2024
The discovery of novel noncoding RNAs in 50 bacterial genomes
Narunsky A, Higgs G, Torres B, Yu D, de Andrade G, Kavita K, Breaker R. The discovery of novel noncoding RNAs in 50 bacterial genomes. Nucleic Acids Research 2024, 52: 5152-5165. PMID: 38647067, PMCID: PMC11109978, DOI: 10.1093/nar/gkae248.Peer-Reviewed Original ResearchBacterial genomesDomains of lifeIntergenic regionNcRNA classesGC-rich intergenic regionsBacterial domain of lifeIndividual bacterial genomesStructured noncoding RNAsNovel noncoding RNAsProtein coding genesNoncoding RNAsNcRNA motifsRiboswitch candidatesBacterial domainRiboswitch classesCoding genesGene regulationCellular processesCytidine nucleotidesBacterial speciesGenomeComputational pipelineNcRNAsDiverse functionsGenes
2019
Genome‐wide Discovery of Rare Riboswitches in Bacteria
Arachchilage G, Atilho R, Stav S, Higgs G, Breaker R. Genome‐wide Discovery of Rare Riboswitches in Bacteria. The FASEB Journal 2019, 33: 778.8-778.8. DOI: 10.1096/fasebj.2019.33.1_supplement.778.8.Peer-Reviewed Original ResearchRiboswitch candidatesBacterial genomesGC-rich intergenic regionsDifferent bacterial genomesGenome-wide discoverySequenced bacterial genomesNascent RNA transcriptsRiboswitch classesThiamin biosynthesisRiboswitch aptamerStructured ncRNAsNcRNA classesIntergenic regionHydroxymethylpyrimidine pyrophosphateRiboswitchBioinformatics pipelineRNA transcriptsTranscription processComputational pipelinePhysiological pathwaysConformational changesNcRNAsGenomeFASEB JournalHoward Hughes Medical Institute
2018
High Throughput Validation of Orphan Riboswitch Candidates
Arachchilage G, Sherlock M, White N, Panchapakesan S, Breaker R. High Throughput Validation of Orphan Riboswitch Candidates. The FASEB Journal 2018, 32: lb18-lb18. DOI: 10.1096/fasebj.2018.32.1_supplement.lb18.Peer-Reviewed Original ResearchRiboswitch candidatesRiboswitch classesIntergenic regionCognate ligandsS-adenosylmethionineLong intergenic regionCis-acting genesDiscovery of riboswitchesExperimental Biology 2018 MeetingImportant biological pathwaysHigh-throughput validationHigh-throughput strategyS-adenosylhomocysteineComparative genomicsRecent bioinformaticsBacterial mRNAsLine probingRNA elementsRiboswitchGenetic validationReporter assaysBiological pathwaysComputational approachThroughput strategyFASEB Journal
2016
Prospects for Noncoding RNA Discovery in Bacteria
Breaker R. Prospects for Noncoding RNA Discovery in Bacteria. The FASEB Journal 2016, 30 DOI: 10.1096/fasebj.30.1_supplement.386.1.Peer-Reviewed Original ResearchNoncoding RNAsNovel biochemical functionLarge noncoding RNAsBacterial noncoding RNAsRNA world organismsSelf-cleaving ribozymesRiboswitch candidatesRNA discoveryBiological validation studiesBiochemical functionsBioinformatics analysisModern cellsWorld organismsRNAGreat diversityStructural diversityNovel ribozymesRibozymeDiversityBacteriaDiscoveryRiboswitchRNAsOrganismsCells