H2AK121ub and H3K27me3 marks have different effects on nucleosome organization in Arabidopsis

Background: Nucleosome organization within chromatin can be altered through the incorporation of histone modifications that in turn affects gene expression. Accordingly, the Polycomb Group (PcG) complexes PRC1 and PRC2 through the incorporation of H2AK121ub and H3K27me3 marks, respectively, maintain the repression of target genes; however, little is known about the exact function of these modifications in shaping nucleosome array at target genes, especially in plants. Results: By using two different MNase-seq datasets we analyzed the nucleosome occupancy profile of different PcG target genes in Arabidopsis. We found that PcG targets strongly differ in their nucleosome organization depending on the marks that they carry. Our data indicate that H2AK121ub marks play a role in fine-tuning +1 nucleosome position, while H3K27me3 marks impact nucleosome spacing and chromatin accessibility at both promoter and gene regions. Furthermore, analyzing the nucleosome profile of transcriptionally active PcG target genes in WT seedlings we found that their apparent activated state may be actually due to transcriptional heterogeneity across different cells. Conclusion: Our findings show that H2AK121ub and H3K27me3 marks differentially affect nucleosome organization in Arabidopsis, displaying additive effects when co-localizing at target genes. Overall design: Nucleosome landscapes of 7DAG Arabidopsis seedlings Col-0 and triple mutants atbmi1a/b/c