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 ResearchMeSH KeywordsAntibodiesBinding SitesCell LineChromatin Immunoprecipitation SequencingDNAHumansTranscription FactorsConceptsMock 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 ResearchMeSH KeywordsAnimalsCaenorhabditis elegansCaenorhabditis elegans ProteinsEmbryo, NonmammalianEmbryonic DevelopmentOocytesTranscription FactorsConceptsEmbryo 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