Abstract
Novel motifs identified in a comparative genomic analysis of bacterial, archaeal and metagenomic data reveals over 100 candidate structured RNAs.
Highlights
Structured noncoding RNAs perform many functions that are essential for protein synthesis, RNA processing, and gene regulation
The predicted RNAs exhibit a great diversity of conserved sequences and structural features, and their genomic locations are indicative of a wide variety of mechanisms of action and putative biologic roles
Our findings suggest that the bacterial and archaeal domains of life will continue to be a rich source of novel structured RNAs
Summary
Structured noncoding RNAs perform many functions that are essential for protein synthesis, RNA processing, and gene regulation. Ongoing efforts to identify and characterize various structured noncoding RNAs from bacteria are revealing the remarkable functions that structured RNAs can perform [1,2,3]. In our recent efforts to identify novel structured RNAs, we applied a scheme based on detecting RNA secondary structures upstream of homologous protein-coding genes [13,14]. This strategy is best suited to finding cis-regulatory RNAs, not noncoding RNAs. some cis-regulatory RNAs such as c-di-. The resulting alignments are scored and analyzed manually to identify the most promising candidates and to infer possible biologic roles
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