title: Identification of unknown RNA partners using MAPS.
abstract: Recent advances in high-throughput sequencing have led to an explosion in the rate of small regulatory RNAs (sRNAs) discovery among bacteria. However, only a handful of them are functionally characterized. Most of the time, little to no targets are known. In Lalaouna et al. (2015), we proposed a new technology to uncover sRNAs targetome, which is based on the MS2-affinity purification (MAPS). We were able to prove its efficiency by applying it on well-characterized sRNAs of Escherichia coli. Thereafter, we adapted the procedure to other kind of RNA (mRNAs and tRNA-derived RNA fragments) and bacteria (pathogenic or Gram-positive strains). Here, we clearly report all improvements and adjustments made to MAPS technology since it was originally reported.
authors.affiliation: Department of Biochemistry, RNA Group, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada.
authors.forename: David
authors.initials: D
authors.lastname: Lalaouna
authors.affiliation: Department of Biochemistry, RNA Group, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada.
authors.forename: Karine
authors.initials: K
authors.lastname: Prévost
authors.affiliation: Department of Biochemistry, RNA Group, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada.
authors.forename: Alex
authors.initials: A
authors.lastname: Eyraud
authors.affiliation: Department of Biochemistry, RNA Group, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada. Electronic address: eric.masse@usherbrooke.ca.
authors.forename: Eric
authors.initials: E
authors.lastname: Massé
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry / Q000378:metabolism; D020029:Base Pairing; D002846:Chromatography, Affinity / Q000379:methods; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000235:genetics* / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D017909:Levivirus / Q000737:chemistry; D058619:Maltose-Binding Proteins / Q000235:genetics / Q000378:metabolism; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D012329:RNA, Bacterial / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D058727:RNA, Small Untranslated / Q000235:genetics* / Q000378:metabolism; D012343:RNA, Transfer / Q000235:genetics / Q000378:metabolism; D011993:Recombinant Fusion Proteins / Q000235:genetics* / Q000378:metabolism; D014764:Viral Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: D052157:Aptamers, Nucleotide; D029968:Escherichia coli Proteins; D058619:Maltose-Binding Proteins; D012329:RNA, Bacterial; D012333:RNA, Messenger; D058727:RNA, Small Untranslated; D011993:Recombinant Fusion Proteins; D014764:Viral Proteins; D012343:RNA, Transfer
keywords: MS2-affinity purification; RNA sequencing (RNAseq); Small RNAs (sRNAs); Targetome; tRNA derived fragments (tRFs)