The nuclear and organellar tRNA-derived RNA fragment population in Arabidopsis thaliana is highly dynamic

Abstract

In the expanding repertoire of small noncoding RNAs (ncRNAs), tRNA-derived RNA fragments (tRFs) have been identified in all domains of life. Their existence in plants has been already proven but no detailed analysis has been performed. Here, short tRFs of 19–26 nucleotides were retrieved from Arabidopsis thaliana small RNA libraries obtained from various tissues, plants submitted to abiotic stress or fractions immunoprecipitated with ARGONAUTE 1 (AGO1). Large differences in the tRF populations of each extract were observed. Depending on the tRNA, either tRF-5D (due to a cleavage in the D region) or tRF-3T (via a cleavage in the T region) were found and hot spots of tRNA cleavages have been identified. Interestingly, up to 25% of the tRFs originate from plastid tRNAs and we provide evidence that mitochondrial tRNAs can also be a source of tRFs. Very specific tRF-5D deriving not only from nucleus-encoded but also from plastid-encoded tRNAs are strongly enriched in AGO1 immunoprecipitates. We demonstrate that the organellar tRFs are not found within chloroplasts or mitochondria but rather accumulate outside the organelles. These observations suggest that some organellar tRFs could play regulatory functions within the plant cell and may be part of a signaling pathway.

Combining tRNA sequencing methods to characterize plant tRNA expression and post-transcriptional modification

“…Plant nuclear tRNAs can be present in numerous copies, some of which are organized into large, tandemly repeated arrays (Theologis et al 2000;Cognat et al 2013). Furthermore, the generation and function of tRNA-derived fragments (tRFs) has come under increasing scrutiny because their presence has been directly linked to plant cell growth and response to stresses (Cognat et al 2017;Park and Kim 2018;Soprano et al 2018). Plants also have a high degree of tRNA compartmentalization and trafficking because of the presence of two endosymbiotically derived organelles, the plastid and the mitochondria.…”

Epigenetic silencing of clustered tDNAs in Arabidopsis

“…To determine whether this lack of detection relies on a transcriptional or on a posttranscriptional regulatory process, we used publicly available small RNA libraries 33 to undertake a degradome analysis of tRNA-derived fragments (tRFs) bearing polymorphic ribonucleotides ( Fig. 2c, Supplementary Fig.…”

“…For 4 days-old seedlings, roots, rosette leaves, inflorescences and green siliques of 7 week-old plants, total RNA was prepared according Chang et al 78 . Total tRNA was enriched from total RNA as described in 33 . This protocol includes a LiCl precipitation step that allows enrichment, in the supernatant, of RNAs of a size smaller than 150 nt (i.e.…”

“…Two small RNA libraries (GSM2301576, GSM2301577) were retrieved from the GEO database (http://www.ncni.nlm.nih.gov/geo/). tRF analysis was performed as described in Cognat et al 33 . The adapter sequence was trimmed for the short read libraries with cutadapt (version 1.18) 79 .…”

History of tRNA research in strasbourg

“…This idea received recently strong support with the finding of unprecedented properties of tRFs. Such fragments were found, for example, in various tissues of A thaliana , and interestingly, their biogenesis in plants was found correlated with stress conditions . Other questions remain partly open, for instance, how does an isoform of mRNA GlyRS control expression and localization of human GlyRS or what are the precise mechanisms of tRNA trafficking and tRNA‐dependent transamidations in mitochondria .…”