Navigation through the twists and turns of RNA sequencing technologies: Application to bacterial regulatory RNAs

Desgranges, Emma; Caldelari, Isabelle; Marzi, Stefano; Lalaouna, David

doi:10.1016/j.bbagrm.2020.194506

Cited by 14 publications

(17 citation statements)

References 103 publications

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“…Several recent reviews describe in detail the diversity of RNA-sequencing technologies developed for different aspects of regulatory RNA analysis [ 203 , 206 ]. Transcriptional start site (TSS) mapping by differential RNA-seq (dRNA-seq) or 5’-end RNA-seq, whole-transcript RNA-seq, small RNA sequencing (sRNA-seq), and Term-seq for 3’-end RNA mapping could be cited among the most powerful unbiased approaches for genome-wide sRNA identification [ 207 , 208 , 209 ].…”

Section: Strategies To Identify Tcs-associated Srnasmentioning

confidence: 99%

“…Experimental validation of in silico predicted sRNA targets is required since these bioinformatics analyses usually lead to a large number of potential targets with a substantial proportion of false positive predictions [ 234 ]. Direct sRNA target identification still remains a challenging task, but several new experimental approaches have been recently developed for unbiased sRNA target discovery (reviewed in [ 206 ]). Among them, MS2-affinity purification coupled with RNA sequencing (MAPS) [ 236 , 237 ] allows sensitive detection of direct sRNA targets by base-pairing with an sRNA of interest, while RIL-seq [ 238 ] and CLASH [ 239 ] are used for global sRNA–RNA interaction analysis and rely on the association of sRNA-target pairs with RNA-binding proteins.…”

Section: Strategies To Identify Tcs-associated Srnasmentioning

confidence: 99%

Section: Global Approaches For Srna Identificationmentioning

confidence: 99%

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Interplay between Regulatory RNAs and Signal Transduction Systems during Bacterial Infection

Piattelli

Peltier

Soutourina

2020

Genes

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The ability of pathogenic bacteria to stably infect the host depends on their capacity to respond and adapt to the host environment and on the efficiency of their defensive mechanisms. Bacterial envelope provides a physical barrier protecting against environmental threats. It also constitutes an important sensory interface where numerous sensing systems are located. Signal transduction systems include Two-Component Systems (TCSs) and alternative sigma factors. These systems are able to sense and respond to the ever-changing environment inside the host, altering the bacterial transcriptome to mitigate the impact of the stress. The regulatory networks associated with signal transduction systems comprise small regulatory RNAs (sRNAs) that can be directly involved in the expression of virulence factors. The aim of this review is to describe the importance of TCS- and alternative sigma factor-associated sRNAs in human pathogens during infection. The currently available genome-wide approaches for studies of TCS-regulated sRNAs will be discussed. The differences in the signal transduction mediated by TCSs between bacteria and higher eukaryotes and the specificity of regulatory RNAs for their targets make them appealing targets for discovery of new strategies to fight against multi-resistant bacteria.

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Section: Strategies To Identify Tcs-associated Srnasmentioning

confidence: 99%

Section: Strategies To Identify Tcs-associated Srnasmentioning

confidence: 99%

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Interplay between Regulatory RNAs and Signal Transduction Systems during Bacterial Infection

Piattelli

Peltier

Soutourina

2020

Genes

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“…Numerous characterizations of significant regulatory roles for sncRNA fragments excised from various types of ncRNAs other than miRNAs have now been reported(10–13). As new high-throughput small RNA sequencing strategies(25) continue to make small RNA-Seq faster and less expensive, there is a clear need for tools capable of digesting large amounts of small RNA-Seq data in order to detect and characterize all small RNA genes including specifically-excised small RNA fragments. Most existing tools (e.g., miRDeep(26), miRSpring(27), miRanalyzer(28), etc.)…”

Section: General Introductionmentioning

confidence: 99%

SALTS – SURFR (sncRNA) And LAGOOn (lncRNA) Transcriptomics Suite

Mv¹,

Houserova²,

Ym³

et al. 2021

Preprint

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The widespread utilization of high-throughput sequencing technologies has unequivocally demonstrated that eukaryotic transcriptomes consist primarily (>98%) of non-coding RNA (ncRNA) transcripts significantly more diverse than their protein-coding counterparts. ncRNAs are typically divided into two categories based on their length. (1) ncRNAs less than 200 nucleotides (nt) long are referred as small non-coding RNAs (sncRNAs) and include microRNAs (miRNAs), piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), transfer ribonucleic RNAs (tRNAs), etc., and the majority of these are thought to function primarily in controlling gene expression. That said, the full repertoire of sncRNAs remains fairly poorly defined as evidenced by two entirely new classes of sncRNAs only recently being reported, i.e., snoRNA-derived RNAs (sdRNAs) and tRNA-derived fragments (tRFs). (2) ncRNAs longer than 200 nt long are known as long ncRNAs (lncRNAs). lncRNAs represent the 2nd largest transcriptional output of the cell (behind only ribosomal RNAs), and although functional roles for several lncRNAs have been reported, most lncRNAs remain largely uncharacterized due to a lack of predictive tools aimed at guiding functional characterizations. Importantly, whereas the cost of high-throughput transcriptome sequencing is now feasible for most active research programs, tools necessary for the interpretation of these sequencings typically require significant computational expertise and resources markedly hindering widespread utilization of these datasets. In light of this, we have developed a powerful new ncRNA transcriptomics suite, SALTS, which is highly accurate, markedly efficient, and extremely user-friendly. SALTS stands for SURFR (sncRNA) And LAGOOn (lncRNA) Transcriptomics Suite and offers platforms for comprehensive sncRNA and lncRNA profiling and discovery, ncRNA functional prediction, and the identification of significant differential expressions among datasets. Notably, SALTS is accessed through an intuitive Web-based interface, can be used to analyze either user-generated, standard next-generation sequencing (NGS) output file uploads (e.g., FASTQ) or existing NCBI Sequence Read Archive (SRA) data, and requires absolutely no dataset pre-processing or knowledge of library adapters/oligonucleotides. SALTS constitutes the first publically available, Web-based, comprehensive ncRNA transcriptomic NGS analysis platform designed specifically for users with no computational background, providing a much needed, powerful new resource capable of enabling more widespread ncRNA transcriptomic analyses. The SALTS WebServer is freely available online at http://salts.soc.southalabama.edu.

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“…A small regulatory RNA (sRNA) named Lpr17 (Lppnc0140 in strain Paris) is encoded complementary to lpg0499 (45,46). sRNA are short RNA molecules involved in post-transcriptional regulation of genes required for virulence and response to various conditions such as sugar metabolism, iron homeostasis, and biofilm formation (47,48). Base-pairing sRNAs are the most common type of sRNA and they act by hybridising to their target mRNA.…”

Section: Introductionmentioning

confidence: 99%

Legionella pneumophila’s Tsp is important for surviving thermal stress in water and inside amoeba

Saoud

Mani

Faucher

2020

Preprint

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Legionella pneumophila (Lp) is an inhabitant of natural and man-made water systems where it replicates within amoebae and ciliates and survives within biofilms. When Lp-contaminated aerosols are breathed in, Lp will enter the lungs and infect human alveolar macrophages, causing a severe pneumonia known as Legionnaires Disease. Lp is often found in hot water distribution systems (HWDS), which are linked to nosocomial outbreaks. Heat treatment is used to disinfect HWDS and reduce the concentration of Lp. However, Lp is often able to recolonize these water systems, indicating an efficient heat-shock response. Tail-specific proteases (Tsp) are typically periplasmic proteases implicated in degrading aberrant proteins in the periplasm and important for surviving thermal stress. In this paper, we show that Tsp, encoded by the lpg0499 gene in Lp Philadelphia-1, is important for surviving thermal stress in water and for optimal infection of amoeba when a shift in temperature occurs during intracellular growth. Tsp is expressed in the post-exponential phase but repressed in the exponential phase. The cis-encoded small regulatory RNA Lpr17 shows opposite expression, suggesting that it represses translation of tsp. In addition, tsp is regulated by CpxR, a major regulator in Lp, in a Lpr17-independent manner. Deletion of CpxR also reduced the ability of Lp to survive heat shock. In conclusion, this study shows that Tsp is an important factor for the survival and growth of Lp in water systems.IMPORTANCELegionella pneumophila (Lp) is a major cause of nosocomial and community-acquired pneumonia. Lp is found in water systems including hot water distribution systems. Heat treatment is a method of disinfection often used to limit Lp’s presence in such systems; however, the benefit is usually short term as Lp is able to quickly recolonize these systems. Presumably, Lp respond efficiently to thermal stress, but so far not much is known about the genes involved. In this paper, we show that the Tail-specific protease (Tsp) and the two-component system CpxRA are required for resistance to thermal stress, when Lp is free in water and when it is inside host cells. Our study identifies critical systems for the survival of Lp in its natural environment under thermal stress.

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Navigation through the twists and turns of RNA sequencing technologies: Application to bacterial regulatory RNAs

Cited by 14 publications

References 103 publications

Interplay between Regulatory RNAs and Signal Transduction Systems during Bacterial Infection

Interplay between Regulatory RNAs and Signal Transduction Systems during Bacterial Infection

SALTS – SURFR (sncRNA) And LAGOOn (lncRNA) Transcriptomics Suite

Legionella pneumophila’s Tsp is important for surviving thermal stress in water and inside amoeba

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