2019
The vault RNA of Trypanosoma brucei plays a role in the production of trans-spliced mRNA
Kolev NG, Rajan KS, Tycowski KT, Toh JY, Shi H, Lei Y, Michaeli S, Tschudi C. The vault RNA of Trypanosoma brucei plays a role in the production of trans-spliced mRNA. Journal Of Biological Chemistry 2019, 294: 15559-15574. PMID: 31439669, PMCID: PMC6816085, DOI: 10.1074/jbc.ra119.008580.Peer-Reviewed Original ResearchConceptsTelomerase-associated protein 1Vault RNAY RNAsRNA quality controlRNA polymerase IIISmall nuclear RNATrans-spliced mRNAPermeabilized cell systemNcRNA repertoireRNP biogenesisMRNA metabolismRNA speciesSequence similarityRNA classesMammalian cellsNuclear RNAPolymerase IIIRo functionTrypanosoma bruceiVtRNAsGene expressionRo proteinBloodstream formsRNACell nuclei
2018
Temperature shift activates bloodstream VSG expression site promoters in Trypanosoma brucei
Kolev NG, Ramsdell TK, Tschudi C. Temperature shift activates bloodstream VSG expression site promoters in Trypanosoma brucei. Molecular And Biochemical Parasitology 2018, 226: 20-23. PMID: 30399391, PMCID: PMC6258174, DOI: 10.1016/j.molbiopara.2018.10.003.Peer-Reviewed Original Research
2017
Metacyclic VSG expression site promoters are recognized by the same general transcription factor that is required for RNA polymerase I transcription of bloodstream expression sites
Kolev NG, Günzl A, Tschudi C. Metacyclic VSG expression site promoters are recognized by the same general transcription factor that is required for RNA polymerase I transcription of bloodstream expression sites. Molecular And Biochemical Parasitology 2017, 216: 52-55. PMID: 28716719, PMCID: PMC5582990, DOI: 10.1016/j.molbiopara.2017.07.002.Peer-Reviewed Original ResearchConceptsBloodstream VSG expression sitesVSG expression sitesVSG ES promoterExpression sitesPol IVSG genesES promoterRNA polymerase I transcriptionGeneral transcription factorsBloodstream expression sitesVariant surface glycoprotein (VSG) coatPolymerase I transcriptionRNA polymerase IDistinct promoter sequencesMetacyclic VSG geneTrypanosoma brucei cellsProcyclin genesTypes of promotersBrucei cellsDevelopmental programDistinct binding affinitiesTranscription factorsI transcriptionInitiation factorsPromoter sequences
2015
Genome-wide analysis of small nucleolar RNAs of Leishmania major reveals a rich repertoire of RNAs involved in modification and processing of rRNA
Eliaz D, Doniger T, Tkacz ID, Biswas VK, Gupta SK, Kolev NG, Unger R, Ullu E, Tschudi C, Michaeli S. Genome-wide analysis of small nucleolar RNAs of Leishmania major reveals a rich repertoire of RNAs involved in modification and processing of rRNA. RNA Biology 2015, 12: 1222-1255. PMID: 25970223, PMCID: PMC4829279, DOI: 10.1080/15476286.2015.1038019.Peer-Reviewed Original ResearchConceptsSmall nucleolar RNAsNucleolar RNAsGenome-wide analysisRNA processing mechanismsRRNA secondary structurePost-transcriptional levelCore proteinProcessing of rRNARNA-seq analysisFunctional homologueGene clusterRNA speciesTrypanosoma bruceiSnoRNAsComplete repertoireGene expressionRRNA cleavageAnalogous functionsSecondary structureRNAProtozoan parasiteRich repertoireOrganismsSpeciesProtein
2012
Developmental Progression to Infectivity in Trypanosoma brucei Triggered by an RNA-Binding Protein
Kolev NG, Ramey-Butler K, Cross GA, Ullu E, Tschudi C. Developmental Progression to Infectivity in Trypanosoma brucei Triggered by an RNA-Binding Protein. Science 2012, 338: 1352-1353. PMID: 23224556, PMCID: PMC3664091, DOI: 10.1126/science.1229641.Peer-Reviewed Original ResearchComparative Genomics Reveals Two Novel RNAi Factors in Trypanosoma brucei and Provides Insight into the Core Machinery
Barnes RL, Shi H, Kolev NG, Tschudi C, Ullu E. Comparative Genomics Reveals Two Novel RNAi Factors in Trypanosoma brucei and Provides Insight into the Core Machinery. PLOS Pathogens 2012, 8: e1002678. PMID: 22654659, PMCID: PMC3359990, DOI: 10.1371/journal.ppat.1002678.Peer-Reviewed Original ResearchConceptsRNA interferenceT. bruceiComparative genomicsTrypanosoma bruceiMechanism of RNAiCatalog of genesCore RNAi machineryWide RNAi screenArgonaute 1 proteinNext-generation IlluminaRepertoire of factorsLoss of fitnessDistinct developmental stagesAncient eukaryotesRNAi factorsCore machineryRNAi machineryRNAi screenRNAi toolTrypanosomatid protozoaDuplex siRNAsRNAi efficiencyHuman parasitesMolecular explorationBrucei
2010
The Transcriptome of the Human Pathogen Trypanosoma brucei at Single-Nucleotide Resolution
Kolev NG, Franklin JB, Carmi S, Shi H, Michaeli S, Tschudi C. The Transcriptome of the Human Pathogen Trypanosoma brucei at Single-Nucleotide Resolution. PLOS Pathogens 2010, 6: e1001090. PMID: 20838601, PMCID: PMC2936537, DOI: 10.1371/journal.ppat.1001090.Peer-Reviewed Original ResearchMeSH KeywordsBase SequenceGene Expression ProfilingGenome, BacterialHigh-Throughput Nucleotide SequencingHumansMolecular Sequence DataRNA Polymerase IIRNA PrecursorsRNA, BacterialSequence Homology, Nucleic AcidTranscription Initiation SiteTranscription, GeneticTrypanosoma brucei bruceiTrypanosomiasis, AfricanConceptsGene clusterNew transcriptsHigh-throughput RNA sequencingInitiation siteOrganization of genesRNA polymerase IISimilar genome organizationPutative initiation siteSingle-nucleotide resolutionTranscription initiation siteGene expression patternsPre-mRNA processingNon-coding RNAsGenome organizationPolymerase IIGenomic mapTranscription initiationInsect vectorsEukaryotic promotersMass spectrometry analysisImportant human pathogenMammalian hostsRNA sequencingTrypanosoma bruceiT. brucei
2008
A manganese-dependent ribozyme in the 3′-untranslated region of Xenopus Vg1 mRNA
Kolev NG, Hartland EI, Huber PW. A manganese-dependent ribozyme in the 3′-untranslated region of Xenopus Vg1 mRNA. Nucleic Acids Research 2008, 36: 5530-5539. PMID: 18753150, PMCID: PMC2553595, DOI: 10.1093/nar/gkn530.Peer-Reviewed Original ResearchConserved motifs in both CPSF73 and CPSF100 are required to assemble the active endonuclease for histone mRNA 3′‐end maturation
Kolev NG, Yario TA, Benson E, Steitz JA. Conserved motifs in both CPSF73 and CPSF100 are required to assemble the active endonuclease for histone mRNA 3′‐end maturation. EMBO Reports 2008, 9: 1013-1018. PMID: 18688255, PMCID: PMC2572124, DOI: 10.1038/embor.2008.146.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid MotifsAmino Acid SequenceBase SequenceCell LineCleavage And Polyadenylation Specificity FactorConserved SequenceEndonucleasesEnzyme ActivationHeLa CellsHistonesHumansMolecular Sequence DataProtein Structure, TertiaryProtein SubunitsRNA 3' End ProcessingRNA PrecursorsRNA, MessengerConceptsPre-messenger RNAPolyadenylation specificity factorMammalian proteinsRNase ZConserved motifsHistone mRNASpecificity factorEndonucleolytic cleavageActive endonucleaseEndonuclease activityMBL familyComplex machineryMessenger RNAPoint mutationsCPSF73CPSF100Process of maturationMaturation processRNAProteinMotifMRNAMaturationEukaryotesCleavage
2006
In vivo assembly of functional U7 snRNP requires RNA backbone flexibility within the Sm-binding site
Kolev NG, Steitz JA. In vivo assembly of functional U7 snRNP requires RNA backbone flexibility within the Sm-binding site. Nature Structural & Molecular Biology 2006, 13: 347-353. PMID: 16547514, DOI: 10.1038/nsmb1075.Peer-Reviewed Original Research
2003
VgRBP71 Stimulates Cleavage at a Polyadenylation Signal in Vg1 mRNA, Resulting in the Removal of a cis-Acting Element that Represses Translation
Kolev NG, Huber PW. VgRBP71 Stimulates Cleavage at a Polyadenylation Signal in Vg1 mRNA, Resulting in the Removal of a cis-Acting Element that Represses Translation. Molecular Cell 2003, 11: 745-755. PMID: 12667456, DOI: 10.1016/s1097-2765(03)00071-6.Peer-Reviewed Original Research3' Untranslated RegionsAnimalsBase SequenceBinding SitesBinding, CompetitiveBlotting, WesternGlutathione TransferaseGlycoproteinsMolecular Sequence DataNucleic Acid ConformationOocytesPlasmidsPolymerase Chain ReactionProtein BindingProtein BiosynthesisProtein Structure, SecondaryReverse Transcriptase Polymerase Chain ReactionRibonucleasesRNARNA HelicasesRNA-Binding ProteinsRNA, MessengerTranscription, GeneticTransforming Growth Factor betaXenopusXenopus Proteins