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
2017
The proteome and transcriptome of the infectious metacyclic form of Trypanosoma brucei define quiescent cells primed for mammalian invasion
Christiano R, Kolev NG, Shi H, Ullu E, Walther TC, Tschudi C. The proteome and transcriptome of the infectious metacyclic form of Trypanosoma brucei define quiescent cells primed for mammalian invasion. Molecular Microbiology 2017, 106: 74-92. PMID: 28742275, PMCID: PMC5607103, DOI: 10.1111/mmi.13754.Peer-Reviewed Original ResearchConceptsInfectious metacyclic formsTsetse fly vectorMetacyclic formsVariant surface glycoprotein expression sitesQuiescent cellsGene expression profilesFly vectorsAvailability of nutrientsMammalian invasionsCell surface componentsCell divisionProcyclic trypanosomesMammalian hostsTrypanosoma bruceiMRNA sequencingExpression profilesExpression sitesMetabolic enzymesBloodstream formsInfectious metacyclicsProtein 6TranscriptomeTsetse fliesProteomeProtein levelsThe Canonical Poly (A) Polymerase PAP1 Polyadenylates Non-Coding RNAs and Is Essential for snoRNA Biogenesis in Trypanosoma brucei
Chikne V, Gupta SK, Doniger T, K. SR, Cohen-Chalamish S, Ben-Asher HW, Kolet L, Yahia NH, Unger R, Ullu E, Kolev NG, Tschudi C, Michaeli S. The Canonical Poly (A) Polymerase PAP1 Polyadenylates Non-Coding RNAs and Is Essential for snoRNA Biogenesis in Trypanosoma brucei. Journal Of Molecular Biology 2017, 429: 3301-3318. PMID: 28456523, DOI: 10.1016/j.jmb.2017.04.015.Peer-Reviewed Original ResearchConceptsNon-coding RNAsPoly (ADP-ribose) polymeraseUnique RNA processing mechanismsCis-spliced intronsRNA processing mechanismsSmall nucleolar RNAsLong non-coding RNAsPolyadenylation of mRNAParasite Trypanosoma bruceiSnoRNA biogenesisTrans splicingPrecursor snoRNASnoRNA processingNucleolar RNAsPAP1Trypanosoma bruceiPolyadenylationMajor substrateSnoRNAsTrypanosoma cruziPAP2RNAPolymerase Pap1TrypanosomesCausative agent
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
2014
Construction of Trypanosoma brucei Illumina RNA-Seq Libraries Enriched for Transcript Ends
Kolev NG, Ullu E, Tschudi C. Construction of Trypanosoma brucei Illumina RNA-Seq Libraries Enriched for Transcript Ends. Methods In Molecular Biology 2014, 1201: 165-175. PMID: 25388113, DOI: 10.1007/978-1-4939-1438-8_9.Peer-Reviewed Original ResearchConceptsHuman pathogen Trypanosoma bruceiHigh-throughput RNA sequencingLong polycistronic precursorsGenome-wide scaleIllumina RNA-seqPathogen Trypanosoma bruceiRNA polymerase IIRNA-seq librariesSingle-nucleotide resolutionTranscript endsTranscript boundariesTranscriptome annotationUnannotated genesPolymerase IICellular abundancePolycistronic precursorsTranscription initiationGene clusterRNA-seqPolyadenylation sitesRNA sequencingMRNA precursorsTrypanosoma bruceiRNA moleculesMRNA moleculesThe emerging role of RNA‐binding proteins in the life cycle of Trypanosoma brucei
Kolev NG, Ullu E, Tschudi C. The emerging role of RNA‐binding proteins in the life cycle of Trypanosoma brucei. Cellular Microbiology 2014, 16: 482-489. PMID: 24438230, PMCID: PMC3974610, DOI: 10.1111/cmi.12268.Peer-Reviewed Original ResearchConceptsParasitic protozoan Trypanosoma bruceiIdentification of RBPsTargets of RBPsSpecific gene networksProtozoan Trypanosoma bruceiPost-transcriptional mechanismsGene regulatory networksGene expression patternsRelated trypanosomatidsTranscriptional machineryCellular fateGene networksRegulatory networksTrypanosoma bruceiExpression patternsRegulatory mechanismsDifferent hostsRBPsLife cyclePathogenic organismsRNAOrganismsProteinDifferent environmentsCrucial role
2012
Comparative 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
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