2024
The genome organization of the Lake Magadi tilapia, Oreochromis Alcolapia grahami, a cichlid extremophile
Bernardi G, Kavembe G, Bergman H, Bucciarelli G, Wood C. The genome organization of the Lake Magadi tilapia, Oreochromis Alcolapia grahami, a cichlid extremophile. Journal Of Great Lakes Research 2024, 50: 102326. DOI: 10.1016/j.jglr.2024.102326.Peer-Reviewed Original ResearchGC-rich isochoresGC-rich regionBase compositionLake Magadi tilapiaGC-poorRepetitive elementsGC-rich genomic regionsGC-poor genomeRepetitive element analysisProtein coding genesGenomes of vertebratesMagadi tilapiaNile tilapiaGenome organizationGenome sequenceGC-richGenomic regionsCoding genesGenomeHot-waterNatural selectionAlcolapia grahamiFish speciesTilapiaCichlidsThe 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
2023
Establishment genomics of the Indo-Pacific damselfish Neopomacentrus cyanomos, in the Greater Caribbean
Bernardi G, Cohn F, Dominguez-Dominguez O, Kingon K, Tornabene L, Robertson D. Establishment genomics of the Indo-Pacific damselfish Neopomacentrus cyanomos, in the Greater Caribbean. Biological Invasions 2023, 26: 1017-1031. DOI: 10.1007/s10530-023-03226-w.Peer-Reviewed Original ResearchNon-native speciesNon-native populationsGreater CaribbeanReef fishesNative rangeNatural selectionTrinidad populationIndo-Pacific reef fishMitochondrial DNA lineagesProtein coding genesSeparate genetic clustersDNA lineagesGenetic differentiationCoding genesAtlantic individualsRocky reefsGenetic clustersGenetic diversityEstablishment successRAD sequencesPopulation structureIsolated populationCoral reefsAdaptable speciesNearby reefsBacillus subtilis Phages Related to SIOphi from Desert Soils of the Southwest United States
Magness L, Delesalle V, Vill A, Strine M, Chaudhry B, Lichty K, Guffey A, DeCurzio J, Krukonis G. Bacillus subtilis Phages Related to SIOphi from Desert Soils of the Southwest United States. PHAGE 2023, 4: 165-172. PMID: 40134792, PMCID: PMC11932521, DOI: 10.1089/phage.2023.0021.Peer-Reviewed Original ResearchPutative protein coding genesDouble-stranded DNA genomeBacillus subtilis phagePhage host rangeLow GC contentProtein coding genesDiversity of phagesAmino acid similarityPhage clusterPhage evolutionPhage genomeGC contentUnique genesBacillus phagesCoding genesDNA genomeReplication genesModel organismsPhageHost rangeMicrobial dynamicsGenetic differencesGenomeGenesDesert soils
2022
Comparative Genomics of Six Lytic Bacillus subtilis Phages from the Southwest United States
Vill A, Delesalle V, Tomko B, Lichty K, Strine M, Guffey A, Burton E, Tanke N, Krukonis G. Comparative Genomics of Six Lytic Bacillus subtilis Phages from the Southwest United States. PHAGE 2022, 3: 171-178. PMID: 36793550, PMCID: PMC9917325, DOI: 10.1089/phage.2022.0030.Peer-Reviewed Original ResearchPutative protein coding genesDouble-stranded DNA genomeLoci encoding proteinsLow GC contentProtein coding genesDiversity of phagesAmino acid similarityPhage evolutionGC contentSmall genesGenomic mosaicismCoding genesDNA genomeEncode proteinsProtein foldingModel organismsPhageMicrobial dynamicsGenomeGenesProteinSiphovirusIndelsGenBankNucleotide
2020
Developmentally Regulated Novel Non-coding Anti-sense Regulators of mRNA Translation in Trypanosoma b rucei
Rajan KS, Doniger T, Cohen-Chalamish S, Rengaraj P, Galili B, Aryal S, Unger R, Tschudi C, Michaeli S. Developmentally Regulated Novel Non-coding Anti-sense Regulators of mRNA Translation in Trypanosoma b rucei. IScience 2020, 23: 101780. PMID: 33294788, PMCID: PMC7683347, DOI: 10.1016/j.isci.2020.101780.Peer-Reviewed Original ResearchRNA regulatorsProtein coding genesDistinct mRNA speciesNon-coding RNAsCoding genesPolycistronic transcriptsTranscriptional regulationMRNA translationRRNA locusMRNA functionMammalian hostsMRNA speciesMRNA stabilityGene expressionConcerted actionRegulatorParasitesRNACausative agentRegulationInsectsPolyadenylationSplicingTranslationAdditional layer
2017
Detection of Regional Variation in Selection Intensity within Protein-Coding Genes Using DNA Sequence Polymorphism and Divergence
Zhao ZM, Campbell MC, Li N, Lee DSW, Zhang Z, Townsend JP. Detection of Regional Variation in Selection Intensity within Protein-Coding Genes Using DNA Sequence Polymorphism and Divergence. Molecular Biology And Evolution 2017, 34: 3006-3022. PMID: 28962009, PMCID: PMC5850860, DOI: 10.1093/molbev/msx213.Peer-Reviewed Original ResearchConceptsPoisson random fieldRandom fieldsEnsemble of modelsRandom field frameworkField frameworkClustering modelHistorical demographic trendsAmino acid-altering substitutionsSelection intensityEnsembleHigh powerUniform selectionProtein-coding genesProtein coding genesHeterogeneity of selectionDNA sequence polymorphismsComparison of polymorphisms
2016
The Human Adrenal Gland Proteome Defined by Transcriptomics and Antibody-Based Profiling
Bergman J, Botling J, Fagerberg L, Hallström B, Djureinovic D, Uhlén M, Pontén F. The Human Adrenal Gland Proteome Defined by Transcriptomics and Antibody-Based Profiling. Endocrinology 2016, 158: 239-251. PMID: 27901589, DOI: 10.1210/en.2016-1758.Peer-Reviewed Original ResearchConceptsImmunohistochemistry-based protein profilingNormal human tissue typesProtein coding genesMessenger RNA sequencingExpression levelsProtein expression patternsHuman tissue typesCoding genesProtein homologsFERM domainRelative expression levelsCorresponding proteinRNA sequencingWide transcriptomicsExpression patternsProtein profilingGreater expression levelsGenesSpecific functionsProteinMolecular landscapeTissue typesProteomeTranscriptomicsElevated expression
2014
Genome-Wide Characterization of Light-Regulated Genes in Neurospora crassa
Wu C, Yang F, Smith KM, Peterson M, Dekhang R, Zhang Y, Zucker J, Bredeweg EL, Mallappa C, Zhou X, Lyubetskaya A, Townsend JP, Galagan JE, Freitag M, Dunlap JC, Bell-Pedersen D, Sachs MS. Genome-Wide Characterization of Light-Regulated Genes in Neurospora crassa. G3: Genes, Genomes, Genetics 2014, 4: 1731-1745. PMID: 25053707, PMCID: PMC4169166, DOI: 10.1534/g3.114.012617.Peer-Reviewed Original ResearchConceptsNeurospora crassaRNA-seqFilamentous fungus Neurospora crassaGenome-wide characterizationProtein coding genesFungus Neurospora crassaPrevious microarray studyRibosome biogenesisCoding genesTranscriptional responseRRNA metabolismCellular metabolismMicroarray studiesGenesCrassaSignificant oxidative stressRNA levelsOrganismsMRNA levelsOxidative stressMRNAMetabolismBiogenesisTranscriptsMyceliumAlternative Capture of Noncoding RNAs or Protein-Coding Genes by Herpesviruses to Alter Host T Cell Function
Guo YE, Riley KJ, Iwasaki A, Steitz JA. Alternative Capture of Noncoding RNAs or Protein-Coding Genes by Herpesviruses to Alter Host T Cell Function. Molecular Cell 2014, 54: 67-79. PMID: 24725595, PMCID: PMC4039351, DOI: 10.1016/j.molcel.2014.03.025.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAntigens, CDAntigens, Differentiation, T-LymphocyteBase SequenceCallithrixEnzyme ActivationGene Expression RegulationGPI-Linked ProteinsGRB2 Adaptor ProteinHEK293 CellsHerpesvirus 2, SaimiriineHigh-Throughput Nucleotide SequencingHost-Pathogen InteractionsHumansImmunoprecipitationInterferon-gammaJurkat CellsLectins, C-TypeLymphocyte ActivationMicroRNAsMitogen-Activated Protein KinasesMolecular Sequence DataReceptors, Antigen, T-CellRNA StabilityRNA, UntranslatedRNA, ViralSemaphorinsSequence Analysis, RNASignal TransductionTime FactorsT-LymphocytesTransfectionConceptsMitogen-activated protein kinaseMiR-27Protein coding genesHerpesvirus saimiriHigh-throughput sequencingTCR-induced activationCell functionHSUR 1Γ-herpesvirusesNoncoding RNAsProtein kinaseEctopic expressionOncogenic γ-herpesvirusesTarget genesInduction of CD69MicroRNA-27Key modulatorRNACommon targetAlHV-1GenesCell receptorDiverse strategiesHost T-cell functionCells
2011
A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets
Cheng C, Yan KK, Yip KY, Rozowsky J, Alexander R, Shou C, Gerstein M. A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets. Genome Biology 2011, 12: r15. PMID: 21324173, PMCID: PMC3188797, DOI: 10.1186/gb-2011-12-2-r15.Peer-Reviewed Original Research
2009
Features of Mammalian microRNA Promoters Emerge from Polymerase II Chromatin Immunoprecipitation Data
Corcoran DL, Pandit KV, Gordon B, Bhattacharjee A, Kaminski N, Benos PV. Features of Mammalian microRNA Promoters Emerge from Polymerase II Chromatin Immunoprecipitation Data. PLOS ONE 2009, 4: e5279. PMID: 19390574, PMCID: PMC2668758, DOI: 10.1371/journal.pone.0005279.Peer-Reviewed Original ResearchConceptsProtein coding genesMiRNA genesCoding genesIntragenic miRNAsPol II chromatin immunoprecipitationNon-coding RNA regulatorsRNA polymerase II promoterChromatin immunoprecipitation dataDiverse biological processesOwn unique promoterPolymerase II promoterTranscription start siteIntergenic miRNAsTranscription regulationMiRNA promotersRNA regulatorsChromatin immunoprecipitationPromoter organizationHost genesPrimary transcriptTranscript organizationStart siteImmunoprecipitation dataUnique promoterBiological processes
2001
Unusual diversity in α-amanitin sensitivity of RNA polymerases in trichomonads
Vaňáčová Š, Tachezy J, Ullu E, Tschudi C. Unusual diversity in α-amanitin sensitivity of RNA polymerases in trichomonads. Molecular And Biochemical Parasitology 2001, 115: 239-247. PMID: 11420110, DOI: 10.1016/s0166-6851(01)00294-8.Peer-Reviewed Original ResearchConceptsUnusual diversityResistant RNA polymerase IIProtein coding genesParasitic protist Trichomonas vaginalisRNA polymerase IIAlpha-amanitin sensitivityProtist Trichomonas vaginalisGenus-specific patternsTritrichomonas foetusLysolecithin-permeabilized cellsUnicellular eukaryotesCoding genesPolymerase IIRNAP IIRNAP IIIRNA polymeraseTrichomonad speciesAlpha-amanitinT. vaginalisRNA synthesisΑ-amanitin sensitivityDiversityTrichomonadsRelated groupsEukaryotes
1996
A Novel Spliceosome Containing U11, U12, and U5 snRNPs Excises a Minor Class (AT–AC) Intron In Vitro
Tarn W, Steitz J. A Novel Spliceosome Containing U11, U12, and U5 snRNPs Excises a Minor Class (AT–AC) Intron In Vitro. Cell 1996, 84: 801-811. PMID: 8625417, DOI: 10.1016/s0092-8674(00)81057-0.Peer-Reviewed Original ResearchMeSH KeywordsBase CompositionBase SequenceBlotting, NorthernCell NucleusHeLa CellsHumansMolecular Sequence DataNucleic Acid ConformationOligodeoxyribonucleotidesPlasmidsPolymerase Chain ReactionRibonuclease HRibonucleoprotein, U5 Small NuclearRibonucleoproteins, Small NuclearRNA PrecursorsRNA SplicingConceptsU5 small nuclear ribonucleoproteinSmall nuclear ribonucleoproteinU12 small nuclear ribonucleoproteinsMinor class intronsProtein coding genesPre-mRNA substrateNative gel electrophoresisCoding genesBranch site sequenceSplicing complexesNuclear ribonucleoproteinPre-mRNAP120 geneLariat intermediateSite sequenceIntronsHeLa cellsEssential roleSplicingGel electrophoresisBranch siteGenesU12Minor classU11
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