title: Mutation of the RDR1 gene caused genome-wide changes in gene expression, regional variation in small RNA clusters and localized alteration in DNA methylation in rice.
abstract: BACKGROUND
  Endogenous small (sm) RNAs (primarily si- and miRNAs) are important trans/cis-acting regulators involved in diverse cellular functions. In plants, the RNA-dependent RNA polymerases (RDRs) are essential for smRNA biogenesis. It has been established that RDR2 is involved in the 24 nt siRNA-dependent RNA-directed DNA methylation (RdDM) pathway. Recent studies have suggested that RDR1 is involved in a second RdDM pathway that relies mostly on 21 nt smRNAs and functions to silence a subset of genomic loci that are usually refractory to the normal RdDM pathway in Arabidopsis. Whether and to what extent the homologs of RDR1 may have similar functions in other plants remained unknown.
  
  
  RESULTS
  We characterized a loss-of-function mutant (Osrdr1) of the OsRDR1 gene in rice (Oryza sativa L.) derived from a retrotransposon Tos17 insertion. Microarray analysis identified 1,175 differentially expressed genes (5.2% of all expressed genes in the shoot-tip tissue of rice) between Osrdr1 and WT, of which 896 and 279 genes were up- and down-regulated, respectively, in Osrdr1. smRNA sequencing revealed regional alterations in smRNA clusters across the rice genome. Some of the regions with altered smRNA clusters were associated with changes in DNA methylation. In addition, altered expression of several miRNAs was detected in Osrdr1, and at least some of which were associated with altered expression of predicted miRNA target genes. Despite these changes, no phenotypic difference was identified in Osrdr1 relative to WT under normal condition; however, ephemeral phenotypic fluctuations occurred under some abiotic stress conditions.
  
  
  CONCLUSIONS
  Our results showed that OsRDR1 plays a role in regulating a substantial number of endogenous genes with diverse functions in rice through smRNA-mediated pathways involving DNA methylation, and which participates in abiotic stress response.
authors: Ningning
authors: N
authors: Wang
authors: Di
authors: D
authors: Zhang
authors: Zhenhui
authors: Z
authors: Wang
authors: Hongwei
authors: H
authors: Xun
authors: Jian
authors: J
authors: Ma
authors: Hui
authors: H
authors: Wang
authors: Wei
authors: W
authors: Huang
authors: Ying
authors: Y
authors: Liu
authors: Xiuyun
authors: X
authors: Lin
authors: Ning
authors: N
authors: Li
authors: Xiufang
authors: X
authors: Ou
authors: Chunyu
authors: C
authors: Zhang
authors: Ming-Bo
authors: MB
authors: Wang
authors: Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China. Baoliu@nenu.edu.cn.
authors: Bao
authors: B
authors: Liu
mesh_terms: D032461:Chromosomes, Plant / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D056426:Genetic Loci; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D016254:Mutagenesis, Insertional / Q000235:genetics; D009154:Mutation / Q000235:genetics*; D012275:Oryza / Q000235:genetics*; D010641:Phenotype; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism; D013312:Stress, Physiological / Q000235:genetics
chemical_list: D035683:MicroRNAs; D010940:Plant Proteins; D018749:RNA, Plant