2020
To mock or not: a comprehensive comparison of mock IP and DNA input for ChIP-seq
Xu J, Kudron MM, Victorsen A, Gao J, Ammouri HN, Navarro FCP, Gevirtzman L, Waterston RH, White KP, Reinke V, Gerstein M. To mock or not: a comprehensive comparison of mock IP and DNA input for ChIP-seq. Nucleic Acids Research 2020, 49: e17-e17. PMID: 33347581, PMCID: PMC7897498, DOI: 10.1093/nar/gkaa1155.Peer-Reviewed Original ResearchConceptsMock immunoprecipitationsSpurious sitesDNA inputCell linesMultiple cell typesOpen chromatinChIP-seqChromatin immunoprecipitationGenomic activityWhole organismNonspecific interactionsIP experimentsImmunoprecipitationCell typesIP antibodyTechnical noiseAbundanceComplex samplesChromatinGenomeSitesGenesOrganismsLinesInteraction
2018
The ModERN Resource: Genome-Wide Binding Profiles for Hundreds of Drosophila and Caenorhabditis elegans Transcription Factors
Kudron MM, Victorsen A, Gevirtzman L, Hillier LW, Fisher WW, Vafeados D, Kirkey M, Hammonds AS, Gersch J, Ammouri H, Wall ML, Moran J, Steffen D, Szynkarek M, Seabrook-Sturgis S, Jameel N, Kadaba M, Patton J, Terrell R, Corson M, Durham TJ, Park S, Samanta S, Han M, Xu J, Yan KK, Celniker SE, White KP, Ma L, Gerstein M, Reinke V, Waterston R. The ModERN Resource: Genome-Wide Binding Profiles for Hundreds of Drosophila and Caenorhabditis elegans Transcription Factors. Genetics 2018, 208: 937-949. PMID: 29284660, PMCID: PMC5844342, DOI: 10.1534/genetics.117.300657.Peer-Reviewed Original ResearchConceptsIndividual transcription factorsTranscription factorsModel organismsGenome-wide binding profilesMajor model organismsKey model organismDifferent transcription factorsTissue-specific patternsFly genomeWorm genomeChromatin immunoprecipitationStock CenterRegulatory pathwaysRegulatory sitesCaenorhabditisDrosophilaOrganismsGenomeBinding profileGenesModENCODESitesGFPImmunoprecipitationVast number
2017
Identification of an RNA Polymerase III Regulator Linked to Disease-Associated Protein Aggregation
Sin O, de Jong T, Mata-Cabana A, Kudron M, Zaini MA, Aprile FA, Seinstra RI, Stroo E, Prins RW, Martineau CN, Wang HH, Hogewerf W, Steinhof A, Wanker EE, Vendruscolo M, Calkhoven CF, Reinke V, Guryev V, Nollen EA. Identification of an RNA Polymerase III Regulator Linked to Disease-Associated Protein Aggregation. Molecular Cell 2017, 65: 1096-1108.e6. PMID: 28306505, PMCID: PMC5364375, DOI: 10.1016/j.molcel.2017.02.022.Peer-Reviewed Original ResearchMeSH KeywordsActive Transport, Cell NucleusAnimalsAnimals, Genetically ModifiedBinding SitesCaenorhabditis elegansCaenorhabditis elegans ProteinsCell NucleusCytosolDisease Models, AnimalNeurodegenerative DiseasesPeptidesPromoter Regions, GeneticProtein AggregatesProtein Aggregation, PathologicalProtein BindingRNA InterferenceRNA Polymerase IIIRNA, Small UntranslatedTranscription FactorsTranscription, GeneticConceptsProtein aggregationSmall non-coding RNAsForward genetic screenAggregation-prone proteinsDrivers of aggregationRNA polymerase IIINon-coding RNAsPolyglutamine-expanded huntingtinGenetic screenCellular homeostasisPolyglutamine aggregationAge-related neurodegenerative disordersPolymerase IIIEndogenous proteinsPolyglutamineCellular mechanismsProteinNeurodegenerative disordersCytosolSuch mechanismsAggregationLIRTranscriptionHuntingtinRNA
2016
A novel small molecule that disrupts a key event during the oocyte-to-embryo transition in C. elegans
Weicksel SE, Mahadav A, Moyle M, Cipriani PG, Kudron M, Pincus Z, Bahmanyar S, Abriola L, Merkel J, Gutwein M, Fernandez AG, Piano F, Gunsalus KC, Reinke V. A novel small molecule that disrupts a key event during the oocyte-to-embryo transition in C. elegans. Development 2016, 143: 3540-3548. PMID: 27510972, PMCID: PMC5087616, DOI: 10.1242/dev.140046.Peer-Reviewed Original ResearchConceptsEmbryo transitionProtein traffickingEarly embryonic eventsCandidate target genesComplex cellular eventsSmall-molecule screenCaenorhabditis elegansInviable embryosC. elegansEmbryonic lethalityMore key componentsEarly embryogenesisTranscription factorsEarly embryosEmbryonic eventsTarget genesCellular eventsSpecies specificityEggshell integrityNovel small moleculesElegansRemarkable specificityKey eventsOsmotic sensitivityDiverse aspects
2013
Tissue-specific direct targets of Caenorhabditis elegans Rb/E2F dictate distinct somatic and germline programs
Kudron M, Niu W, Lu Z, Wang G, Gerstein M, Snyder M, Reinke V. Tissue-specific direct targets of Caenorhabditis elegans Rb/E2F dictate distinct somatic and germline programs. Genome Biology 2013, 14: r5. PMID: 23347407, PMCID: PMC4053757, DOI: 10.1186/gb-2013-14-1-r5.Peer-Reviewed Original ResearchConceptsRb/E2FLin-35Target genesGenome-wide binding profilesGene expressionTissue-specific gene regulationLin-35 mutantsDistinct cell fatesSmall RNA pathwaysEffector target genesDirect target geneBinding profileGermline programHPL-2Chromatin associationH3K36 methylationRNA pathwaysCSR-1Germline transformationC. elegansGene regulationCell fateE2FDirect targetMultiple tissues
2008
C. elegans Nucleostemin Is Required for Larval Growth and Germline Stem Cell Division
Kudron MM, Reinke V. C. elegans Nucleostemin Is Required for Larval Growth and Germline Stem Cell Division. PLOS Genetics 2008, 4: e1000181. PMID: 18725931, PMCID: PMC2515194, DOI: 10.1371/journal.pgen.1000181.Peer-Reviewed Original ResearchConceptsRibosome biogenesisGermline stem cell divisionLarval arrest phenotypeGerm line functionGermline stem cellsStem cell divisionCell growthNematode C. elegansN-terminal domainStem cellsExhibit reduced levelsCell cycle arrestArrest phenotypeNucleolar factorsC. elegansRRNA transcriptionGrowth defectNucleolar functionGerm lineCell divisionLarval growthTransgenic studiesBiogenesisStable expressionProliferative state
2006
RecA Dimers Serve as a Functional Unit for Assembly of Active Nucleoprotein Filaments †
Forget A, Kudron M, McGrew D, Calmann M, Schiffer C, Knight K. RecA Dimers Serve as a Functional Unit for Assembly of Active Nucleoprotein Filaments †. Biochemistry 2006, 45: 13537-13542. PMID: 17087507, PMCID: PMC2522307, DOI: 10.1021/bi060938q.Peer-Reviewed Original ResearchConceptsNucleoprotein filamentDNA strand exchange activityCo-protease activityActive nucleoprotein filamentStrand exchange activityDNA strand exchangeRadA proteinVivo DNA repairHomologous recombinationDNA repairStrand exchangeFilament assemblyDimer proteinRecAImportant functional unitsFunctional unitsExchange activityCoordinated activityStructural studiesProteinAssemblyFilamentsRAD51DNAATPase