Strand-specific RNA sequencing uncovers chloroplast ribonuclease functions

Organellar gene expression incorporates ribonucleases as indispensable participants. Here, we explored the capacity of strand-specific RNA sequencing (RNA-Seq) as a tool to analyze chloroplast ribonuclease functions using the 3′→5′ exoribonuclease polynucleotide phosphorylase (PNPase) as a proof of concept. The role of PNPase in transcript 3′ end maturation was easily monitored, and additional targeted mRNAs were discovered. Moreover, a role in tRNA precursor degradation was predicted and validated. These results, together with previously published data, suggest that RNA-Seq represents a unique opportunity to decipher the roles of organellar ribonucleases and deepen our understanding of chloroplast gene expression.