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Highly Efficient Ligation of Small RNA Molecules for MicroRNA Quantitation by High-Throughput Sequencing
Published on: November 18, 2014
Stem-loops direct precise processing of 3' UTR-derived small RNA MicL.
Taylor B Updegrove1, Andrew B Kouse1, Katarzyna J Bandyra2
1Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892-5430, USA.
Nucleic Acids Research
|November 22, 2018
Summary
Tandem stem-loops downstream of the cleavage site are key for precise bacterial small regulatory RNA (sRNA) processing by RNase E. Different sRNAs show varied sensitivity to this enzyme.
Area of Science:
- Bacteriology
- Molecular Biology
- RNA Biology
Background:
- Small regulatory RNAs (sRNAs) derived from 3' untranslated regions (3'UTRs) are increasingly identified in bacteria.
- RNase E, a major endoribonuclease in enterobacteria, is implicated in processing these sRNAs from longer transcripts.
- Previous research on RNase E processing determinants has yielded conflicting conclusions.
Purpose of the Study:
- To elucidate the sequence and structural determinants governing the precise processing of 3'UTR-derived sRNAs.
- To investigate the role of downstream elements in the cleavage of the MicL sRNA by RNase E.
Main Methods:
- In vivo and in vitro cleavage assays were performed on mutant and chimeric derivatives of the MicL sRNA.
- Analysis of RNase E sensitivity across multiple sRNAs, including MicL, ArcZ, and CpxQ.
Main Results:
- Tandem stem-loops located 3' to the cleavage site were identified as critical for optimal and correctly positioned cleavage of MicL.
- The study demonstrated differential sensitivity of MicL, ArcZ, and CpxQ to RNase E.
- These findings suggest a hierarchy of sRNA features influencing endonuclease recognition.
Conclusions:
- Optimal processing of bacterial 3'UTR-derived sRNAs by RNase E is significantly influenced by tandem stem-loop structures downstream of the cleavage site.
- Bacterial sRNAs exhibit distinct sensitivities to RNase E, reflecting a complex recognition mechanism by the enzyme.
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