Transfer RNA-derived non-coding RNAs (tncRNAs): Uncovering hidden regulators of transcriptional regulatory circuits in plants

Abstract The lateral emergence of distinct classes of non-coding RNAs has led to better insights into the eukaryotic regulatory networks. Among them, the existence of transfer RNA (tRNA)-derived non-coding RNAs (tncRNAs) demands their exploration in the plant kingdom. Here, we have designed a methodology to uncover the bigger picture of tncRNAome in plants. Using this, we have identified diverse tncRNAs of length 14-50 nt in ~2500 small RNA sequencing (sRNA-seq) samples of six major angiosperms, and further studied their various features including length, codon-usage, cleavage pattern, and modified tRNA nucleosides. Codon-dependent generation of tncRNAs indicates that the process is highly specific rather than being mere random tRNA degradation. Analysis for nucleotide composition of tncRNA cleavage positions indicates that they are generated through precise endoribonucleolytic machinery. Certain tRNA nucleoside modifications on tncRNAs were found to be conserved across the plants, and hence may influence tRNA cleavage, as well as tncRNA functions. Pathway enrichment analysis revealed that common tncRNA targets were majorly involved in the metabolic and developmental processes of plants. Also, many tRFs were found to be associated with transposable elements. Distinct tissue-specific tncRNA clusters indicate their role in plant development under normal physiological conditions. Furthermore, the identification of a significant number of differentially expressed tncRNAs under several abiotic and biotic stresses highlights their probable role as gene expression modulators during various stress conditions. Thus, this study will be beneficial to investigate the emerging role of tncRNAs as prospective biomarkers in plant development and stress. Highlights Computational pipeline for accurate identification of genuine transfer RNA-derived non-coding RNAs (tncRNAs) using small RNA sequencing (sRNA-seq) datasets. Six major tncRNA classes of length ranging from 14 to 50 nt were identified in ~2,500 sRNA-seq datasets in six different angiosperms. tRNA nucleoside modifications may affect tncRNA cleavage in plants. Conserved tncRNAs target transcripts are involved in plant growth, development, and metabolism. tncRNAs are expressed in a tissue-dependent, and stress-specific manner in plants.