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Additional file 7. Review history.

Additional file 1: Fig. S1. Divergent transcriptomic changes of leaves and flowers in heat. Fig. S2. Comparison of m6A enrichment in two biological replications. Fig. S3. Detected sequence motifs of m6A-modified sites. Fig. S4. m6A peaks detected in different clusters. Fig. S5. Correlation between m6A and expression levels. Fig. S6. Correlation between FC m6A and FC expression. Fig. S7. Increased m6A RNA modification in Arabidopsis flowers. Fig. S8. Overlap of lowly variable genes identified from different datasets. Fig. S9. Inverse correlation of m6A levels and gene expression variability. Fig. S10. Lowly variable genes show stronger m6A RNA modification. Fig. S11. Enrichment of genes associated with low expression variability. Fig. S12. Expression profiling of genes encoding RNA demethylases. Fig. S13. An exemplary locus for increased m6A in 10b-1. Fig. S14. Density distribution of m6A enrichment in Arabidopsis leaves. Fig. S15. Exemplary loci with decreased expression variability in 10b-1. Fig. S16. Stress-granule association of lowly variable transcripts.

Additional file 2.

Transposable elements (TEs) are often regarded as harmful genomic factors and indeed they are strongly suppressed by the epigenetic silencing mechanisms. On the other hand, the mobilization of TEs brings about variability of genome and transcriptome which are essential in the survival and evolution of the host species. The vast majority of such controlling TEs influence the neighboring genes in cis by either promoting or repressing the transcriptional activities. Although TEs are highly repetitive in the genomes and transcribed in specific stress conditions or developmental stages, the trans-acting regulatory roles of TE-derived RNAs have been rarely studied. It was only recently that TEs were investigated for their regulatory roles as a form of RNA. Particularly in plants, TEs are ample source of small RNAs such as small interfering (si) RNAs and micro (mi) RNAs. Those TE-derived small RNAs have potentials to affect non-TE transcripts by sequence complementarity, thereby generating novel gene regulatory networks including stress resistance and hybridization barrier. Apart from the small RNAs, a number of long non-coding RNAs (lncRNAs) are originated from TEs in plants. For example, a retrotransposon-derived lncRNA expressed in rice root acts as a decoy RNA or miRNA target mimic which negatively controls miRNA171. The post-transcriptional suppression of miRNA171 in roots ensures the stabilization of the target transcripts encoding SCARECROW-LIKE transcription factors, the key regulators of root development. In this review article, the recent discoveries of the regulatory roles of TE-derived RNAs in plants will be highlighted.