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Published on: July 9, 2021

Identifying and characterizing Hfq-RNA interactions

M A Faner¹, A L Feig

¹Department of Chemistry, Wayne State University, 5101 Cass Ave., Detroit, MI, United States.

Methods (San Diego, Calif.)

|May 28, 2013

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.

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

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