylation of KSPK. To identify factors involved in this suppression mechanism, we performed a synthetic screen in fission yeast expressing a mimic of the Arabidopsis H2A.W.7. Among those factors was the BRCT-domain protein Mdb1. We showed that phosphorylation of KSPK prevents binding of the BRCT-domain protein Mdb1 to phosphorylated SQ and as a result hampers response to DNA damage. Hence, cross-talks between motif-specific PTMs interfere with the vital functions of H2A variants. Such interference could be responsible for the mutual exclusion of specific motifs between distinct H2A variants. We conclude that sequence innovations in H2A variants have potentiated the acquisition of many specific PTMs with still unknown functions. These add a layer of complexity to the nucleosome properties and their impact in chromatin regulation.

synthetic biology↗