ArticleGenome biology2005
Identification of cyanobacterial non-coding RNAs by comparative genome analysis.
Article in Genome biology, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
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Who cites it
68 citing papers in PubMed, 133 citations in OpenAlex.
- Codon bias shapes bacterial small RNA binding sites within protein-coding sequences.RNA (New York, N.Y.) · 2026Article
- Exploring the regulatory potential of RNA structures in 202 cyanobacterial genomes.Nucleic acids research · 2026Article
- Bioinformatics Approaches in Noncoding RNAs Research.Experientia supplementum (2012) · 2026Review
- Review
- Key players in regulatory RNA realm of bacteria.Biochemistry and biophysics reports · 2022Review
- Review
- Cyanobacterial Genome Sequencing, Annotation, and Bioinformatics.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Discovery of 17 conserved structural RNAs in fungi.Nucleic acids research · 2021Article
- Review
- A framework for the computational prediction and analysis of non-coding RNAs in microbial environmental populations and their experimental validation.The ISME journal · 2020Article
- Article
- Interplay and Targetome of the Two Conserved Cyanobacterial sRNAs Yfr1 and Yfr2 in Prochlorococcus MED4.Scientific reports · 2019Article
- Sequence-based bacterial small RNAs prediction using ensemble learning strategies.BMC bioinformatics · 2018Article
- A glutamine riboswitch is a key element for the regulation of glutamine synthetase in cyanobacteria.Nucleic acids research · 2018Article
- The GntR family transcriptional regulator PMM1637 regulates the highly conserved cyanobacterial sRNA Yfr2 in marine picocyanobacteria.DNA research : an international journal for rapid publication of reports on genes and genomes · 2018Article
- Regulatory sRNAs in Cyanobacteria.Frontiers in microbiology · 2018Review
- 6S RNA plays a role in recovery from nitrogen depletion in Synechocystis sp. PCC 6803.BMC microbiology · 2017Article
- Small Antisense RNA RblR Positively Regulates RuBisCo inFrontiers in microbiology · 2017Article
- Mycoplasma non-coding RNA: identification of small RNAs and targets.BMC genomics · 2016Article
- Network analysis of transcriptomics expands regulatory landscapes in Synechococcus sp. PCC 7002.Nucleic acids research · 2016Article
8 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWhole genome sequencing of marine cyanobacteria has revealed an unprecedented degree of genomic variation and streamlining. With a size of 1.66 megabase-pairs, Prochlorococcus sp. MED4 has the most compact of these genomes and it is enigmatic how the few identified regulatory proteins efficiently sustain the lifestyle of an ecologically successful marine microorganism. Small non-coding RNAs (ncRNAs) control a plethora of processes in eukaryotes as well as in bacteria; however, systematic searches for ncRNAs are still lacking for most eubacterial phyla outside the enterobacteria.
resultsBased on a computational prediction we show the presence of several ncRNAs (cyanobacterial functional RNA or Yfr) in several different cyanobacteria of the Prochlorococcus-Synechococcus lineage. Some ncRNA genes are present only in two or three of the four strains investigated, whereas the RNAs Yfr2 through Yfr5 are structurally highly related and are encoded by a rapidly evolving gene family as their genes exist in different copy numbers and at different sites in the four investigated genomes. One ncRNA, Yfr7, is present in at least seven other cyanobacteria. In addition, control elements for several ribosomal operons were predicted as well as riboswitches for thiamine pyrophosphate and cobalamin.
conclusionThis is the first genome-wide and systematic screen for ncRNAs in cyanobacteria. Several ncRNAs were both computationally predicted and their presence was biochemically verified. These RNAs may have regulatory functions and each shows a distinct phylogenetic distribution. Our approach can be applied to any group of microorganisms for which more than one total genome sequence is available for comparative analysis.
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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.