When junk DNA turns functional: transposon-derived non-coding RNAs in plants

Abstract

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.

The Dynamism of Transposon Methylation for Plant Development and Stress Adaptation

“…Transposable elements (TEs), also known as jumping genes or mobile genetic elements, are key players in plant biological systems and genome evolution [1][2][3][4][5]. TEs were previously considered as genomic parasites since these self-replicating entities are ubiquitous [6,7] and abundant in nature [8]. In recent years, several evolutionary studies in eukaryote genomes emphasized the biological significance of TEs in animals and plant genomes [9][10][11].…”

The Evolutionary Volte-Face of Transposable Elements: From Harmful Jumping Genes to Major Drivers of Genetic Innovation

“…TE-derived ncRNAs can also act in trans to regulate the expression of host genes at the transcriptional or post-transcriptional level. Besides, when embedded in a transcribed host mRNA, they can contribute to a plethora of mechanisms governing the mRNA outcome [ 158 , 243 , 244 , 245 ]. Although all these processes might not reflect genuine exaptation events, they clearly demonstrate that interaction between TEs and their host also occurs at the level of the RNA molecule ( Figure 3 B).…”

“…Comparative analyses performed in 40 plant species revealed more than 14,000 overlaps between TE and lncRNAs. While vertebrate lncRNAs appear to be lineage-specific, plant lncRNAs are generally poorly conserved between the same family species [ 158 , 244 ]. There is, however, a substantial number of TE-derived lncRNAs that are conserved among Brassicaceae species, suggesting conserved biological functions between these lncRNAs [ 250 ].…”

“…As mentioned above, TE-derived small RNAs have been widely described in plants, especially in the process of siRNA-mediated heterochromatinization (for recent reviews see also [ 158 , 244 , 245 ]). Different evolutionary scenarios depict how TE-derived small RNAs control host gene expression.…”

Editorial: Mobile Elements and Plant Genome Evolution, Comparative Analyzes and Computational Tools

“…These numerous families of interspersed repeats were often called "junk DNA" as first, they were not associated with any vital protein-coding processes. Now, more and more clues indicate that such repeated DNA might play major roles in the genome as functional "non-coding" DNA (Pennisi, 2012;Ariel and Manavella, 2021). Transposable elements (TEs), such as DNA transposons and retrotransposons, are the main part of these interspersed repeats (Vitte et al, 2014).…”