Small RNA profiling in Chlamydomonas: insights into chloroplast RNA metabolism

Abstract : In Chlamydomonas reinhardtii, regulation of chloro-plast gene expression is mainly post-transcriptional. It requires nucleus-encoded transacting protein factors for maturation/stabilization (M factors) or translation (T factors) of specific target mRNAs. We used long-and small-RNA sequencing to generate a detailed map of the transcriptome. Clusters of sRNAs marked the 5 end of all mature mRNAs. Their absence in M-factor mutants reflects the protection of transcript 5 end by the cognate factor. Enzymatic removal of 5-triphosphates allowed identifying those cosRNA that mark a transcription start site. We detected another class of sRNAs derived from low abundance transcripts, antisense to mRNAs. The formation of antisense sRNAs required the presence of the complementary mRNA and was stimulated when translation was inhibited by chloramphenicol or lin-comycin. We propose that they derive from degradation of double-stranded RNAs generated by pairing of antisense and sense transcripts, a process normally hindered by the traveling of the ribosomes. In addition, chloramphenicol treatment, by freezing ri-bosomes on the mRNA, caused the accumulation of 32–34 nt ribosome-protected fragments. Using this 'in vivo ribosome footprinting', we identified the function and molecular target of two candidate transacting factors.
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Nucleic Acids Research, Oxford University Press, 2017, 45 (18), pp.10783 - 10799. 〈10.1093/nar/gkx668〉
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Marina Cavaiuolo, Richard Kuras, Francis‐andré Wollman, Yves Choquet, Olivier Vallon. Small RNA profiling in Chlamydomonas: insights into chloroplast RNA metabolism. Nucleic Acids Research, Oxford University Press, 2017, 45 (18), pp.10783 - 10799. 〈10.1093/nar/gkx668〉. 〈hal-01629554〉

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