This master Project focused on an RNA degrading enzyme called RNase J in Staphylococcus aureus. This enzyme has two functions; degrading RNA from its 5' end (exonucleolitic activity) and cleaving RNA strands (endonucleolitic activity). This study focused on the exonucleolitic activity of the enzyme. The RNA-seq protocol was coupled to a time-course experiment where rifampicine was used to block cellular transcription. The whole experiment allowed studying degradation independently from transcription at a whole transcriptome scale in a wild-type strain compared to an RNase J knock out strain. Bioinformatics was used to analyze the results at Open Reading Frame level but also at single base resolution. The analysis per ORF showed that RNase J is a main degrading enzyme in S.aureus, affecting a vast majority of transcripts' stability. Studying the half-life at single base resolution of several individual transcripts revealed non linear degradation of some RNA in the absence of RNase J. The integration of EMOTE data, that detects cleavages in RNA, showed that RNase J has primordial function in the degradation of pre-cleaved RNA. Indeed we could observe that the absence of RNase J induced very high half-life of the downstream piece of a cleaved RNA.