The rice NAD(+)-dependent histone deacetylase OsSRT1 targets preferentially to stress- and metabolism-related genes and transposable elements

PLoS One. 2013 Jun 25;8(6):e66807. doi: 10.1371/journal.pone.0066807. Print 2013.

Abstract

Histone acetylation/deacetylation is an important chromatin modification for epigenetic regulation of gene expression. Silent information regulation2 (Sir2)-related sirtuins are nicotinamide-adenine dinucleotide (NAD(+))-dependent histone deacetylases (HDAC). The mammalian sirtuin family comprises 7 members (SIRT1-7) that act in different cellular compartments to regulate metabolism and aging. The rice genome contains only two Sir2-related genes: OsSRT1 (or SRT701) and OsSRT2 (orSRT702). OsSRT1 is closely related to the mammalian SIRT6, while OsSRT2 is homologous to SIRT4. Previous work has shown that OsSRT1 is required for the safeguard against genome instability and cell damage in rice plant. In this work we investigated the role of OsSRT1 on genome-wide acetylation of histone H3 lysine 9 (H3K9ac) and studied the genome-wide binding targets of OsSRT1. The study reveals that OsSRT1 binds to loci with relatively low levels of H3K9ac and directly regulates H3K9ac and expression of many genes that are related to stress and metabolism, indicating that OsSRT1 is an important site-specific histone deacetylase for gene regulation in rice. In addition, OsSRT1 is found to also target to several families of transposable elements, suggesting that OsSRT1 is directly involved in transposable element repression.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acetylation
  • Base Sequence
  • DNA Transposable Elements / genetics*
  • DNA, Plant / genetics
  • DNA, Plant / metabolism
  • Gene Expression Regulation, Plant
  • Genes, Plant / genetics*
  • Group III Histone Deacetylases / deficiency
  • Group III Histone Deacetylases / genetics
  • Group III Histone Deacetylases / metabolism*
  • Histones / metabolism
  • Oryza / enzymology*
  • Oryza / genetics*
  • Oryza / metabolism
  • Oryza / physiology
  • RNA Interference
  • Stress, Physiological / genetics*
  • Substrate Specificity

Substances

  • DNA Transposable Elements
  • DNA, Plant
  • Histones
  • Group III Histone Deacetylases

Grants and funding

This work was supported by the Chinese Ministry of Science and Technology “863” project (2012AA10A303); the Fundamental Research Funds for the Central Universities (“2011PY051” and “2012ZYTS057”); and the French Agence Nationale de la Recherche (ANR) program Blanc (NERDPATH). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.