Perturbation of H2A.Z enrichment and variant composition in Arabidopsis thaliana is sufficient to alter H3K27me3 distribution and abundance in a locus-specific fashion

Abstract Background H3K27me3 is a histone modification associated with transcriptional repression that plays a pivotal role in differentiation and development in plants and animals. H2A.Z, a histone variant of H2A, is often colocalized with H3K27me3 in Arabidopsis. Previous genome-wide studies have raised the possibility that H2A.Z contributes to H3K27me3 homeostasis in plants. To examine the contribution of H2A.Z to H3K27me3, we made use of hta9 hta11 plants, which are defective in two of three genes that code for H2A.Z. Results Use of the quantitative siQ-ChIP pipeline to examine H2A.Z enrichment reveals that hta9 hta11 plants exhibit a two-fold global reduction of H2A.Z abundance. Concurrent analysis of histone protein abundance in the chromatin of hta9 hta11 plants by mass spectrometry confirms a global reduction of H2A.Z and also reveals an altered relative abundance of H2A.Z variants. A similar characterization of H3K27me3 reveals an altered normalized distribution of this histone modification in the genome of hta9 hta11 plants. There is a slight decrease in the global abundance of H3K27me3 at non-expressed genes in hta9 hta11 plants, and hundreds of individual loci exhibit reduced H3K27me3 enrichment. Further, genes marked with H3K27me3 are substantially overrepresented among genes exhibiting differential expression in hta9 hta11 plants. Intriguingly, our analyses raise the possibility that ectopic expression of the transcriptional regulator FUS3 in hta9 hta11 seedlings contributes to altered H3K27me3 enrichment of target genes. Conclusions Our combined analyses reveal that perturbation of H2A.Z is sufficient to alter H3K27me3 homeostasis in a locus-specific fashion and are consistent with the possibility of a functional relationship between these conserved chromatin features in plants.