Noncoding RNAs have been extensively described in plant and animal transcriptomes by using high-throughput sequencing technology. Of these non-coding RNAs, a growing number of long intergenic noncoding RNAs (lincRNAs) have been described in multicellular organisms, however the origins and functions of many lincRNAs remain to be explored. In many eukaryotic genomes, transposable elements (TEs) are widely distributed and often account for large fractions of plant and animal genomes yet the contribution of TEs to lincRNAs is largely unknown. By using strand-specific RNA sequencing, researchers from the Shanghai Center for Plant Stress Biology profiled the expression patterns of lincRNAs in Arabidopsis, rice and maize, and identified 47, 611 and 398 TE-associated lincRNAs (TE-lincRNAs), respectively. TE-lincRNAs were more often derived from retrotransposons than DNA transposons and as retrotransposon copy number in both rice and maize genomes so did TE-lincRNAs. The researchers validated the expression of these TE-lincRNAs by strand-specific RT-PCR and also demonstrated tissue specific transcription and stress induced TE-lincRNAs either after salt, abscisic acid (ABA) or cold treatments. For Arabidopsis TE-lincRNA11195, 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 lincRNAs including TE-lincRNAs were generated from the preceding untranscribed regions and interestingly inherited in a wild type background in subsequent generations. These findings not only demonstrate that TE-associated lincRNAs play important roles in plant abiotic stress responses but lincRNAs and TE-lincRNAs might act as an adaptive reservoir in eukaryotes.
Gene differential expression analysis of TE-lincRNA11195 mutant using RNA-seq
(A) Volcano plot showing log2 fold changes versus statistical significances of genes. Blue dots represent statistically significant differentially expressed genes (Benjamini-Hochberg method adjusted p-value < 0.05). (B) GO enrichment analysis of 100 most significantly differentially expressed genes. (C) Genomic distribution of 100 most significantly differentially expressed genes. Gene labels with blue colour are top 10 most significantly expressed genes. Scatter plot inside inner track represents log2 fold changes of genes, therefore, red and blue dots represent up- and down- regulated genes respectively. Links inside circle plot represent 5 genes associated with most significant over-represented GO term “response to salicylic acid stimulus”, blue and red lines represent between- and in- chromosome connections respectively