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When junk DNA turns functional: transposon-derived noncoding RNAs in plants.

Transposable elements (TEs) are major contributors to genome complexity in eukaryotes. TE mobilization may cause genome instability, although it can also drive genome diversity throughout evolution. TE transposition may influence the transcriptional activity of neighboring genes by modulating the epigenomic profile of the region or by altering the relative position of regulatory elements. Notably, TEs have emerged in the last few years as an important source of functional long and small noncoding RNAs. A plethora of small RNAs derived from TEs have been linked to the trans-regulation of gene activity at the transcriptional and post-transcriptional levels. Furthermore, TE-derived long noncoding RNAs have been shown to modulate gene expression by interacting with protein partners, sequestering active small RNAs, and forming duplexes with DNA or other RNA molecules. In this review, we revise our current knowledge about the functional and mechanistic paradigms of TE-derived long and small noncoding RNAs and discuss their role in plant development and evolution.