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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. 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. In addition, analyses of mutants impaired in miRNA processing, splicing, or mRNA quality control reveal the existence of many transcripts that are undetectable in wild-type plants such as transcripts that are adjacent to silenced transposons. Such RNAs might constitute unstable, but important regulatory molecules of the Arabidopsis transcriptome, RNA processing intermediates that are eliminated during RNA maturation, or simply ghosts of past evolution. We will discuss the identification of previously unknown RNAs and potential new RNA maturation pathways, and conclude by giving an outlook on RNA-seq applications.