Biology subjects

Hummel, G.

Publications and source records attributed to Hummel, G..

3 recordsLinked to original sources

bioRxiv2023

Transcriptional reactivation of the tRNASer/tRNATyr gene cluster in Arabidopsis thaliana root tip

Plants retain a repetitious tRNA gene content in their nuclear genome. How important are these individuals, how exactly plants orchestrate their usage, and for what purposes, is poorly understood. Arabidopsis thaliana chromosome 1 holds a cluster of tandemly repeated serine- and tyrosine-decoding tRNA genes (SYY cluster). They intersect with constitutive heterochromatin and are silenced in most parts of the plant. Yet, the natural conditions leading to their transcription remain unknown. Here, we resolve the tissular expression pattern of this cluster along seedling establishment. We show that the root cap columella and few adjacent lateral root cap cells are the main sources of SYY cluster tRNAs. The transcriptional reactivation of the SYY cluster occurs in these tissues although elevated DNA methylation levels. Furthermore, we evidence that these cells are able to accumulate high levels of a transgenic glycoprotein rich in serine, tyrosine, and proline, and that the CRISPR/Cas9 deletion of the SYY cluster alters the phenomenon. Altogether, our work sheds light on pioneering evidence of a developmental and cell-specific expression program for a plant tRNA gene. We provide new perspectives on the role of peculiar tRNA genes in conferring a potential for the high synthesis of glycoproteins in protective tissues of the meristem.

plant biology↗

bioRxiv2020

Epigenetic silencing of clustered tDNAs in Arabidopsis

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. Our data highlight that the combination of both genomic environment and epigenomic landscape contribute to fine tune the differential expression of dispersed versus clustered tDNAs in Arabidopsis.

plant biology↗

bioRxiv2019

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

Differences in tRNA expression have been implicated in a remarkable number of biological processes. There is growing evidence that tRNA genes can play dramatically different roles depending on both expression and post-transcriptional modification, yet sequencing tRNAs to measure abundance and detect modifications remains challenging. Their secondary structure and extensive post-transcriptional modifications interfere with RNA-seq library preparation methods and have limited the utility of high-throughput sequencing technologies. Here, we combine two modifications to standard RNA-seq methods by treating with the demethylating enzyme AlkB and ligating with tRNA-specific adapters in order to sequence tRNAs from four species of flowering plants, a group that has been shown to have some of the most extensive rates of post-transcriptional tRNA modifications. This protocol has the advantage of detecting full-length tRNAs and sequence variants that can be used to infer many post-transcriptional modifications. We used the resulting data to produce a modification index of almost all unique reference tRNAs in Arabidopsis thaliana, which exhibited many anciently conserved similarities with humans but also positions that appear to be \"hot spots\" for modifications in angiosperm tRNAs. We also found evidence based on northern blot analysis and droplet digital PCR that, even after demethylation treatment, tRNA-seq can produce highly biased estimates of absolute expression levels most likely due to biased reverse transcription. Nevertheless, the generation of full-length tRNA sequences with modification data is still promising for assessing differences in relative tRNA expression across treatments, tissues or subcellular fractions and help elucidate the functional roles of tRNA modifications.

molecular biology↗