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Genome-wide discovery of structured noncoding RNAs in bacteria
Shira Stav1, Ruben M Atilho2, Gayan Mirihana Arachchilage3
1Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, USA.
BMC Microbiology
|March 24, 2019
Summary
Researchers developed a computational pipeline to discover novel structured noncoding RNAs (ncRNAs), including rare riboswitches, in bacterial genomes. This method identified 30 new ncRNA motifs, advancing the search for these crucial regulatory elements.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Structured noncoding RNAs (ncRNAs) are vital for diverse biological processes.
- Riboswitches, a common class of bacterial ncRNAs, regulate metabolic and signaling pathways.
- Many novel riboswitch classes remain undiscovered, posing challenges for current detection methods.
Purpose of the Study:
- To develop an efficient computational pipeline for identifying novel structured ncRNAs.
- To overcome limitations in current bioinformatics techniques for detecting rare ncRNA candidates.
Main Methods:
- Utilized a computational search pipeline to analyze intergenic regions.
- Applied the pipeline to five bacterial genomes for ncRNA identification.
Main Results:
- Identified nearly 70 novel genetic elements, including 30 candidate ncRNA motifs.
- Discovered a novel riboswitch candidate involved in thiamin biosynthesis regulation.
Conclusions:
- The computational pipeline effectively identifies novel structured ncRNAs.
- Further genomic analysis will reveal more ncRNAs and expand understanding of bacterial and archaeal ncRNA diversity.
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