Microarray analysis and new sequencing technologies have revealed that the majority of the genome is transcribed in many eukaryotes. Much of the RNA appears to be non-coding and an ongoing debate is how much of a functional role it has. Different mechanisms by which ncRNA can be regulatory have been described: direct ncRNA effects on transcription; recruitment of chromatin modifiers; formation of silent nuclear compartments. These have been documented chiefly in yeasts and mammals but examples are now appearing in plants. To date RNA-mediated transcriptional silencing studies in plants have focused on siRNAs, but data now show longer ncRNAs are also involved in this silencing. Roles for long ncRNAs in the phenotypic plasticity of plants are also suggested by whole genome analysis showing widespread effects of different external cues on ncRNA expression.
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