Terminome-seq

Terminome-seq maps chloroplast transcript termini in Arabidopsis thaliana to catalog primary and processed 5' and 3' ends and to study RNA processing and regulation.

Key Features:

• Systematic Mapping: Identifies both 5' and 3' termini, reporting 215 primary transcription start sites (TSS), 1628 processed 5' ends, and 1299 3' ends.
• Location Diversity: Locates termini in intergenic regions, within coding sequences, and in introns, including several major TSS at unexpected positions.
• Clustering of Terminations: Detects clustering of 5' and 3' termini, indicating imprecision in transcription initiation or RNA processing.
• Correlation with RNA Structures: Finds many termini that correlate with small RNA footprints or predicted stem-loop structures, consistent with passive RNA protection.
• Functional Insights from Mutants: Applied to the pnp1-1 mutant lacking polynucleotide phosphorylase, revealing nearly 2000 altered termini and implicating PNPase in shaping the transcriptome.

Scientific Applications:

• Chloroplast RNA biology: Provides a detailed map of chloroplast transcript ends in Arabidopsis thaliana to study RNA population diversity and stability.
• RNA processing and quality control studies: Enables analysis of the interplay between transcription initiation, RNA processing, and quality-control mechanisms.
• Functional genomics of organellar expression: Identifies mutation-dependent changes (e.g., pnp1-1) and unexpected TSS locations that inform models of organellar gene expression.

Methodology:

High-throughput sequencing of transcript ends to delineate transcription start sites and processed 5' and 3' ends.