Michelle Kudron, PhD, AB
she/her/hers
Associate Research Scientist in GeneticsDownloadHi-Res Photo
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Associate Research Scientist in Genetics
Biography
Michelle Kudron attended Smith College and received her AB degree in Biology in 2002. In 2001, she completed a Smith summer internship in the laboratory of Celia Schiffer in the Department of Biochemistry and Molecular Pharmacology at UMASS Medical School studying Human Immunodeficiency Virus. Following graduation, she returned to the Schiffer lab and Knight Lab to work as a Research Laboratory Associate uncovering a novel role for dimeric RecA in the assembly of nucleoprotein filaments and homologous recombination (Kudron et al., 2006). In 2003, she attended Yale University and earned her Ph.D. in Genetics in the laboratory of Valerie Reinke in 2009 studying the role for C. elegans nucleostemin in regulating cell growth and proliferation by modulating ribosome biogenesis (Kudron MM and Reinke V, 2008).
Since obtaining her doctorate, Michelle has been interested in the role that transcription factors play at both the tissue-specific level as well as more globally in C. elegans.
Appointments
Education & Training
- PhD
- Yale School of Medicine (2009)
- AB
- Smith College, Biology (2002)
Research
Overview
I am interested in the role that transcription factors (TFs) play at both the tissue-specific level as well as more globally in C. elegans. I pioneered the first in depth examination of tissue-specific binding of the Rb/E2F pathway in vivo. More recently, I have been a lead member of modERN (Model Organism Encyclopendia of Regulatory Networks) which is a multi-lab effort to capture the genome-wide binding sites of all the TFs in both worm and fly.
Research at a Glance
Yale Co-Authors
Frequent collaborators of Michelle Kudron's published research.
Publications Timeline
A big-picture view of Michelle Kudron's research output by year.
Valerie Reinke, PhD
Guilin Wang, PhD
8Publications
326Citations
Publications
2024
Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships.
Kudron M, Gewirtzman L, Victorsen A, Lear B, Vafeados D, Gao J, Xu J, Samanta S, Frink E, Tran-Pearson A, Hyunh C, Hammonds A, Fisher W, Wall M, Wesseling G, Hernandez V, Lin Z, Kasparian M, White K, Allada R, Gerstein M, Hillier L, Celniker S, Reinke V, Waterston R. Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships. Genome Research 2024, gr.279037.124. PMID: 39438113, DOI: 10.1101/gr.279037.124.Peer-Reviewed Original ResearchConceptsHigh-occupancy targetC. elegans transcription factorsSingle cell RNA-seq dataRegulatory relationshipsTranscription factor (TFChromatin immunoprecipitation sequencing dataTF-target relationshipsChIP-seq dataConsensus sequence motifRNA-seq dataDrosophila melanogaster</i>Promote target gene expressionTarget gene expressionChIP-seqSequence motifsSequence dataRegulatory networksEvents in vivoStock CenterModel organismsTranscription factorsTF functionGene expressionBinding sitesCell types
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 ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsMock 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 ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsIndividual 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 ResearchCitationsAltmetricMeSH Keywords and ConceptsMeSH 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 ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsEmbryo 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 ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsRb/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 ResearchCitationsMeSH Keywords and ConceptsConceptsRibosome 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 ResearchCitationsMeSH Keywords and ConceptsConceptsNucleoprotein 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