title: Transcriptome profiling and methyl homeostasis of an Arabidopsis mutant deficient in S-adenosylhomocysteine hydrolase1 (SAHH1).
abstract: Transcriptome profiling was conducted to detect genes whose expression is significantly changed in an Arabidopsis mutant deficient in S-adenosylhomocysteine hydrolase1 (SAHH1) during early seedling development when mutant phenotypes could be clearly observed. A total of 2,040 differentially expressed genes were identified, representing approximately 6.7% of the 30,385 DNA oligonucleotide targets on the microarray. Among these differential expressed genes, many were mapped to pathways essential to plant growth and development including those of primary, secondary and hormone metabolisms. A significant proportion of up-regulated genes encoded transposable elements which were mapped to the centromeric and pericentromeric regions of the Arabidopsis chromosomes that were analyzed. A number of down-regulated genes were found to be involved in root hair formation, which might have contributed to the root hair defective phenotype of the mutant. Analysis of genes encoding transposable elements and those associating with root hair development indicated that these genes were highly co-expressed during seedling development. Despite SAHH1 deficiency, the expression of genes encoding methyltransferase remained largely unchanged in the sahh1 mutant. Bisulfite sequencing analysis of the transposable elements and the FWA gene revealed that their sequences in the mutant were deficient of 5-methylcytosines. Analysis of mutant genomic DNA using restriction endonucleases that were unable to cut methylated DNA suggested a genome-wide hypomethylation had occurred in the mutant. These results indicated that SAHH1 plays a critical role in methyl homeostasis, and its deficiency is a major contributing factor to the change of global gene expression, metabolic pathways and activation of transposable elements in the sahh1 mutant.
authors.affiliation: Plant Biotechnology Institute, National Research Council of Canada (NRC), 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada.
authors.forename: Bo
authors.initials: B
authors.lastname: Ouyang
authors.forename: Zhangjun
authors.initials: Z
authors.lastname: Fei
authors.forename: Je-Gun
authors.initials: JG
authors.lastname: Joung
authors.forename: Allan
authors.initials: A
authors.lastname: Kolenovsky
authors.forename: Chushin
authors.initials: C
authors.lastname: Koh
authors.forename: Jacek
authors.initials: J
authors.lastname: Nowak
authors.forename: Allan
authors.initials: A
authors.lastname: Caplan
authors.forename: Wilfred A
authors.initials: WA
authors.lastname: Keller
authors.forename: Yuhai
authors.initials: Y
authors.lastname: Cui
authors.forename: Adrian J
authors.initials: AJ
authors.lastname: Cutler
authors.forename: Edward W T
authors.initials: EW
authors.lastname: Tsang
mesh_terms: D043383:Adenosylhomocysteinase / Q000235:genetics* / Q000378:metabolism; D017360:Arabidopsis / Q000201:enzymology* / Q000235:genetics* / Q000254:growth & development; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000378:metabolism; D019175:DNA Methylation / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D015971:Gene Expression Regulation, Enzymologic; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D006706:Homeostasis; D053858:Metabolic Networks and Pathways / Q000235:genetics; D008954:Models, Biological; D009154:Mutation; D010641:Phenotype; D018517:Plant Roots / Q000254:growth & development
chemical_list: D029681:Arabidopsis Proteins; D004251:DNA Transposable Elements; D018744:DNA, Plant; D043383:Adenosylhomocysteinase; C505419:HOG1 protein, Arabidopsis