The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria
Open accessAbstract
Recent bioinformatics-aided searches have identified many new small RNAs (sRNAs) in the intergenic regions of the bacterium Escherichia coli. Here, a shot-gun cloning approach (RNomics) was used to generate cDNA libraries of small sized RNAs. Besides many of the known sRNAs, we found new species that were not predicted previously. The present work brings the number of sRNAs in E.coli to 62. Experimental transcription start site mapping showed that some sRNAs were encoded from independent genes, while others were processed from mRNA leaders or trailers, indicative of a parallel transcriptional output generating sRNAs co-expressed with mRNAs. Two of these RNAs (SroA and SroG) consist of known (THI and RFN) riboswitch elements. We also show that two recently identified sRNAs (RyeB and SraC/RyeA) interact, resulting in RNase III-dependent cleavage. To the best of our knowledge, this represents the first case of two non-coding RNAs interacting by a putative antisense mechanism. In addition, intracellular metabolic stabilities of sRNAs were determined, including ones from previous screens. The wide range of half-lives (<2 to >32 min) indicates that sRNAs cannot generally be assumed to be metabolically stable. The experimental characterization of sRNAs analyzed here suggests that the definition of an sRNA is more complex than previously assumed.
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Cites
Mfold web server for nucleic acid folding and hybridization prediction
Zuker, M. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg595 · Cited by 13,404
Identification of Novel Genes Coding for Small Expressed RNAs
Lagos-Quintana, M., Rauhut, R., Lendeckel, W., & Tuschl, T. (2001) · Science · doi:10.1126/science.1064921 · Cited by 4,956
Identification of novel small RNAs using comparative genomics and microarrays
Wassarman, K. M., Repoila, F., Rosenow, C., Storz, G., & Gottesman, S. (2001) · Genes & Development · doi:10.1101/gad.901001 · Cited by 723
Cited by
Single-cell RNA-seq: advances and future challenges
Saliba, A.-E., Westermann, A. J., Gorski, S. A., & Vogel, J. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku555 · Cited by 847
Self-citationQuantitative Characteristics of Gene Regulation by Small RNA
Levine, E., Zhang, Z., Kuhlman, T., & Hwa, T. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050229 · Cited by 384
AN ABUNDANCE OF RNA REGULATORS
Storz, G., Altuvia, S., & Wassarman, K. M. (2005) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.74.082803.133136 · Cited by 371
Regulatory mechanisms employed by cis-encoded antisense RNAs
Brantl, S. (2007) · Current Opinion in Microbiology · doi:10.1016/j.mib.2007.03.012 · Cited by 323
Hfq-dependent regulation of OmpA synthesis is mediated by an antisense RNA
Udekwu, K. I., Darfeuille, F., Vogel, J., Reimegård, J., Holmqvist, E., & Wagner, E. G. H. (2005) · Genes & Development · doi:10.1101/gad.354405 · Cited by 320
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Metadata
- Authors
- Vogel, J.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2003-11-15
- Volume
- 31
- Issue
- 22
- Pages
- 6435-6443
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2145943422
- Cited by
- 445
- References
- 3
- FWCI
- 12.06
- Type
- journal article
- Language
- en
- Open access
- bronze
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