Decoding the tissue-specific regulatory roles of H2A.Z in maize leaf and endosperm

The histone variant H2A.Z is a key regulator of transcription, but its function in maize (Zea mays subsp. mays) is largely unknown. In this study, we mapped the genome-wide distribution patterns of H2A.Z in maize leaf and endosperm tissues to understand its role in gene regulation. We found that H2A.Z is mainly located around genes in both tissues, and can affect gene expression together with other epigenetic modifications. Moreover, while most intergenic H2A.Z peaks are associated with non-coding transcripts probably derived from regulatory enhancers, some are associated with transcripts with protein-coding potential. These suggest that H2A.Z signals can be used to assist genome annotation of regulatory elements and protein-coding genes. Furthermore, H2A.Z deposition pattern around genes exhibited variations between endosperm and leaf, which correlates well with expression levels of the genes in these two tissues. Interestingly, genes with higher H2A.Z levels around promoters in leaf compared with endosperm tend to show higher expression in leaf, and these genes are enriched for photosynthetic activity, suggesting a possible role of H2A.Z in photosynthetic pathway. In support of this, higher net photosynthetic rate was observed in H2A.Z overexpression lines. In summary, our study provides new insights into the epigenetic control of gene expression and tissue development in maize.