Epigenetic silencing of clustered tRNA genes in Arabidopsis

Abstract

Beyond their key role in translation, cytosolic transfer RNAs (tRNAs) are involved in a wide range of other biological processes. Nuclear tRNA genes (tDNAs) are transcribed by the RNA polymerase III (RNAP III) and cis-elements, trans-factors as well as genomic features are known to influence their expression. In Arabidopsis, besides a predominant population of dispersed tDNAs spread along the 5 chromosomes, some clustered tDNAs have been identified. Here, we demonstrate that these tDNA clusters are transcriptionally silent and that pathways involved in the maintenance of DNA methylation play a predominant role in their repression. Moreover, we show that clustered tDNAs exhibit repressive chromatin features whilst their dispersed counterparts contain permissive euchromatic marks. This work demonstrates that both genomic and epigenomic contexts are key players in the regulation of tDNAs transcription. The conservation of most of these regulatory processes suggests that this pioneering work in Arabidopsis can provide new insights into the regulation of RNA Pol III transcription in other organisms, including vertebrates.

PlantRNA 2.0: an updated database dedicated to tRNAs of photosynthetic eukaryotes

“…In embryophytes (Figure 1), about 5% of them possess a classical intronic sequence between positions 37 and 38, and correspond to two tRNA gene families (tRNA Tyr and tRNA eMet ). This proportion increases up to 13.8% in Brassicaceae, such as Arabidopsis thaliana, where a cluster of tRNA Tyr genes exist (Hummel et al, 2020). In gymnosperms, Ginkgo biloba and P. taeda, tRNA Ile (TAT) genes also contain classical intronic The color code is as follows: true tRNA genes in blue; tRNA-like/tRNA pseudogenes in orange; tRNA genes inserted into the nuclear genome or due to contamination by mitochondrial or plastidial DNA in gray; and tRNA genes corresponding to external bacterial contamination in yellow.…”

Characterization of tRNA expression profiles in large offspring syndrome

“…Distinct sets of tissue-specific methylation patterns in cattle have been described, yet the regulatory impacts of these regions are poorly understood [ 11 ]. A report found that 24.59% and 22.43% of transfer RNA (tRNA) genes are methylated in fetal and adult bovine muscle tissue [ 12 ] and elevated methylation levels at tRNA gene clusters have been identified which resulted in transcriptional repression and demonstrated that epigenetic mechanisms can fine tune tRNA expression [ 13 ]. In addition, recent tRNA studies in human cancer have indicated that DNA methylation interferes with the binding of the transcriptional machinery (RNA polymerase III & TFIIIC) to the promoter of tRNA genes and inhibits tRNA expression [ 14 ].…”

PlantRNA 2.0: an updated database dedicated to tRNAs of photosynthetic eukaryotes

“…In embryophytes (Figure 1), around 5% of them possess a classical intronic sequence between positions 37 and 38 and correspond to two tRNA gene families (tRNA Tyr and tRNA eMet ). This proportion increases up to 13.8% in Brassicaceae, such as A. thaliana, where a cluster of tRNA Tyr genes exist (10). In streptophyte algae and chlrorophytes, the number and identity of intron-containing nuclear tRNA genes is more variable and usually higher.…”

“…(6) (7) (8) (9)). These genes are either scattered or clustered throughout the genomes (10) (11). Their number greatly varies between the nuclear genomes of eukaryotes (8), and likely their genomic distribution varies as well but this remains poorly explored.…”