Identification of bacterial small non-coding RNAs: experimental approaches

Shoshy Altuvia*

*Corresponding author for this work

Research output: Contribution to journalReview articlepeer-review

120 Scopus citations

Abstract

Almost 140 bacterial small RNAs (sRNAs; sometimes referred to as non-coding RNAs) have been discovered in the past six years. The majority of these sRNAs were discovered in Escherichia coli, and a smaller subset was characterized in other bacteria, many of which were pathogenic. Many of these genes were identified as a result of systematic screens using computational prediction of sRNAs and experimental-based approaches, including microarray and shotgun cloning. A smaller number of sRNAs were discovered by direct labeling or by functional genetic screens. Many of the discovered genes, ranging in size from 50 to 500 nucleotides, are conserved and located in intergenic regions, in-between open reading frames. The expression of many of these genes is growth phase dependent or stress related. As each search employed specific parameters, this led to the identification of genes with distinct characteristics. Consequently, unique sRNAs such as those that are species-specific, sRNA genes that are transcribed under unique conditions or genes located on the antisense strand of protein-encoding genes, were probably missed.

Original languageAmerican English
Pages (from-to)257-261
Number of pages5
JournalCurrent Opinion in Microbiology
Volume10
Issue number3
DOIs
StatePublished - Jun 2007

Bibliographical note

Funding Information:
I thank Hilla Giladi and Gisela Storz for editorial comments. Supported by The Israel Science Foundation founded by The Israel Academy of Sciences and Humanities, grant number 663/02, The United States-Israel Binational Science Foundation, grant number 2001032, The Israel Science Foundation-Bikura Program, grant number 1342/05, The Israeli Ministry of Science, grant number 3/2559 and by BACRNAs, a Specific Targeted Research Project supported by European Union's FP6 Life Science, Genomics and Biotechnology for Health, LSHM-CT-2005-018618.

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