ArticleNucleic acids research2010
Mining regulatory 5'UTRs from cDNA deep sequencing datasets.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 22 citations in OpenAlex.
- Identification of small RNAs abundant in Burkholderia cenocepacia biofilms reveal putative regulators with a potential role in carbon and iron metabolism.Scientific reports · 2017Article
- CRISPR/Cas9-mediated mutation of tyrosinase (Tyr) 3' UTR induce graying in rabbit.Scientific reports · 2017Article
- A Transcriptome Map of Actinobacillus pleuropneumoniae at Single-Nucleotide Resolution Using Deep RNA-Seq.PloS one · 2016Article
- Whole-genome mapping of 5' RNA ends in bacteria by tagged sequencing: a comprehensive view in Enterococcus faecalis.RNA (New York, N.Y.) · 2015Article
- Non-protein coding RNA genes as the novel diagnostic markers for the discrimination of Salmonella species using PCR.PloS one · 2015Article
- Ultra deep sequencing of Listeria monocytogenes sRNA transcriptome revealed new antisense RNAs.PloS one · 2014Article
- Parallel evolution of genome structure and transcriptional landscape in the Epsilonproteobacteria.BMC genomics · 2013Article
- How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?BMC genomics · 2012Article
- Transcriptomic profiling of the oyster pathogen Vibrio splendidus opens a window on the evolutionary dynamics of the small RNA repertoire in the Vibrio genus.RNA (New York, N.Y.) · 2012Article
- Riboswitch control of Rho-dependent transcription termination.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Deep sequencing uncovers numerous small RNAs on all four replicons of the plant pathogen Agrobacterium tumefaciens.RNA biology · 2012Article
- Genome-wide detection of novel regulatory RNAs in E. coli.Genome research · 2011Article
- The intracellular sRNA transcriptome of Listeria monocytogenes during growth in macrophages.Nucleic acids research · 2011Article
- Prokaryotic whole-transcriptome analysis: deep sequencing and tiling arrays.Microbial biotechnology · 2010Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
Regulatory 5' untranslated regions (r5'UTRs) of mRNAs such as riboswitches modulate the expression of genes involved in varied biological processes in both bacteria and eukaryotes. New high-throughput sequencing technologies could provide powerful tools for discovery of novel r5'UTRs, but the size and complexity of the datasets generated by these technologies makes it difficult to differentiate r5'UTRs from the multitude of other types of RNAs detected. Here, we developed and implemented a bioinformatic approach to identify putative r5'UTRs from within large datasets of RNAs recently identified by pyrosequencing of the Vibrio cholerae small transcriptome. This screen yielded only approximately 1% of all non-overlapping RNAs along with 75% of previously annotated r5'UTRs and 69 candidate V. cholerae r5'UTRs. These candidates include several putative functional homologues of diverse r5'UTRs characterized in other species as well as numerous candidates upstream of genes involved in pathways not known to be regulated by r5'UTRs, such as fatty acid oxidation and peptidoglycan catabolism. Two of these novel r5'UTRs were experimentally validated using a GFP reporter-based approach. Our findings suggest that the number and diversity of pathways regulated by r5'UTRs has been underestimated and that deep sequencing-based transcriptomics will be extremely valuable in the search for novel r5'UTRs.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.