Relationships between nucleosome positioning and gene Expression in plant

Nucleosome positioning influences the access of transcription factors (TFs) to DNA and gene expression. Studies in multiple models demonstrate similar nucleosome positioning patterns along genes and correlations between occupancy and expression. However, the relationships among nucleosome positioning, cis-regulatory element accessibility, and gene expression in plants remain undefined. We found that plant nucleosome depletion occurs on specific 6-mer motifs and this sequence-specific nucleosome depletion is predictive of expression levels in Arabidopsis thaliana. Importantly, 6-mer motif sites with significantly reduced nucleosome occupancy have higher DNase I hypersensitivity and are flanked by strongly phased nucleosomes, consistent with known TF binding sites. Intriguingly, this 6-mer specific nucleosome depletion pattern occurs not only in promoter but also in genic regions and is significantly correlated with higher gene expression, a pattern that is also found in rice but not yeast. Finally, to evaluate the influence of hormonal treatment, we compared the global nucleosome occupancy pattern prior and after treating plants with the defense hormone jasmonate. Intriguingly, there is no significant change in occupancy before and after, suggesting that these sites are pre-conditioned to enable rapid response without changing chromatin state significantly. Our study provides a global assessment of the joint contribution of nucleosome occupancy and motif sequences that are likely cis-elements to the control of gene expression in plants. Our findings pave the way for further understanding the impact of chromatin state on plant transcriptional regulatory circuits.