Data from: 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.组蛋白去乙酰化酶（Histone deacetylases, HDACs）可通过移除赖氨酸残基上的乙酰基，调控组蛋白乙酰化水平。玉米（Zea mays）HDAC家族成员HDA101能够影响植株多项发育进程，包括籽粒大小；但目前HDA101调控籽粒发育的分子机制仍不明晰。本研究发现，HDA101可调控传递细胞（transfer cell）特异性基因的表达，提示其表达失调可能与hda101突变体的传递细胞分化缺陷及籽粒变小相关。为探究HDA101在种子发育早期的功能，我们对HDA101的结合位点开展了全基因组定位分析。结果显示，HDA101主要靶向高表达及中表达基因。尽管HDA101的缺失会导致其直接靶基因发生组蛋白高度乙酰化，但这通常并不会伴随转录水平的变化。另有一小部分在籽粒发育过程中需被负向调控的沉默基因，同样是HDA101的靶标；HDA101的缺失会引发这些基因的组蛋白高度乙酰化，并使其表达水平上调。最后，我们发现HDA101可与多种染色质重塑复合物的成员互作，例如NFC103/MSI1以及SNL1/SIN3样共阻遏因子。综上，本研究揭示了HDA101在种子发育过程中调控的复杂遗传网络，并为解析HDA101介导的转录激活与沉默基因的不同调控机制提供了新见解。