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
2009
Distinct and overlapping roles for two Dicer-like proteins in the RNA interference pathways of the ancient eukaryote Trypanosoma brucei
Patrick KL, Shi H, Kolev NG, Ersfeld K, Tschudi C, Ullu E. Distinct and overlapping roles for two Dicer-like proteins in the RNA interference pathways of the ancient eukaryote Trypanosoma brucei. Proceedings Of The National Academy Of Sciences Of The United States Of America 2009, 106: 17933-17938. PMID: 19815526, PMCID: PMC2764927, DOI: 10.1073/pnas.0907766106.Peer-Reviewed Original ResearchConceptsDicer-like enzymesRNA interferenceRNAi pathwayBiogenesis of siRNAsDicer-like proteinsNuclear RNAi pathwaySingle Argonaute proteinEnd modificationReverse genetic analysisRNAi-deficient cellsRNA interference (RNAi) pathwayWild-type cellsAncient eukaryotesArgonaute proteinsRNAi responseAncient traitRepeat transcriptsInterference pathwayCytoplasmic proteinsImportant human pathogenTrypanosoma bruceiGenetic analysisRNAi triggersFunctional analysisIntermediate transcripts
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 groupsEukaryotesCharacterization of a candidate Trypanosoma brucei U1 small nuclear RNA gene
Djikeng A, Ferreira L, D'Angelo M, Dolezal P, Lamb T, Murta S, Triggs V, Ulbert S, Villarino A, Renzi S, Ullu E, Tschudi C. Characterization of a candidate Trypanosoma brucei U1 small nuclear RNA gene. Molecular And Biochemical Parasitology 2001, 113: 109-115. PMID: 11254959, DOI: 10.1016/s0166-6851(00)00384-4.Peer-Reviewed Original Research
2000
Cotranscriptional Cap 4 Formation on the Trypanosoma brucei Spliced Leader RNA*
Mair G, Ullu E, Tschudi C. Cotranscriptional Cap 4 Formation on the Trypanosoma brucei Spliced Leader RNA*. Journal Of Biological Chemistry 2000, 275: 28994-28999. PMID: 10880518, DOI: 10.1074/jbc.m004193200.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsRNA CapsRNA, ProtozoanRNA, Spliced LeaderTranscription, GeneticTrypanosoma brucei bruceiConceptsCap 4 structureSL RNAMRNA cap formationT. brucei cellsSpliced leader RNARNA cap structureSpliced leader sequenceTranscriptional arrestTrypanosomatid protozoaBrucei cellsLeader RNACap 4Cotranscriptional mechanismLeader sequenceTrypanosoma bruceiCap structureRNA transcriptsRibonucleoprotein formationAdenosine residuesPosition 117RNATranscriptsCap formationNucleotidesEukaryotes
1998
Physical and transcriptional analysis of the Trypanosoma brucei genome reveals a typical eukaryotic arrangement with close interspersionof RNA polymerase II- and III-transcribed genes
Marchetti M, Tschudi C, Silva E, Ullu E. Physical and transcriptional analysis of the Trypanosoma brucei genome reveals a typical eukaryotic arrangement with close interspersionof RNA polymerase II- and III-transcribed genes. Nucleic Acids Research 1998, 26: 3591-3598. PMID: 9671824, PMCID: PMC147737, DOI: 10.1093/nar/26.15.3591.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceChloramphenicol O-AcetyltransferaseDNA, ProtozoanEukaryotic CellsGene DosageGenome, ProtozoanMolecular Sequence DataPromoter Regions, GeneticProtozoan ProteinsRibonucleoprotein, U2 Small NuclearRibonucleoproteins, Small NuclearRNA Polymerase IIRNA Polymerase IIIRNA, MessengerTranscription, GeneticTrypanosoma brucei bruceiConceptsPol II transcription unitsPol III genesSmall nuclear RNAU3 small nuclear RNACAT gene cassettePol IITranscription unitRNA genesTranscriptional domainsPol IIICAT mRNAU2 small nuclear RNARNA gene lociPol II genesRNA polymerase IIGene cassettesMRNA processing signalsPolymerase IITranscriptional mapTranscriptional analysisCosmid clonesNuclear RNADistinct initiation sitesCAT geneGene locus
1997
Transcription of the Trypanosoma brucei spliced leader RNA gene is dependent only on the presence of upstream regulatory elements
Günzl A, Ullu E, Dörner M, Fragoso S, Hoffmann K, Milner J, Morita Y, Nguu E, Vanacova S, Wünsch S, Dare A, Kwon H, Tschudi C. Transcription of the Trypanosoma brucei spliced leader RNA gene is dependent only on the presence of upstream regulatory elements. Molecular And Biochemical Parasitology 1997, 85: 67-76. PMID: 9108549, DOI: 10.1016/s0166-6851(96)02816-2.Peer-Reviewed Original Research
1995
Accurate Transcription of the Trypanosoma brucei U2 Small Nuclear RNA Gene in a Homologous Extract *
Günzl A, Tschudi C, Nakaar V, Ullu E. Accurate Transcription of the Trypanosoma brucei U2 Small Nuclear RNA Gene in a Homologous Extract *. Journal Of Biological Chemistry 1995, 270: 17287-17291. PMID: 7542235, DOI: 10.1074/jbc.270.29.17287.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceGenes, ProtozoanMolecular Sequence DataMutationRNARNA Polymerase IIIRNA, Small NuclearTranscription, GeneticTrypanosoma brucei bruceiConceptsIntragenic control regionRNA polymerase IIIControl regionPolymerase IIIU2 small nuclear RNA genesTranscription systemSmall nuclear RNA genesGene expressionInsect form trypanosomesNuclear RNA genesU2 snRNA genesSnRNA gene promotersB-box elementsFull transcriptional activitySeries of mutationsSnRNA genesRNA genesInsect formsRNA polymeraseGene promoterTrypanosoma bruceiCell-free extractsTransient expressionBox elementTranscriptional activity
1994
Upstream tRNA genes are essential for expression of small nuclear and cytoplasmic RNA genes in trypanosomes.
Nakaar V, Dare A, Hong D, Ullu E, Tschudi C. Upstream tRNA genes are essential for expression of small nuclear and cytoplasmic RNA genes in trypanosomes. Molecular And Cellular Biology 1994, 14: 6736-6742. PMID: 7523857, PMCID: PMC359204, DOI: 10.1128/mcb.14.10.6736.Peer-Reviewed Original ResearchConceptsSmall RNA genesTRNA genesRNA genesSmall nuclear RNARegulatory elementsU6 small nuclear RNAUpstream tRNA genesIntragenic promoter elementsT. brucei cellsU6 snRNA genesRNA polymerase IIIB-box elementsSnRNA lociGenome organizationSnRNA genesRNA lociSmall RNAsBrucei cellsB-boxSubstitution mutantsPolymerase IIIFamily TrypanosomatidaeNuclear RNAGene transcriptionPromoter elementsRNA polymerase III-mediated transcription of the trypanosome U2 small nuclear RNA gene is controlled by both intragenic and extragenic regulatory elements.
Fantoni A, Dare A, Tschudi C. RNA polymerase III-mediated transcription of the trypanosome U2 small nuclear RNA gene is controlled by both intragenic and extragenic regulatory elements. Molecular And Cellular Biology 1994, 14: 2021-2028. PMID: 8114733, PMCID: PMC358562, DOI: 10.1128/mcb.14.3.2021.Peer-Reviewed Original ResearchMeSH KeywordsAmanitinsAnimalsBase SequenceConsensus SequenceDNA, ProtozoanGenes, ProtozoanMolecular Sequence DataPromoter Regions, GeneticRegulatory Sequences, Nucleic AcidRNA Polymerase IIIRNA, Small NuclearSequence AlignmentSequence DeletionSequence Homology, Nucleic AcidTranscription, GeneticTrypanosomaConceptsU2 small nuclear RNA genesSmall nuclear RNA genesNuclear RNA genesU2 snRNA genesSnRNA genesRNA genesCis-acting regulatory sequencesRNA polymerase III transcriptsInsect form trypanosomesSnRNA gene expressionRNA polymerase IIInternal control regionRNA polymerase IIIPolymerase III transcriptsTranscription start siteIII-like enzymeTRNA genesPolymerase IIRNA polymeraseRegulatory sequencesU2 snRNAControl regionPolymerase IIIStart siteRegulatory elements
1991
Trans splicing in trypanosomes requires methylation of the 5' end of the spliced leader RNA.
Ullu E, Tschudi C. Trans splicing in trypanosomes requires methylation of the 5' end of the spliced leader RNA. Proceedings Of The National Academy Of Sciences Of The United States Of America 1991, 88: 10074-10078. PMID: 1719544, PMCID: PMC52870, DOI: 10.1073/pnas.88.22.10074.Peer-Reviewed Original Research
1990
Permeable trypanosome cells as a model system for transceiption and trans-splicing
Ullu E, Tschudi C. Permeable trypanosome cells as a model system for transceiption and trans-splicing. Nucleic Acids Research 1990, 18: 3319-3326. PMID: 2356121, PMCID: PMC330939, DOI: 10.1093/nar/18.11.3319.Peer-Reviewed Original ResearchConceptsAlpha-tubulin RNASL RNAFree linear moleculesHigh molecular weight RNAMolecular weight RNARNA speciesLeader RNATrypanosome cellsDifferent genesWeight RNARNATranscriptionModel systemCritical rolePermeable cellsConcentrations of monovalentIntronsCellsGenesLesser extentHigh potassium concentrationSpeciesTrypanosomaMgCl2 concentrationLinear moleculesDestruction of U2, U4, or U6 small nuclear RNA blocks Trans splicing in trypanosome cells
Tschudi C, Ullu E. Destruction of U2, U4, or U6 small nuclear RNA blocks Trans splicing in trypanosome cells. Cell 1990, 61: 459-466. PMID: 1692263, DOI: 10.1016/0092-8674(90)90527-l.Peer-Reviewed Original ResearchConceptsTrans splicingU snRNAsPre-mRNAU6 small nuclear RNAU4/U6 snRNPsAlpha-tubulin transcriptsSmall nuclear RNAHigh molecular weight RNAMolecular weight RNASite-directed cleavageSL sequenceLeader RNATrypanosome cellsU6 snRNPsNuclear RNAU6 snRNATrypanosoma bruceiSplicing processSplicingWeight RNASnRNAEarly stepsRNAase HRNAIntrons
1988
Polygene transcripts are precursors to calmodulin mRNAs in trypanosomes.
Tschudi C, Ullu E. Polygene transcripts are precursors to calmodulin mRNAs in trypanosomes. The EMBO Journal 1988, 7: 455-463. PMID: 3366120, PMCID: PMC454342, DOI: 10.1002/j.1460-2075.1988.tb02833.x.Peer-Reviewed Original ResearchConceptsCalmodulin mRNACultured procyclic trypanosomesAbundant RNA speciesSteady-state RNAPulse-labeled RNAAuthentic precursorIntergenic regionRNA speciesProcyclic trypanosomesCalmodulin genePolyadenylation sitesAfrican trypanosomesHybridization probesTranscriptsStreptavidin-agaroseDiscrete endsSmall familyTrypanosomesMRNAGenesRNASpeciesCalmodulinTrypanosoma brucei gambienseBrucei gambiense
1984
Alu sequences are processed 7SL RNA genes
Ullu E, Tschudi C. Alu sequences are processed 7SL RNA genes. Nature 1984, 312: 171-172. PMID: 6209580, DOI: 10.1038/312171a0.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceBiological EvolutionDrosophila melanogasterGenesHumansRNASpecies SpecificityTranscription, GeneticXenopusConceptsRNA genesAlu sequencesMiddle repetitive DNA sequencesAbundant cytoplasmic RNARepetitive DNA sequencesHuman 7SL RNAInsect sequencesAlu domainMammalian radiationDrosophila melanogasterEvolutionary distanceXenopus sequenceAbundant familyDNA sequencesNucleotide sequenceCDNA copyCytoplasmic RNAPair sequencePrimary structureProtein secretionRNAGenesHuman counterpartSequenceSignificant block