title: Strand-specific RNA sequencing uncovers chloroplast ribonuclease functions.
abstract: 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.
authors: Boyce Thompson Institute for Plant Research, Ithaca, NY 14853-1801, USA.
authors: Benoît
authors: B
authors: Castandet
authors: Amber M
authors: AM
authors: Hotto
authors: Zhangjun
authors: Z
authors: Fei
authors: David B
authors: DB
authors: Stern
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism*; D002736:Chloroplasts / Q000235:genetics / Q000378:metabolism*; D005095:Exoribonucleases / Q000235:genetics / Q000378:metabolism*; D018506:Gene Expression Regulation, Plant; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism*; D012322:RNA Precursors / Q000235:genetics / Q000378:metabolism; D018747:RNA, Chloroplast / Q000235:genetics / Q000378:metabolism*; D012343:RNA, Transfer / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods; D024363:Transcription Initiation Site; D061785:Transcription Initiation, Genetic; D020506:Untranslated Regions
chemical_list: D010940:Plant Proteins; D012322:RNA Precursors; D018747:RNA, Chloroplast; D020506:Untranslated Regions; D012343:RNA, Transfer; D005095:Exoribonucleases
keywords: Chloroplast; PNPase; RNA maturation; RNA-Seq; Ribonuclease; tRNA