Small RNA biology is systems biology

Jost, Daniel; Nowojewski, Andrzej; Levine, Erel

doi:10.5483/bmbrep.2011.44.1.11

Cited by 34 publications

(28 citation statements)

References 106 publications

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“…mall noncoding RNAs (sRNAs) are known to be one of the major players in the regulation of gene expression in the Prokaryota in both Bacteria and Archaea (20,25,55). A number of sRNA studies, particularly of Bacteria, have been undertaken in the last decade (1,20).…”

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confidence: 99%

Metatranscriptomic Analysis of Microbes in an Oceanfront Deep-Subsurface Hot Spring Reveals Novel Small RNAs and Type-Specific tRNA Degradation

Murakami

Fujishima

Tomita

et al. 2012

Appl Environ Microbiol

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Studies of small noncoding RNAs (sRNAs) have been conducted predominantly using culturable organisms, and the acquisition of further information about sRNAs from global environments containing uncultured organisms now is very important. In this study, hot spring water (57°C, pH 8.1) was collected directly from the underground environment at depths of 250 to 1,000 m in Yunohama, Japan, and small RNA sequences obtained from the environment were analyzed. A phylogenetic analysis of both archaeal and bacterial 16S rRNA gene sequences was conducted, and the results suggested the presence of unique species in the environment, corresponding to the Archaeal Richmond Mine Acidophilic Nanoorganisms (ARMAN) group and three new Betaproteobacteria. A metatranscriptomic analysis identified 64,194 (20,057 nonredundant) cDNA sequences. Of these cDNAs, 90% were either tRNAs, tRNA fragments, rRNAs, or rRNA fragments, whereas 2,181 reads (10%) were classified as previously uncharacterized putative candidate sRNAs. Among these, 15 were particularly abundant, 14 of which showed no sequence similarity to any known noncoding RNA, and at least six of which form very stable RNA secondary structures. The analysis of a large number of tRNA fragments suggested that unique relationships exist between the anticodons of the tRNAs and the sites of tRNA degradation. Previous bacterial tRNA degradation studies have been limited to specific organisms, such as Escherichia coli and Streptomyces coelicolor, and the current results suggest that specific tRNA decay occurs more frequently than previously expected.

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confidence: 99%

Metatranscriptomic Analysis of Microbes in an Oceanfront Deep-Subsurface Hot Spring Reveals Novel Small RNAs and Type-Specific tRNA Degradation

Murakami

Fujishima

Tomita

et al. 2012

Appl Environ Microbiol

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“…MiRNAs are non-coding RNA molecules of 18 to 22 nucleotides in length, and regulate gene expression at the post-transcriptional level (55)(56)(57). Several recent studies have demonstrated that many miRNAs showed tissue-specific expression patterns (58,59).…”

Section: Microrna Profiling Methodsmentioning

confidence: 99%

Body fluid identification in forensics

et al. 2012

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“…siRNA molecules induce gene silencing by binding to complementary target RNA molecules in association with the nucleolytic cytoplasmic protein complex known as the RNA-induced silencing complex (87). Nowadays, siRNA is being designed to reduce the production of angiogenic molecules providing potent therapies for ocular neovascularization in patients with AMD.…”

Section: Small Interference Rna (Sirna)mentioning

confidence: 99%