Genome-wide mapping of targets of maize histone deacetylase hda101 reveals its function and regulatory mechanism during seed development

Histone deacetylases (HDACs) control histone acetylation levels by removing acetyl group from lysine residues. Maize (Zea mays) HDAC HDA101 influences several aspects of development, including kernel size; however, the molecular mechanism by which HDA101 affects kernel development remains unknown. In this study, we find HDA101 regulates the expression of transfer cell-specific genes, suggesting their mis-regulation may be associated with defects in differentiation of transfer cells and smaller kernels of hda101 mutants. To investigate HDA101 function during early stages of seed development, we performed genome-wide mapping of HDA101 binding sites. We observed that HDA101 mainly targets highly and intermediately expressed genes. Although loss of HDA101 can induce histone hyper-acetylation of its direct targets, this often does not involve variation in transcription. A small subset of inactive genes that must be negatively regulated during kernel development are also targeted by HDA101 and its loss leads to hyper-acetylation and increased expression of these genes. Finally, we report HDA101 interacts with members of different chromatin remodeling complexes, such as NFC103/MSI1 and SNL1/SIN3-like co-repressors. Taken together, our results reveal a complex genetic network regulated by HDA101 during seed development and provide insights into the different mechanisms of HDA101-mediated regulation of transcriptionally active and inactive genes.