Transposable elements ( TE s) contribute to stress‐related long intergenic noncoding RNA s in plants

Summary Noncoding RNA s have been extensively described in plant and animal transcriptomes by using high‐throughput sequencing technology. Of these noncoding RNA s, a growing number of long intergenic noncoding RNA s (linc RNA s) have been described in multicellular organisms, however the origins and functions of many linc RNA s remain to be explored. In many eukaryotic genomes, transposable elements ( TE s) are widely distributed and often account for large fractions of plant and animal genomes yet the contribution of TE s to linc RNA s is largely unknown. By using strand‐specific RNA ‐sequencing, we profiled the expression patterns of linc RNA s in Arabidopsis, rice and maize, and identified 47 611 and 398 TE ‐associated linc RNA s ( TE ‐linc RNA s), respectively. TE ‐linc RNA s were more often derived from retrotransposons than DNA transposons and as retrotransposon copy number in both rice and maize genomes so did TE ‐linc RNA s. We validated the expression of these TE ‐linc RNA s by strand‐specific RT ‐ PCR and also demonstrated tissue‐specific transcription and stress‐induced TE ‐linc RNA s either after salt, abscisic acid ( ABA ) or cold treatments. For Arabidopsis TE ‐linc RNA 11195, mutants had reduced sensitivity to ABA as demonstrated by longer roots and higher shoot biomass when compared to wild‐type. Finally, by altering the chromatin state in the Arabidopsis chromatin remodelling mutant ddm1 , unique linc RNA s including TE ‐linc RNA s were generated from the preceding untranscribed regions and interestingly inherited in a wild‐type background in subsequent generations. Our findings not only demonstrate that TE ‐associated linc RNA s play important roles in plant abiotic stress responses but linc RNA s and TE ‐linc RNA s might act as an adaptive reservoir in eukaryotes.