A game of tag: MAPS catches up on RNA interactomes

Carrier, Marie-Claude; Lalaouna, David; Massé, Éric

doi:10.1080/15476286.2016.1156830

Cited by 17 publications

(20 citation statements)

References 39 publications

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“…The above data confirm the ability of the LIGR-seq technique to identify new potential sRNA–mRNA interactions in bacteria. This method is complementary to those focusing on individual RNAs such as MAPS ( 54 ) or those based on specific RNA binding proteins such as RIL-seq ( 23 ) or CLASH ( 25 ), but has the advantage of not requiring prior knowledge about the different partners.…”

Section: Resultsmentioning

confidence: 99%

Identification of an RNA sponge that controls the RoxS riboregulator of central metabolism in Bacillus subtilis

Durand

Callan-Sidat

McKeown

et al. 2021

Nucleic Acids Research

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sRNAs are a taxonomically-restricted but transcriptomically-abundant class of post-transcriptional regulators. While of major importance for adaption to the environment, we currently lack global-scale methodology enabling target identification, especially in species without known RNA hub proteins (e.g. Hfq). Using psoralen RNA cross-linking and Illumina-sequencing we identify RNA–RNA interacting pairs in vivo in Bacillus subtilis, resolving previously well-described interactants. Although sRNA–sRNA pairings are rare (compared with sRNA–mRNA), we identify a robust example involving the conserved sRNA RoxS and an unstudied sRNA RosA (Regulator of sRNA A). We show RosA to be the first confirmed RNA sponge described in a Gram-positive bacterium. RosA interacts with at least two sRNAs, RoxS and FsrA. The RosA/RoxS interaction not only affects the levels of RoxS but also its processing and regulatory activity. We also found that the transcription of RosA is repressed by CcpA, the key regulator of carbon-metabolism in B. subtilis. Since RoxS is already known to be transcriptionally controlled by malate via the transcriptional repressor Rex, its post-transcriptional regulation by CcpA via RosA places RoxS in a key position to control central metabolism in response to varying carbon sources.

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Section: Resultsmentioning

confidence: 99%

Identification of an RNA sponge that controls the RoxS riboregulator of central metabolism in Bacillus subtilis

Durand

Callan-Sidat

McKeown

et al. 2021

Nucleic Acids Research

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“…Besides sRNA pulse-expression, several alternative methods have been described to discover target genes of bacterial sRNAs. For instance, in the MAPS (MS2 affinity purification coupled with RNA-sequencing) approach an sRNA of interest is fused to a MS2 aptamer tag, purified from cell lysates and bound interaction partners are identified using RNA-seq (Carrier, Lalaouna, & Masse, 2016) (see chapter "On the prowl: An in vivo method to identify RNA partners of a sRNA" by Carrier, Morin, & Mass e). A related method is GRIL-seq (Global small noncoding RNA target identification by ligation and sequencing), which is based on the in vivo coexpression of an RNA ligase that fuses the sRNA to its targets.…”

Section: Discussionmentioning

confidence: 99%

Transcriptomic Approaches for Studying Quorum Sensing in Vibrio cholerae

Herzog

Papenfort

2018

Methods in Enzymology

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Transcriptome analysis using RNA-sequencing (RNA-seq) has now become the standard approach to determine the transcriptional output of an organism. Various modifications to this technology have been developed over the years, usually aiming to improve the annotation of transcript borders, or to identify novel classes of RNAs, such as small regulatory RNAs (sRNAs) and antisense transcripts. RNA-seq has also led to the identification of dozens of new sRNAs in the major human pathogen, Vibrio cholerae. Several of these sRNAs function in the context of a cell-to-cell communication process, called quorum sensing (QS). QS is key for pathogenicity and biofilm formation of V. cholerae and the

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“…An MS2-GST protein (MS2 protein fused to the Glutathione S-transferase protein) can also be used, instead of the MS2-GFP one, to pull-down the fusion RNA-MS2 complex through sepharose beads paired with GSH (MS2-TRAP) [93]. In addition, an MS2-MBP protein (MS2 protein fused to the Maltose Binding Protein) immobilized on an amylose resin can be employed to avoid the overexpression of the fusion protein into the cell [94,95]. After many washes and an elution of the associated-miRNAs, the identification and quantification phases have to be done.…”

Section: Ms2-ripmentioning

confidence: 99%

Definition and identification of small RNA sponges: Focus on miRNA sequestration

Migault

Donnou‐Fournet

Galibert

et al. 2017

Methods

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Targeting RNAs appears as an important opportunity to modulate biological processes. Here, we overviewed critical parameters implied in RNAs competition to bind small RNAs. These competitions influence small RNA availability and thereby gene expression and cell fate. We focused on the ability of RNAs to sequester small RNA, mainly the microRNAs (miRNAs) and proposed experimental workflows to demonstrate the existence and activity of RNA-sponge. From this basic science, we detailed tailored oligonucleotides, developed to challenge the binding of small RNA. In vitro and in vivo, these tailored oligonucleotides efficiently restore small RNA activity by preventing their sequestration on RNA-sponges.

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A game of tag: MAPS catches up on RNA interactomes

Cited by 17 publications

References 39 publications

Identification of an RNA sponge that controls the RoxS riboregulator of central metabolism in Bacillus subtilis

Identification of an RNA sponge that controls the RoxS riboregulator of central metabolism in Bacillus subtilis

Transcriptomic Approaches for Studying Quorum Sensing in Vibrio cholerae

Definition and identification of small RNA sponges: Focus on miRNA sequestration

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