New molecular phenotypes in the dst mutants of Arabidopsis revealed by DNA microarray analysis.
In this study, DNA microarray analysis was used to expand our understanding of the dst1 mutant of Arabidopsis. The dst (downstream) mutants were isolated originally as specifically increasing the steady state level and the half-life of DST-containing transcripts. As such, txhey offer a unique opportunity to study rapid sequence-specific mRNA decay pathways in eukaryotes. These mutants show a threefold to fourfold increase in mRNA abundance for two transgenes and an endogenous gene, all containing DST elements, when examined by RNA gel blot analysis; however, they show no visible aberrant phenotype. Here, we use DNA microarrays to identify genes with altered expression levels in dst1 compared with the parental plants. In addition to verifying the increase in the transgene mRNA levels, which were used to isolate these mutants, we were able to identify new genes with altered mRNA abundance in dst1. RNA gel blot analysis confirmed the microarray data for all genes tested and also was used to catalog the first molecular differences in gene expression between the dst1 and dst2 mutants. These differences revealed previously unknown molecular phenotypes for the dst mutants that will be helpful in future analyses. Cluster analysis of genes altered in dst1 revealed new coexpression patterns that prompt new hypotheses regarding the nature of the dst1 mutation and a possible role of the DST-mediated mRNA decay pathway in plants.
Pérez-Amador
M A
MA
Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, USA.
Lidder
P
P
Johnson
M A
MA
Landgraf
J
J
Wisman
E
E
Green
P J
PJ
D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins; D001483:Base Sequence; D016000:Cluster Analysis; D005095:Exoribonucleases / Q000235:genetics* / Q000378:metabolism; D020224:Expressed Sequence Tags; D018506:Gene Expression Regulation, Plant; D005819:Genetic Markers; D008969:Molecular Sequence Data; D016296:Mutagenesis; D020411:Oligonucleotide Array Sequence Analysis; D010641:Phenotype; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins; D017386:Sequence Homology, Amino Acid; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism; D035165:Transcription Factors, General; D035602:Transcriptional Elongation Factors
D029681:Arabidopsis Proteins; D005819:Genetic Markers; D010940:Plant Proteins; C086789:SAUR-AC1 protein, Arabidopsis; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors; D035165:Transcription Factors, General; D035602:Transcriptional Elongation Factors; C018648:transcription factor S-II; D005095:Exoribonucleases; C068398:XRN1 protein, S cerevisiae