Genome-wide Nucleosome Occupancy and Organization Modulates the Plasticity of Gene Transcriptional Status in Maize

Nucleosomes are fundamental units of chromatin that play critical roles in gene regulation by modulating DNA accessibility. However, their roles in regulating tissue-specific gene transcription are poorly understood. Here, we present genome-wide nucleosome maps of maize shoot and endosperm generated by sequencing the micrococcal nuclease digested nucleosomal DNA. The changes of gene transcriptional status between shoot and endosperm were accompanied by preferential nucleosome loss from the promoters and shifts in the first nucleosome downstream of the transcriptional start sites (+1 nucleosome) and upstream of transcriptional termination sites (-1 nucleosome). Intrinsically DNA-encoded nucleosome organization was largely associated with the capacity of a gene to alter its transcriptional status among different tissues. Compared with tissue-specific genes, constitutively expressed genes showed more pronounced 5' and 3' nucleosome-depleted regions as well as further +1 nucleosome to transcriptional start sites and -1 nucleosome to transcriptional termination sites. Moreover, nucleosome organization was more highly correlated with the plasticity of gene transcriptional status than with its expression level when examined using in vivo and predicted nucleosome data. In addition, the translational efficiencies of tissue-specific genes appeared to be greater than those of constitutively expressed genes. Taken together, our results indicate that intrinsically DNA-encoded nucleosome organization is important, beyond its role in regulating gene expression levels, in determining the plasticity of gene transcriptional status.