tncRNAs

tncRNAs identifies and characterizes transfer RNA-derived non-coding RNAs (tncRNAs) from plant small RNA sequencing (small RNA-seq) datasets to analyze their sequences, positions, modifications, and expression.

Key Features:

• Identification: Detects tncRNAs ranging from 14 to 50 nucleotides (nt) across 2448 small RNA-seq samples from six angiosperms.
• Detailed annotation: Reports tncRNA type, associated tRNA details, position on the tRNA, strand orientation, sequence, and length.
• Quantification: Provides read counts and RPM (Reads Per Million) for tncRNA expression levels.
• Modification mapping: Identifies modification sites and conserved nucleoside modifications on tRNAs associated with tncRNA generation.
• Length and cleavage analysis: Analyzes length distributions and cleavage patterns of tncRNAs.
• Codon usage analysis: Evaluates codon usage to reveal codon-dependent patterns of tncRNA generation.
• Endoribonucleolytic cleavage inference: Supports inference of specific endoribonucleolytic cleavage mechanisms based on cleavage pattern analysis.
• Differential expression: Detects tncRNAs exhibiting differential expression under abiotic and biotic stresses.
• Tissue-specific clustering: Identifies tissue-specific tncRNA clusters implicating developmental roles.
• Pathway enrichment: Enables identification of common tncRNA targets enriched in metabolic and developmental pathways.

Scientific Applications:

• Gene Regulation: Investigates how conserved nucleoside modifications and cleavage patterns influence tRNA cleavage and tncRNA functionality in plants.
• Pathway Enrichment Analysis: Identifies metabolic and developmental pathways enriched for common tncRNA targets.
• Stress Response: Characterizes tncRNAs that are differentially expressed under abiotic and biotic stresses to study stress-related regulatory roles.
• Developmental Biology: Examines tissue-specific tncRNA clusters to explore roles in plant growth and development.

Methodology:

The pipeline analyzes 2448 small RNA-seq samples from six angiosperms to identify tncRNAs of 14–50 nt, annotates tncRNA type, associated tRNA, position, strand, sequence, length, read counts and RPM, maps modification sites, and performs analyses of length distribution, codon usage, cleavage patterns and modified nucleosides.