histone deacetylase OsHDAC1 epigenetically regulates the OsNAC6 gene that controls seedling root growth in rice

• Published in: The Plant journal : for cell and molecular biology Vol. 59; no. 5; pp. 764 - 776
• Main Authors: Chung, Pil Joong, Kim, Yeon Shic, Jeong, Jin Seo, Park, Su-Hyun, Nahm, Baek Hie, Kim, Ju-Kon
• Format: Journal Article
• Language: English
• Published: Oxford, UK Oxford, UK : Blackwell Publishing Ltd 01.09.2009; Blackwell Publishing Ltd; Blackwell
• Subjects: Biological and medical sciences; Botany; chromatin immunoprecipitation; Epigenesis, Genetic; epigenetic regulation; Freshwater; Fundamental and applied biological sciences. Psychology; Gene expression; Gene Expression Regulation, Plant; Genetics; histone acetylation; histone deacetylase; Histone Deacetylases - genetics; Histone Deacetylases - metabolism; Oligonucleotide Array Sequence Analysis; Oryza - enzymology; Oryza - genetics; Oryza - growth & development; Oryza sativa; Plant physiology and development; Plant Proteins - genetics; Plant Proteins - metabolism; Plant Roots - enzymology; Plant Roots - genetics; Plant Roots - growth & development; Rice; rice root growth; RNA, Plant - genetics; Seedlings - enzymology; Seedlings - genetics; Seedlings - growth & development; Transgenic plants; Histone deacetylase; Monocotyledones; Root; Growth; epigenetic regulation; Seedlings; chromatin immunoprecipitation; Oryza sativa; Regulation(control); Gene; Gramineae; Angiospermae; Epigenetics; rice root growth; Spermatophyta; Acetylation; histone acetylation
• ISSN: 0960-7412; 1365-313X
• DOI: 10.1111/j.1365-313X.2009.03908.x

We have previously isolated a rice gene encoding a histone deacetylase, OsHDAC1, and observed that its transgenic overexpression increases seedling root growth. To identify the transcriptional repression events that occur as a result of OsHDAC1 overexpression (OsHDAC1OE), a global profiling of root-expressed genes was performed on OsHDAC1OE or HDAC inhibitor-treated non-transgenic (NT) roots, in comparison with untreated NT roots. We selected 39 genes that are induced and repressed in HDAC inhibitor-treated NT and OsHDAC1OE roots, compared with NT roots, respectively. Interestingly, OsNAC6, a member of the NAM-ATAF-CUC (NAC) family, was identified as a key component of the OsHDAC1 regulon, and was found to be epigenetically repressed by OsHDAC1 overexpression. The root phenotype of OsNAC6 knock-out seedlings was observed to be similar to that of the OsHDAC1OE seedlings. Conversely, the root phenotype of the OsNAC6 overexpressors was similar to that of the OsHDAC1 knock-out seedlings. These observations indicate that OsHDAC1 negatively regulates the OsNAC6 gene that primarily mediates the alteration in the root growth of the OsHDAC1OE seedlings. Chromatin immunoprecipitation assays of the OsNAC6 promoter region using antibodies specific to acetylated histones H3 and H4 revealed that OsHDAC1 epigenetically represses the expression of OsNAC6 by deacetylating K9, K14 and K18 on H3 and K5, K12 and K16 on H4.