RNA modification 5-methylcytosine (m5C) is associated with small RNA biogenesis in Arabidopsis thaliana

Small RNAs (sRNAs) are essential in regulating the development in plants and animals. While the biogenesis pathways of many sRNAs is clear, the biogenesis pathway for novel small RNAs like tRNA- and rRNA-derived fragments (tRFs and rRFs) is less so. Many diverse cellular RNAs including mRNAs, long-non-coding RNAs, tRNAs and rRNAs in plants have covalent post-transcriptional modifications and their function is only starting to be elucidated. Here, we determine if the RNA modification 5-methylcytosine (m⁵C) plays a role in sRNA biogenesis in Arabidopsis thaliana. To this effect, we Illumina-sequenced sRNAs from wild type and m5C methyltransferase mutant tRNA methyltransferase 4b (trm4b). Our bioinformatics analysis identified 158 sRNAs loci that increased in abundance and two sRNA loci that decreased in abundance in the trm4b compared to the wild type control. Comparison with RNA bisulphite sequencing data confirmed that most of the top differentially abundant sRNAs have m⁵C sites. In summary, our results suggest that m⁵C RNA modifications is associated with sRNA biogenesis in Arabidopsis thaliana.