Transcriptomics

Dataset Information

22

Unstable transcripts in Arabidopsis allotetraploids are associated with nonadditive gene expression in response to abiotic and biotic stresses


ABSTRACT: Genome-wide analysis of gene expression has documented differential gene expression between closely related species in plants or animals and nonadditive gene expression in hybrids and allopolyploids compared to the parents. In Arabidopsis, 15-43% of genes are expressed differently between the related species, A. thaliana and A. arenosa, and the majority of them are nonadditvely expressed (differently from mid-parent value) in allotetraploids relative to the parents. The gene expression variation is associated with transcriptional and posttranscriptional mechanisms. Although transcriptional regulation by epigenetic mechanisms plays a role in nonadditive gene expression, the effects of posttranscriptional regulation on nonadditive gene expression is largely unknown. Here we reported a comprehensive genome-wide analysis of mRNA decay in Arabidopsis allotetraploids using oligo gene microarrays. Among ~26,000 annotated genes on the arrays, over 1% of genes showed a rapid decay rate with an estimated half-life of less than 60 min, and these genes are known as genes with unstable transcripts (GUTs). Interestingly, 30% of GUTs matched the nonadditively expressed genes, and their expression levels were significantly negatively correlated. These nonadditively expressed GUTs are highly enriched with a 2-8-fold increase compared to the proportion of all genes in the Gene Ontology (GO) classifications in response to stress, abiotic and biotic stimulus, signal transduction, and transcription. The data are consistent with the enrichment of nonadditvely-expressed genes in those categories in allopolyploids of Arabidopsis, wheat and cotton. Interestingly, the GUTs include some key transcription factors including circadian clock regulators, suggesting a mechanism for rapid response to light signalling and clock regulation in allotetraploids. These data collectively suggest an important role of mRNA stability in nonadditive expression of homoeologous genes in allopolyploids. Overall design: A total of 8 slides were used for comparison (0 min vs. 120 min), including two biological and four technical replications. Each biological replication consists of two technical replications (four slides) that were hybridized with reverse-labeled probes .

INSTRUMENT(S): Z. Jeffrey Chen Laboratory Spotted Arabidopsis 70mer Oligo Microarray version 1.0

ORGANISM(S): Arabidopsis  

SUBMITTER: Z Jeffrey Jeffrey Chen  

PROVIDER: GSE26065 | GEO | 2011-09-16

SECONDARY ACCESSION(S): PRJNA135575

REPOSITORIES: GEO

Similar Datasets

2011-09-15 | E-GEOD-26065 | ArrayExpress
2009-07-30 | E-GEOD-15443 | ArrayExpress
2009-07-31 | GSE15443 | GEO
2008-11-20 | GSE9513 | GEO
2008-11-20 | GSE13468 | GEO
2008-03-30 | GSE9512 | GEO
| GSE83371 | GEO
| GSE83372 | GEO
| GSE50715 | GEO
| PRJNA135575 | ENA