title: Genome-Wide Mapping of Targets of Maize Histone Deacetylase HDA101 Reveals Its Function and Regulatory Mechanism during Seed Development.
abstract: Histone deacetylases (HDACs) regulate histone acetylation levels by removing the acetyl group from lysine residues. The maize (Zea mays) HDACHDA101 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 that HDA101 regulates the expression of transfer cell-specific genes, suggesting that their misregulation may be associated with the defects in differentiation of endosperm transfer cells and smaller kernels observed in hda101 mutants. To investigate HDA101 function during the early stages of seed development, we performed genome-wide mapping of HDA101 binding sites. We observed that, like mammalian HDACs, HDA101 mainly targets highly and intermediately expressed genes. Although loss of HDA101 can induce histone hyperacetylation of its direct targets, this often does not involve variation in transcript levels. A small subset of inactive genes that must be negatively regulated during kernel development is also targeted by HDA101 and its loss leads to hyperacetylation and increased expression of these inactive genes. Finally, we report that HDA101 interacts with members of different chromatin remodeling complexes, such as NFC103/MSI1 and SNL1/SIN3-like protein corepressors. Taken together, our results reveal a complex genetic network regulated by HDA101 during seed development and provide insight into the different mechanisms of HDA101-mediated regulation of transcriptionally active and inactive genes.
authors.affiliation: State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, PR China.
authors.forename: Hua
authors.initials: H
authors.lastname: Yang
authors.affiliation: State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, PR China.
authors.forename: Xinye
authors.initials: X
authors.lastname: Liu
authors.affiliation: State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, PR China.
authors.forename: Mingming
authors.initials: M
authors.lastname: Xin
authors.affiliation: State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, PR China.
authors.forename: Jinkun
authors.initials: J
authors.lastname: Du
authors.affiliation: State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, PR China.
authors.forename: Zhaorong
authors.initials: Z
authors.lastname: Hu
authors.affiliation: State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, PR China.
authors.forename: HuiRu
authors.initials: H
authors.lastname: Peng
authors.affiliation: Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Unità di Ricerca per la Maiscoltura, I-24126 Bergamo, Italy.
authors.forename: Vincenzo
authors.identifier: http://orcid.org/0000-0001-9746-2583
authors.initials: V
authors.lastname: Rossi
authors.affiliation: State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, PR China.
authors.forename: Qixin
authors.initials: Q
authors.lastname: Sun
authors.affiliation: State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, PR China.
authors.forename: Zhongfu
authors.initials: Z
authors.lastname: Ni
authors.affiliation: State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, PR China yingyin@cau.edu.cn.
authors.forename: Yingyin
authors.initials: Y
authors.lastname: Yao
mesh_terms: D002874:Chromosome Mapping; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D053263:Gene Regulatory Networks / Q000187:drug effects*; D056572:Histone Deacetylase Inhibitors / Q000494:pharmacology*; D006655:Histone Deacetylases / Q000235:genetics* / Q000378:metabolism; D006657:Histones / Q000187:drug effects* / Q000235:genetics / Q000378:metabolism; D010940:Plant Proteins / Q000037:antagonists & inhibitors / Q000235:genetics / Q000378:metabolism; D012639:Seeds / Q000187:drug effects / Q000201:enzymology* / Q000235:genetics / Q000254:growth & development; D017423:Sequence Analysis, RNA; D020798:Two-Hybrid System Techniques; D003313:Zea mays / Q000187:drug effects / Q000201:enzymology* / Q000235:genetics / Q000254:growth & development
chemical_list: D056572:Histone Deacetylase Inhibitors; D006657:Histones; D010940:Plant Proteins; D006655:Histone Deacetylases