S. Y. Tong, J. S. Davis, E. Eichenberger, T. L. Holland, V. G. Fowler et al., Staphylococcus aureus Infections: Epidemiology, Pathophysiology, Clinical Manifestations, and Management, Clinical Microbiology Reviews, vol.28, issue.3, pp.603-6611000134, 1128.
DOI : 10.1128/CMR.00134-14

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4451395

I. Caldelari, Y. Chao, P. Romby, and J. Vogel, RNA-mediated regulation in pathogenic bacteria. Cold Spring Harb Perspect Med 3, 2013.
DOI : 10.1101/cshperspect.a010298

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753719

E. G. Wagner and P. Romby, Small RNAs in Bacteria and Archaea, Adv Genet, vol.90, pp.133-208, 2015.
DOI : 10.1016/bs.adgen.2015.05.001

A. Jousselin, L. Metzinger, and B. Felden, On the facultative requirement of the bacterial RNA chaperone, Hfq, Trends in Microbiology, vol.17, issue.9, pp.399-405, 2009.
DOI : 10.1016/j.tim.2009.06.003

URL : https://hal.archives-ouvertes.fr/inserm-00712130

G. Storz, J. Vogel, and K. M. Wassarman, Regulation by Small RNAs in Bacteria: Expanding Frontiers, Molecular Cell, vol.43, issue.6, pp.880-891, 2011.
DOI : 10.1016/j.molcel.2011.08.022

URL : http://doi.org/10.1016/j.molcel.2011.08.022

T. Mizuno, M. Y. Chou, and M. Inouye, A unique mechanism regulating gene expression: translational inhibition by a complementary RNA transcript (micRNA)., Proceedings of the National Academy of Sciences, vol.81, issue.7, pp.1966-1970, 1984.
DOI : 10.1073/pnas.81.7.1966

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC345405/pdf

R. P. Novick, S. Iordanescu, S. J. Projan, J. Kornblum, and I. Edelman, plasmid replication is regulated by a countertranscriptdriven transcriptional attenuator, Cell, vol.59, issue.89, pp.181-395, 1989.
DOI : 10.1016/0092-8674(89)90300-0

L. F. Abu-qatouseh, Identification of differentially expressed small non-protein-coding RNAs in Staphylococcus aureus displaying both the normal and the small-colony variant phenotype, Journal of Molecular Medicine, vol.42, issue.6, pp.565-57510, 2010.
DOI : 10.1007/s00109-010-0597-2

K. L. Anderson, Characterization of the Staphylococcus aureus Heat Shock, Cold Shock, Stringent, and SOS Responses and Their Effects on Log-Phase mRNA Turnover, Journal of Bacteriology, vol.188, issue.19, pp.6739-67561886739, 2006.
DOI : 10.1128/JB.00609-06

M. Beaume, Cartography of Methicillin-Resistant S. aureus Transcripts: Detection, Orientation and Temporal Expression during Growth Phase and Stress Conditions, PLoS ONE, vol.191, issue.5, 2010.
DOI : 10.1371/journal.pone.0010725.s005

URL : https://hal.archives-ouvertes.fr/hal-00526375

C. Bohn, Experimental discovery of small RNAs in Staphylococcus aureus reveals a riboregulator of central metabolism, Nucleic Acids Research, vol.38, issue.19, pp.6620-6636, 2010.
DOI : 10.1093/nar/gkq462

URL : https://hal.archives-ouvertes.fr/hal-00534360

T. Geissmann, A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation, Nucleic Acids Research, vol.37, issue.21, pp.7239-7257, 2009.
DOI : 10.1093/nar/gkp668

URL : https://hal.archives-ouvertes.fr/hal-00451250

B. P. Howden, Analysis of the Small RNA Transcriptional Response in Multidrug-Resistant Staphylococcus aureus after Antimicrobial Exposure, Antimicrobial Agents and Chemotherapy, vol.57, issue.8, pp.3864-387410, 2013.
DOI : 10.1128/AAC.00263-13

U. Mader, Staphylococcus aureus Transcriptome Architecture: From Laboratory to Infection-Mimicking Conditions, PLOS Genetics, vol.80, issue.Suppl 5, 2016.
DOI : 10.1371/journal.pgen.1005962.s013

A. Marchais, C. Bohn, P. Bouloc, and D. Gautheret, RsaOG, a new Staphylococcal family of highly transcribed non-coding RNA, RNA Biology, vol.7, issue.2, pp.116-119, 2010.
DOI : 10.4161/rna.7.2.10925

URL : https://hal.archives-ouvertes.fr/hal-00506399

J. M. Morrison, Characterization of SSR42, a Novel Virulence Factor Regulatory RNA That Contributes to the Pathogenesis of a Staphylococcus aureus USA300 Representative, Journal of Bacteriology, vol.194, issue.11, pp.2924-293806708, 2012.
DOI : 10.1128/JB.06708-11

C. Pichon and B. Felden, From The Cover: Small RNA genes expressed from Staphylococcus aureusgenomic and pathogenicity islands with specific expression among pathogenic strains, Proceedings of the National Academy of Sciences, vol.48, issue.6, pp.14249-142540503838102, 2005.
DOI : 10.1046/j.1365-2958.2003.03526.x

C. Roberts, Characterizing the Effect of the Staphylococcus aureus Virulence Factor Regulator, SarA, on Log-Phase mRNA Half-Lives, Journal of Bacteriology, vol.188, issue.7, pp.2593-2603, 2006.
DOI : 10.1128/JB.188.7.2593-2603.2006

T. Xue, X. Zhang, H. Sun, and B. Sun, ArtR, a novel sRNA of Staphylococcus aureus, regulates ??-toxin expression by targeting the 5??? UTR of sarT mRNA, Medical Microbiology and Immunology, vol.79, issue.6, pp.1-12, 2014.
DOI : 10.1128/IAI.01180-10

R. K. Carroll, Genome-wide Annotation, Identification, and Global Transcriptomic Analysis of Regulatory or Small RNA Gene Expression in Staphylococcus aureus, MBio, vol.7, issue.10, pp.1990-2005, 1128.

M. Sassi, regulatory RNA database, RNA, vol.21, issue.5, pp.1005-1017114, 2015.
DOI : 10.1261/rna.049346.114

URL : https://hal.archives-ouvertes.fr/inserm-01136506

T. Baba, T. Bae, O. Schneewind, F. Takeuchi, and K. Hiramatsu, Genome Sequence of Staphylococcus aureus Strain Newman and Comparative Analysis of Staphylococcal Genomes: Polymorphism and Evolution of Two Major Pathogenicity Islands, Journal of Bacteriology, vol.190, issue.1, pp.300-31001000, 2008.
DOI : 10.1128/JB.01000-07

N. Sayed, A. Jousselin, and B. Felden, A cis-antisense RNA acts in trans in Staphylococcus aureus to control translation of a human cytolytic peptide, Nature Structural & Molecular Biology, vol.1, issue.1, pp.105-11210, 2012.
DOI : 10.1038/nprot.2006.4

URL : https://hal.archives-ouvertes.fr/inserm-00696345

L. Pabic, H. Germain-amiot, N. Bordeau, V. Felden, and B. , A bacterial regulatory RNA attenuates virulence, spread and human host cell phagocytosis, Nucleic acids research, vol.43, pp.9232-924810, 2015.
URL : https://hal.archives-ouvertes.fr/inserm-01194696

M. Kathirvel, H. Buchad, and M. Nair, Enhancement of the pathogenicity of Staphylococcus aureus strain Newman by a small noncoding RNA SprX1, Medical Microbiology and Immunology, vol.193, issue.6, pp.10-1007, 2016.
DOI : 10.1128/JB.00027-11

C. Toffano-nioche, Detection of non-coding RNA in bacteria and archaea using the DETR???PROK Galaxy pipeline, Methods, vol.63, issue.1, pp.60-65, 2013.
DOI : 10.1016/j.ymeth.2013.06.003

T. Bae, Staphylococcus aureus virulence genes identified by bursa aurealis mutagenesis and nematode killing, Proceedings of the National Academy of Sciences, vol.50, issue.2, pp.12312-12317, 2004.
DOI : 10.1073/pnas.0730515100

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC514475

E. S. Duthie and L. L. Lorenz, Staphylococcal Coagulase: Mode of Action and Antigenicity, Microbiology, vol.6, issue.1-2, pp.95-10710, 1952.
DOI : 10.1099/00221287-6-1-2-95

S. Anders, P. T. Pyl, and W. Huber, HTSeq -A Python framework to work with high-throughput sequencing data, Bioinformatics, vol.doi, p.638, 2014.

S. Anders and W. Huber, Differential expression analysis for sequence count data, Genome Biol, vol.11, 2010.
DOI : 10.1038/npre.2010.4282.1

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218662/pdf

A. Mortazavi, B. A. Williams, K. Mccue, L. Schaeffer, and B. Wold, Mapping and quantifying mammalian transcriptomes by RNA-Seq, Nature Methods, vol.14, issue.7, pp.621-62810, 2008.
DOI : 10.1128/MCB.14.3.1647

T. Carver, S. R. Harris, M. Berriman, J. Parkhill, and J. A. Mcquillan, Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data, Bioinformatics, vol.28, issue.4, pp.464-46910, 2012.
DOI : 10.1093/bioinformatics/btr703

G. Marincola, and its role in the activation of virulence genes, Molecular Microbiology, vol.193, issue.5, pp.817-832, 2012.
DOI : 10.1128/JB.05939-11

M. Sassi, B. Felden, and Y. Augagneur, Draft Genome Sequence of Staphylococcus aureus subsp. aureus Strain HG003, an NCTC8325 Derivative, Genome Announcements, vol.2, issue.4, pp.10-1128, 2014.
DOI : 10.1128/genomeA.00855-14

URL : https://hal.archives-ouvertes.fr/inserm-01059715

M. Sassi, D. Sharma, S. R. Brinsmade, B. Felden, and Y. Augagneur, Genome Sequence of the Clinical Isolate Staphylococcus aureus subsp. aureus Strain UAMS-1, Genome Announcements, vol.3, issue.1, pp.10-1128, 2015.
DOI : 10.1128/genomeA.01584-14

URL : https://hal.archives-ouvertes.fr/inserm-01123874

B. A. Diep, Complete genome sequence of USA300, an epidemic clone of community-acquired meticillin-resistant Staphylococcus aureus, The Lancet, vol.367, issue.9512, pp.731-73910, 2006.
DOI : 10.1016/S0140-6736(06)68231-7

M. Kuroda, Whole genome sequencing of meticillin-resistant Staphylococcus aureus, The Lancet, vol.357, issue.9264, pp.1225-1240, 2001.
DOI : 10.1016/S0140-6736(00)04403-2

I. Lasa, Genome-wide antisense transcription drives mRNA processing in bacteria, Proceedings of the National Academy of Sciences, vol.39, issue.7, pp.20172-201771113521108, 2011.
DOI : 10.1093/nar/gkr012

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3250193

M. L. Pinel-marie, R. Brielle, and B. Felden, Dual Toxic-Peptide-Coding Staphylococcus aureus RNA under Antisense Regulation Targets Host Cells and Bacterial Rivals Unequally, Cell Reports, vol.7, issue.2, pp.424-435, 2014.
DOI : 10.1016/j.celrep.2014.03.012

URL : https://hal.archives-ouvertes.fr/inserm-00976764

D. Gautheret and A. Lambert, Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles 1 1Edited by J. Doudna, Journal of Molecular Biology, vol.313, issue.5, pp.1003-10115102, 2001.
DOI : 10.1006/jmbi.2001.5102

V. J. Torres, G. Pishchany, M. Humayun, O. Schneewind, and E. P. Skaar, Staphylococcus aureus IsdB Is a Hemoglobin Receptor Required for Heme Iron Utilization, Journal of Bacteriology, vol.188, issue.24, pp.8421-842910, 2006.
DOI : 10.1128/JB.01335-06

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1698231

I. Biswas, J. K. Jha, and N. Fromm, Shuttle expression plasmids for genetic studies in Streptococcus mutans, Microbiology, vol.154, issue.8, pp.2275-2282019265, 2008.
DOI : 10.1099/mic.0.2008/019265-0

S. Li, Phenol-soluble modulins: novel virulence-associated peptides of staphylococci, Future Microbiology, vol.9, issue.2, pp.203-216, 2014.
DOI : 10.2217/fmb.13.153

A. Peschel and M. Otto, Phenol-soluble modulins and staphylococcal infection, Nature Reviews Microbiology, vol.39, issue.10, pp.667-673, 2013.
DOI : 10.1042/BST0390807

J. Song, The Expression of Small Regulatory RNAs in Clinical Samples Reflects the Different Life Styles of Staphylococcus aureus in Colonization vs. Infection, PLoS ONE, vol.55, issue.2, 2012.
DOI : 10.1371/journal.pone.0037294.s003

A. Eyraud, P. Tattevin, S. Chabelskaya, and B. Felden, A small RNA controls a protein regulator involved in antibiotic resistance in Staphylococcus aureus, Nucleic Acids Research, vol.42, issue.8, p.149, 2014.
DOI : 10.1093/nar/gku149

URL : https://hal.archives-ouvertes.fr/inserm-00951043

D. M. Aanensen, ABSTRACT, mBio, vol.7, issue.3, pp.444-460, 1128.
DOI : 10.1128/mBio.00444-16

L. Li, BSRD: a repository for bacterial small regulatory RNA, Nucleic Acids Research, vol.41, issue.D1, pp.233-23810, 2013.
DOI : 10.1093/nar/gks1264

URL : http://doi.org/10.1093/nar/gks1264

E. P. Nawrocki, Rfam 12.0: updates to the RNA families database. Nucleic acids research 43, pp.130-13710, 2015.

P. Bengert and T. Dandekar, Riboswitch finder--a tool for identification of riboswitch RNAs, Nucleic Acids Research, vol.32, issue.Web Server, pp.154-15910, 2004.
DOI : 10.1093/nar/gkh352

R. M. Lacatena and G. Cesareni, Base pairing of RNA I with its complementary sequence in the primer precursor inhibits ColE1 replication, Nature, vol.43, issue.5842, pp.623-626, 1981.
DOI : 10.1101/SQB.1979.043.01.013

M. Wight and A. Werner, The functions of natural antisense transcripts, Essays In Biochemistry, vol.12, pp.91-10110, 2013.
DOI : 10.1042/BST0381144

M. Overgaard, J. Borch, and K. Gerdes, RelB and RelE of Escherichia coli Form a Tight Complex That Represses Transcription via the Ribbon???Helix???Helix Motif in RelB, Journal of Molecular Biology, vol.394, issue.2, pp.183-196, 2009.
DOI : 10.1016/j.jmb.2009.09.006

M. A. Griffin, J. H. Davis, and S. A. Strobel, Bacterial Toxin RelE: A Highly Efficient Ribonuclease with Exquisite Substrate Specificity Using Atypical Catalytic Residues, Biochemistry, vol.52, issue.48, pp.8633-864210, 2013.
DOI : 10.1021/bi401325c

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3910103

G. Y. Li, Y. Zhang, M. Inouye, and M. Ikura, RelE-RelB Toxin-Antitoxin Module Involves a Helix Displacement Near an mRNA Interferase Active Site, Journal of Biological Chemistry, vol.1, issue.21, pp.14628-1463610, 2009.
DOI : 10.1107/S0907444902010090

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2682910

P. Kumari and K. Sampath, cncRNAs: Bi-functional RNAs with protein coding and non-coding functions, Seminars in Cell & Developmental Biology, vol.47, issue.48, pp.47-48, 2015.
DOI : 10.1016/j.semcdb.2015.10.024

URL : http://doi.org/10.1016/j.semcdb.2015.10.024

C. K. Vanderpool, D. Balasubramanian, and C. R. Lloyd, Dual-function RNA regulators in bacteria, Biochimie, vol.93, issue.11, 1943.
DOI : 10.1016/j.biochi.2011.07.016

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3185123

H. Li, The Sequence Alignment/Map format and SAMtools, Bioinformatics, vol.25, issue.16, pp.2078-2079, 2009.
DOI : 10.1093/bioinformatics/btp352

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723002

K. Kuwahara-arai, N. Kondo, S. Hori, E. Tateda-suzuki, and K. Hiramatsu, Suppression of methicillin resistance in a mecAcontaining pre-methicillin-resistant Staphylococcus aureus strain is caused by the mecI-mediated repression of PBP 2? production, Antimicrobial agents and chemotherapy, vol.40, pp.2680-2685, 1996.

S. Herbert, Repair of Global Regulators in Staphylococcus aureus 8325 and Comparative Analysis with Other Clinical Isolates, Infection and Immunity, vol.78, issue.6, pp.2877-288910, 2010.
DOI : 10.1128/IAI.00088-10

B. N. Kreiswirth, The toxic shock syndrome exotoxin structural gene is not detectably transmitted by a prophage, Nature, vol.72, issue.5936, pp.709-712, 1983.
DOI : 10.1093/infdis/143.4.509

N. Sayed, S. Nonin-lecomte, S. Rety, and B. Felden, Apoptotic-like Membrane Peptide from a Toxin-Antitoxin Module, Journal of Biological Chemistry, vol.23, issue.52, pp.43454-4346310, 2012.
DOI : 10.1021/bi1005128

URL : https://hal.archives-ouvertes.fr/inserm-00762197