| Popup Text: | ABSTRACT
Many recent publications report about the pervasive transcription of almost the entire genome of several different model organisms. In the model plant Arabidopsis thaliana, 32,000 protein-coding genes, pseudogenes and non-coding RNAs are annotated and this number is still expected to rise. But what is the best method to gain a comprehensive view in the transcriptional activity of the Arabidopsis genome? We utilized whole genome tiling arrays and found more then 1,000 ???intergenic??? regions that are actively transcribed during the life cycle of wild-type plants as well as novel transcripts that occur only under certain stress conditions such as salt, heat or cold stress. However, we still might have missed many transcripts, especially those that are processed very rapidly such as primary microRNA transcripts. Indeed, whole genome tiling array analyses of Arabidopsis mutants impaired in miRNA pro
cessing, splicing, or mRNA quality control reveal the existence of many transcript that are undetectable in wild-type plants. These RNAs might constitute unstable, but important regulatory molecules of the Arabidopsis transcriptome or RNA processing intermediates that are eliminated during RNA maturation. Taken together, our results highlight the potential of identifying novel RNAs and RNA maturation pathways by in depth transcriptome analyses of RNA processing mutants.
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