title: Identifying and characterizing Hfq-RNA interactions.
abstract: To regulate stress responses and virulence, bacteria use small regulatory RNAs (sRNAs). These RNAs can up or down regulate target mRNAs through base pairing by influencing ribosomal access and RNA decay. A large class of these sRNAs, called trans-encoded sRNAs, requires the RNA binding protein Hfq to facilitate base pairing between the regulatory RNA and its target mRNA. The resulting network of regulation is best characterized in Escherichia coli and Salmonella typhimurium, but the importance of Hfq dependent sRNA regulation is recognized in a diverse population of bacteria. In this review we present the approaches and methods used to discover Hfq binding RNAs, characterize their interactions and elucidate their functions.
authors.affiliation: Department of Chemistry, Wayne State University, 5101 Cass Ave., Detroit, MI, United States.
authors.forename: M A
authors.initials: MA
authors.lastname: Faner
authors.forename: A L
authors.initials: AL
authors.lastname: Feig
mesh_terms: D001419:Bacteria / Q000235:genetics* / Q000378:metabolism; D024202:Electrophoretic Mobility Shift Assay; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D035001:Host Factor 1 Protein / Q000302:isolation & purification / Q000378:metabolism*; D047468:Immunoprecipitation; D008958:Models, Molecular; D011485:Protein Binding; D040901:Proteomics; D012329:RNA, Bacterial / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D058727:RNA, Small Untranslated / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D052156:SELEX Aptamer Technique
chemical_list: D035001:Host Factor 1 Protein; D012329:RNA, Bacterial; D058727:RNA, Small Untranslated
keywords: (ARN)(x); 2-methylnicotinic acid imidizolide; 5′ phosphate dependent terminator endonuclease; 5′ rapid amplification of cDNA ends; 5′RACE; CLIP; CLR; EMSA; HTS; Hfq; ITC; LC–MS; MALDI-TOF; MAST; MEME; N-methylisatoic anhydride; NAI; NMIA; Protein–RNA interactions; RNP; RT; SELEX; SHAPE; SPR; TBE; TEX; Tris/Borate/EDTA; co-IP; coimmunoprecipitation; context likelihood of relatedness; cross-linking and immunoprecipitation; electrophoretic mobility gel shift assay; high through-put sequencing; isothermal titration calorimetry; liquid chromatography–mass spectrometry; matrix-assisted laser desorption/ionization time-of-flight; motif alignment and search tool; multiple em for motif elicitation; ncRNA; qRT-PCR; quantitative reverse transcription polymerase chain reaction; reverse transcription; ribonucleoprotein; sRNA; sRNAs; selective 2′-hydroxyl acylation analyzed by primer extension; small regulatory RNAs; surface plasmon resonance; systematic evolution of ligands by exponential enrichment; where A is adenine, R is adenine or guanosine, and N is any nucleotide