Identification of novel small RNAs using comparative genomics and microarrays.

By K. Wassarman, Francis Repoila, Carsten Rosenow, Gisela Storz, Susan Gottesman. Genes & Development, 2001

750 citations recorded by the source corpus.

A burgeoning list of small RNAs with a variety of regulatory functions has been identified in both prokaryotic and eukaryotic cells. However, it remains difficult to identify small RNAs by sequence inspection. We used the high conservation of small RNAs among closely related bacterial species, as well as analysis of transcripts detected by high-density oligonucleotide probe arrays, to predict the presence of novel small RNA genes in the intergenic regions of the Escherichia coli genome. The existence of 23 distinct new RNA species was confirmed by Northern analysis. Of these, six are predicted to encode short ORFs, whereas 17 are likely to be novel functional small RNAs. We discovered that many of these small RNAs interact with the RNA-binding protein Hfq, pointing to a global role of the Hfq protein in facilitating small RNA function. The approaches used here should allow identification of small RNAs in other organisms.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/ff20694e945df96f05b93eb5bd98209fda1a7a3f

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Citations in the corpus

Non–coding RNA genes and the modern RNA world (2001, background): “Karen Wassarman et al. 20 looked for intergenic regions that showed conservation to other genomes.”
The microRNAs of Caenorhabditis elegans. (2003, background): “Recent advances have been made in the computational identification of ncRNA genes through comparative genomics, and complex algorithms have been developed to identify ncRNAs in general (Argaman et al. 2001; Rivas et al. 2001; Wassarman et al. 2001), as well as specific ncRNA families such as tRNAs a”
Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification (2021, background): “…for improvements regarding the following issues: (i) despite the discovery of previously overlooked conserved short ORFs (sORFs) two decades ago [13], they neither predict nor detect coding sequences (CDSs) of nowadays well-known small proteins shorter than 29 amino acids, due to technical gene…”
DNA Microarray-Mediated Transcriptional Profiling of the Escherichia coli Response to Hydrogen Peroxide (2001, background): “Given the unusually high conservation of the sufA-ydiH intragenic region ( 34 ), it is likely that the regulation of sufA expression is complex.”
σE Regulates and Is Regulated by a Small RNA in Escherichia coli (2007, background): “Steady-state levels of RybB could be detected only in stationary phase in rich media (57, 62).”
Systematic deletion of Salmonella small RNA genes identifies CyaR, a conserved CRP‐dependent riboregulator of OmpX synthesis (2008, background): “Comparison with co-migrating size markers (not shown) strongly suggests that CyaR accumulates as the 86 nt primary transcript, in agreement with observations in E. coli (Wassarman et al., 2001).”
The Crp-Activated Small Noncoding Regulatory RNA CyaR (RyeE) Links Nutritional Status to Group Behavior (2008, background): “(66), expression of cyaR was fivefold higher in a late-log-phase culture 464 DE LAY AND GOTTESMAN J.”
Computational identification of noncoding RNAs in E. coli by comparative genomics. (2001, background): “It must also be noted that not the intergenic regions of the E. coli genome sequence all ncRNA genes conserve an intramolecular secondary [32, 33].”