2025
CACNA1G, A Heterotaxy Candidate Gene, Plays a Role in Ciliogenesis and Left‐Right Patterning in Xenopus tropicalis
Kostiuk V, Kabir R, Akbari R, Rushing A, González D, Kim A, Kim A, Zenisek D, Khokha M. CACNA1G, A Heterotaxy Candidate Gene, Plays a Role in Ciliogenesis and Left‐Right Patterning in Xenopus tropicalis. Genesis 2025, 63: e70009. PMID: 40008628, PMCID: PMC11867209, DOI: 10.1002/dvg.70009.Peer-Reviewed Original ResearchConceptsCongenital heart diseaseCACNA1GLow-voltage-activated calcium channelsExpression of Cacna1gCalcium channelsPatient cohortCardiac functionLR patterningHeterotaxyLR organizerChannel familyCACNA1SHeart diseaseLeft-rightG expressionXenopus tropicalisAbnormal expressionProcess of cilia formationCardiac loopingMultiple organsSignaling cascadesLR asymmetryPatientsT-typeEmbryonic developmentNup107 contributes to the maternal-to-zygotic transition by preventing the premature nuclear export of pri-miR427
Kostiuk V, Kabir R, Levangie K, Empke S, Morgan K, Owens N, Lusk C, Khokha M. Nup107 contributes to the maternal-to-zygotic transition by preventing the premature nuclear export of pri-miR427. Development 2025, 152: dev202865. PMID: 39791357, PMCID: PMC11829755, DOI: 10.1242/dev.202865.Peer-Reviewed Original ResearchConceptsMaternal transcriptsMaternal-to-zygotic transitionMaternal RNA clearanceZinc-finger transcription factorDegradation of maternal transcriptsEctodermal cell fatesMaternal-zygotic transitionNuclear pore complexNucleoporin functionZygotic transcriptionNuclear exportTranscript stabilityCell fateNuclear retentionTranscription factorsPore complexNup107TranscriptionEarly embryosRecognition sitesRNA clearanceGastrulationGerm layersTime course
2023
SMC5 Plays Independent Roles in Congenital Heart Disease and Neurodevelopmental Disability
O'Brien M, Pryzhkova M, Lake E, Mandino F, Shen X, Karnik R, Atkins A, Xu M, Ji W, Konstantino M, Brueckner M, Ment L, Khokha M, Jordan P. SMC5 Plays Independent Roles in Congenital Heart Disease and Neurodevelopmental Disability. International Journal Of Molecular Sciences 2023, 25: 430. PMID: 38203602, PMCID: PMC10779392, DOI: 10.3390/ijms25010430.Peer-Reviewed Original ResearchCFAP45, a heterotaxy and congenital heart disease gene, affects cilia stability
Deniz E, Pasha M, Guerra M, Viviano S, Ji W, Konstantino M, Jeffries L, Lakhani S, Medne L, Skraban C, Krantz I, Khokha M. CFAP45, a heterotaxy and congenital heart disease gene, affects cilia stability. Developmental Biology 2023, 499: 75-88. PMID: 37172641, PMCID: PMC10373286, DOI: 10.1016/j.ydbio.2023.04.006.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBody PatterningCiliaHeart Defects, CongenitalHeterotaxy SyndromeMutation, MissensePhenotypeXenopusXenopus ProteinsConceptsLeft-right organizerCilia stabilityLeft-right patterningCongenital heart disease genesApical surfaceCell apical surfaceLive confocal imagingLeftward fluid flowHeart disease genesRecessive missense mutationLethal birth defectMotile monociliaProtein familyEarly embryogenesisMulticiliated cellsCiliary axonemeDisease genesFrog embryosGenetic underpinningsWhole-exome sequencingMissense mutationsConfocal imagingEmbryosCiliaCongenital heart disease
2020
Disrupted ER membrane protein complex-mediated topogenesis drives congenital neural crest defects
Marquez J, Criscione J, Charney RM, Prasad MS, Hwang WY, Mis EK, García-Castro MI, Khokha MK. Disrupted ER membrane protein complex-mediated topogenesis drives congenital neural crest defects. Journal Of Clinical Investigation 2020, 130: 813-826. PMID: 31904590, PMCID: PMC6994125, DOI: 10.1172/jci129308.Peer-Reviewed Original ResearchConceptsEndoplasmic reticulum (ER) membrane protein complexMultipass membrane proteinsNeural crest cellsMembrane proteinsHuman NCC developmentER membrane proteinsMembrane protein complexesCell-cell signalsMyriad of functionsNCC defectsNCC developmentProtein complexesUnbiased proteomicsXenopus modelTransmembrane proteinFunction allelesPatient phenotypesCrest cellsMolecular connectionNeural crestMolecular mechanismsBirth defectsPatient variantsEMC1Β-catenin
2019
Expression, purification and crystallization of the novel Xenopus tropicalis ALDH16B1, a homologue of human ALDH16A1
Pantouris G, Dioletis E, Chen Y, Thompson DC, Vasiliou V, Lolis EJ. Expression, purification and crystallization of the novel Xenopus tropicalis ALDH16B1, a homologue of human ALDH16A1. Chemico-Biological Interactions 2019, 304: 168-172. PMID: 30894314, PMCID: PMC6746316, DOI: 10.1016/j.cbi.2019.03.009.Peer-Reviewed Original ResearchConceptsAldehyde dehydrogenaseCritical Cys residuesPreliminary crystallographic analysisGenomic analysisSf9 cellsCys residuesALDH16A1Novel familyLower animalsSize exclusion chromatographyActive siteStructure determinationMetabolomics studiesCrystallographic analysisCellsMammalsHomologuesGenesExclusion chromatographyFishStructural characteristicsFrogsPathogenesis of goutUnique structural characteristicsResiduesNon-acylated Wnts Can Promote Signaling
Speer KF, Sommer A, Tajer B, Mullins MC, Klein PS, Lemmon MA. Non-acylated Wnts Can Promote Signaling. Cell Reports 2019, 26: 875-883.e5. PMID: 30673610, PMCID: PMC6429962, DOI: 10.1016/j.celrep.2018.12.104.Peer-Reviewed Original Research
2018
RPSA, a candidate gene for isolated congenital asplenia, is required for pre-rRNA processing and spleen formation in Xenopus
Griffin JN, Sondalle SB, Robson A, Mis EK, Griffin G, Kulkarni SS, Deniz E, Baserga SJ, Khokha MK. RPSA, a candidate gene for isolated congenital asplenia, is required for pre-rRNA processing and spleen formation in Xenopus. Development 2018, 145: dev166181. PMID: 30337486, PMCID: PMC6215398, DOI: 10.1242/dev.166181.Peer-Reviewed Original ResearchConceptsPre-rRNA processingSmall ribosomal subunitCommon disease-associated mutationDisease-associated mutationsRpsA mRNARibosome biogenesisRibosome productionRibosome functionRibosomal subunitCandidate genesHuman mRNAsProtein componentsImpairs expressionSpleen developmentMolecular patterningRPSASpleen anlageMutationsXenopusGenesFirst animal modelUniversal requirementMRNAMutations in multiple components of the nuclear pore complex cause nephrotic syndrome
Braun DA, Lovric S, Schapiro D, Schneider R, Marquez J, Asif M, Hussain MS, Daga A, Widmeier E, Rao J, Ashraf S, Tan W, Lusk CP, Kolb A, Jobst-Schwan T, Schmidt JM, Hoogstraten CA, Eddy K, Kitzler TM, Shril S, Moawia A, Schrage K, Khayyat AIA, Lawson JA, Gee HY, Warejko JK, Hermle T, Majmundar AJ, Hugo H, Budde B, Motameny S, Altmüller J, Noegel AA, Fathy HM, Gale DP, Waseem SS, Khan A, Kerecuk L, Hashmi S, Mohebbi N, Ettenger R, Serdaroğlu E, Alhasan KA, Hashem M, Goncalves S, Ariceta G, Ubetagoyena M, Antonin W, Baig SM, Alkuraya FS, Shen Q, Xu H, Antignac C, Lifton RP, Mane S, Nürnberg P, Khokha MK, Hildebrandt F. Mutations in multiple components of the nuclear pore complex cause nephrotic syndrome. Journal Of Clinical Investigation 2018, 128: 4313-4328. PMID: 30179222, PMCID: PMC6159964, DOI: 10.1172/jci98688.Peer-Reviewed Original ResearchConceptsNuclear pore complexSteroid-resistant nephrotic syndromeCRISPR/Cas9 knockoutOrgan-specific phenotypesNephrotic syndromeRing subunitsMorpholino knockdownEssential genesEnd-stage renal diseasePore complexNPC subunitsCoimmunoprecipitation experimentsAllelic effectsNUP85CRISPR/Nup107Hypomorphic mutationsNup133WT mRNAEarly lethalityGenesImportant effectorsSubunitsMutationsRenal diseaseThe age-regulated zinc finger factor ZNF367 is a new modulator of neuroblast proliferation during embryonic neurogenesis
Naef V, Monticelli S, Corsinovi D, Mazzetto M, Cellerino A, Ori M. The age-regulated zinc finger factor ZNF367 is a new modulator of neuroblast proliferation during embryonic neurogenesis. Scientific Reports 2018, 8: 11836. PMID: 30087422, PMCID: PMC6081467, DOI: 10.1038/s41598-018-30302-2.Peer-Reviewed Original ResearchConceptsGene co-regulation networksEmbryonic neurogenesisWeighted-gene co-expression network analysisAge-regulated genesCo-regulation networkCo-expression network analysisNeuroblast cell cycleProgression of mitosisCandidate gene approachAdult neural stem cellsGene lossSpindle checkpointNext-generation sequencingTranscription factorsZNF367Neural stem cellsGene approachCell cycleDisease coincidePhysiological functionsKey controllerCentral nervous systemNew modulatorsNeuroblast proliferationStem cells
2016
Expression of ribosomopathy genes during Xenopus tropicalis embryogenesis
Robson A, Owens ND, Baserga SJ, Khokha MK, Griffin JN. Expression of ribosomopathy genes during Xenopus tropicalis embryogenesis. BMC Developmental Biology 2016, 16: 38. PMID: 27784267, PMCID: PMC5081970, DOI: 10.1186/s12861-016-0138-5.Peer-Reviewed Original ResearchConceptsRibosome biogenesis factorsBiogenesis factorsVentral blood islandsHuman congenital diseasesCranial neural crestRNA-seq dataAntisense mRNA probesBlood islandsEmbryonic developmentDistinct tissuesNeural crestProtein productionDifferential expressionTranscript numbersMachinery componentsSpecific tissuesSpecific phenotypesRibosomopathiesSitu hybridizationMRNA probesRibosomesExpressionTissue localizationPhenotypeFactor expression
2015
Hepatocystin is Essential for TRPM7 Function During Early Embryogenesis
Overton JD, Komiya Y, Mezzacappa C, Nama K, Cai N, Lou L, Fedeles SV, Habas R, Runnels LW. Hepatocystin is Essential for TRPM7 Function During Early Embryogenesis. Scientific Reports 2015, 5: 18395. PMID: 26671672, PMCID: PMC4680877, DOI: 10.1038/srep18395.Peer-Reviewed Original ResearchConceptsXenopus laevis embryosEmbryonic lethalityTRPM7 functionLaevis embryosProtein kinase C substrate 80KEarly embryonic lethalityNoncatalytic beta subunitXenopus laevis embryogenesisEmbryonic day E11.5TRPM7 ion channelVertebrate gastrulationGastrulation defectsResident enzymesEarly embryogenesisPolycystin-2TRPM7 protein expressionDay E11.5KDa proteinGlucosidase IIEndoplasmic reticulumBeta subunitOverexpression of TRPM7Second alleleSomatic lossIon channelsThe NIMA-like kinase Nek2 is a key switch balancing cilia biogenesis and resorption in the development of left-right asymmetry
Endicott SJ, Basu B, Khokha M, Brueckner M. The NIMA-like kinase Nek2 is a key switch balancing cilia biogenesis and resorption in the development of left-right asymmetry. Development 2015, 142: 4068-4079. PMID: 26493400, PMCID: PMC4712839, DOI: 10.1242/dev.126953.Peer-Reviewed Original ResearchAnimalsBody PatterningCentriolesCiliaGene Expression Regulation, DevelopmentalGene Knockdown TechniquesHistone Deacetylase 6Histone DeacetylasesHomeodomain ProteinsHumansIntercellular Signaling Peptides and ProteinsMiceMicroscopy, FluorescenceMutationNIMA-Related KinasesNuclear Pore Complex ProteinsProtein Serine-Threonine KinasesRNA InterferenceSignal TransductionTranscription FactorsXenopusXenopus Proteins
2014
A Tarantula-Venom Peptide Antagonizes the TRPA1 Nociceptor Ion Channel by Binding to the S1–S4 Gating Domain
Gui J, Liu B, Cao G, Lipchik AM, Perez M, Dekan Z, Mobli M, Daly NL, Alewood PF, Parker LL, King GF, Zhou Y, Jordt SE, Nitabach MN. A Tarantula-Venom Peptide Antagonizes the TRPA1 Nociceptor Ion Channel by Binding to the S1–S4 Gating Domain. Current Biology 2014, 24: 473-483. PMID: 24530065, PMCID: PMC3949122, DOI: 10.1016/j.cub.2014.01.013.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsBinding SitesDrug Evaluation, PreclinicalFemaleGene LibraryHumansMolecular Sequence DataNAV1.2 Voltage-Gated Sodium ChannelOocytesPeptidesProtein Structure, TertiarySpider VenomsTransient Receptor Potential ChannelsVoltage-Gated Sodium Channel BlockersXenopus ProteinsConceptsTransient receptor potential ankyrin 1Ion channel modifiersProTxIon channel transient receptor potential ankyrin 1Channel modifiersPeptide toxinsSpecific peptidesIon channelsVoltage-gated sodium channelsContext of painS1-S4Spider venomPotential clinical applicationsTRPA1 antagonistTRPA1 functionAnkyrin 1PeptidesModifiersPeptide antagonistAntagonistSodium channelsPharmacological reagentsReagentsClinical applicationNav1.2
2012
Exon capture and bulk segregant analysis: rapid discovery of causative mutations using high-throughput sequencing
del Viso F, Bhattacharya D, Kong Y, Gilchrist MJ, Khokha MK. Exon capture and bulk segregant analysis: rapid discovery of causative mutations using high-throughput sequencing. BMC Genomics 2012, 13: 649. PMID: 23171430, PMCID: PMC3526394, DOI: 10.1186/1471-2164-13-649.Peer-Reviewed Original ResearchConceptsBulk segregant analysisForward genetic screenSegregant analysisGenetic screenGenome assemblyExon captureCausative mutationsVertebrate model systemHigh-throughput sequencingHuman genetic analysisThousands of SNPsAssembly of scaffoldsModel systemGenomic resourcesVertebrate modelXenopus tropicalisFine mappingGenetic analysisCapture sequencingSequence variantsSequencingMutationsRapid discoveryMutantsExome sequencingEmbryonic poly(A)-binding protein (ePAB) phosphorylation is required for Xenopus oocyte maturation
Friend K, Brook M, Bezirci FB, Sheets MD, Gray NK, Seli E. Embryonic poly(A)-binding protein (ePAB) phosphorylation is required for Xenopus oocyte maturation. Biochemical Journal 2012, 445: 93-100. PMID: 22497250, PMCID: PMC3955212, DOI: 10.1042/bj20120304.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBlotting, WesternCytoplasmFemaleFluorescent Antibody TechniqueGene Expression Regulation, DevelopmentalImmunoprecipitationMutationOocytesOogenesisPhosphorylationPoly APoly(A)-Binding ProteinsPolyadenylationProtein BiosynthesisProtein Processing, Post-TranslationalRNA, MessengerXenopus laevisXenopus ProteinsConceptsCytoplasmic polyadenylationOocyte maturationPost-transcriptional regulatorsEarly embryonic developmentPost-translational modificationsXenopus oocyte maturationMaternal mRNAsProtein phosphorylationResidue clustersTranslational activationEmbryonic developmentXenopus laevis oocytesProtein activityPhosphorylationFirst insightLaevis oocytesPolyadenylationInherent abilityEPABMaturationPhosphoproteinRegulatorMutationsMRNAOocytes
2011
Nucleosome Disruption by DNA Ligase III-XRCC1 Promotes Efficient Base Excision Repair
Odell ID, Barbour JE, Murphy DL, Della-Maria JA, Sweasy JB, Tomkinson AE, Wallace SS, Pederson DS. Nucleosome Disruption by DNA Ligase III-XRCC1 Promotes Efficient Base Excision Repair. Molecular And Cellular Biology 2011, 31: 4623-4632. PMID: 21930793, PMCID: PMC3209256, DOI: 10.1128/mcb.05715-11.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsDeoxyribonuclease (Pyrimidine Dimer)DNADNA DamageDNA GlycosylasesDNA Ligase ATPDNA LigasesDNA Polymerase betaDNA RepairDNA-(Apurinic or Apyrimidinic Site) LyaseDNA-Binding ProteinsHumansLytechinusNucleosomesPoly-ADP-Ribose Binding ProteinsReactive Oxygen SpeciesX-ray Repair Cross Complementing Protein 1XenopusXenopus ProteinsConceptsBase excision repairNucleosome disruptionApurinic endonucleaseExcision repairEfficient base excision repairNucleated human cellsDNA polymerase βNucleosome substratesRibosomal DNASingle base gapHuman cellsNucleosomesDNA ligasePolymerase βPol βRate-limiting stepHNTH1Ternary complexDNAUnique roleChromatinLigaseDisruptionEndonucleaseLesions form
2010
APCDD1 is a novel Wnt inhibitor mutated in hereditary hypotrichosis simplex
Shimomura Y, Agalliu D, Vonica A, Luria V, Wajid M, Baumer A, Belli S, Petukhova L, Schinzel A, Brivanlou A, Barres B, Christiano A. APCDD1 is a novel Wnt inhibitor mutated in hereditary hypotrichosis simplex. Nature 2010, 464: 1043-1047. PMID: 20393562, PMCID: PMC3046868, DOI: 10.1038/nature08875.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsbeta CateninCell DifferentiationCell LineCell ProliferationChick EmbryoChromosome MappingChromosomes, Human, Pair 18Genes, DominantGenes, ReporterHairHair FollicleHumansHypotrichosisIntracellular Signaling Peptides and ProteinsMembrane GlycoproteinsMembrane ProteinsMiceMutant ProteinsNeuronsPoint MutationScalpSignal TransductionSkinSpinal CordStem CellsWnt ProteinsXenopus laevisXenopus ProteinsConceptsHereditary hypotrichosis simplexSignal transduction pathwaysHypotrichosis simplexMesenchymal cell compartmentGenetic linkage analysisNovel Wnt inhibitorsMembrane-bound glycoproteinTransduction pathwaysHuman hair folliclesLinkage analysisAPCDD1Functional studiesHair folliclesWnt inhibitorsCell compartmentDowny hairsGenesImportant componentThick hairPathwayHairGlycoproteinCompartmentsDegenerative processFamily
2009
Cadherin Adhesion, Tissue Tension, and Noncanonical Wnt Signaling Regulate Fibronectin Matrix Organization
Dzamba BJ, Jakab KR, Marsden M, Schwartz MA, DeSimone DW. Cadherin Adhesion, Tissue Tension, and Noncanonical Wnt Signaling Regulate Fibronectin Matrix Organization. Developmental Cell 2009, 16: 421-432. PMID: 19289087, PMCID: PMC2682918, DOI: 10.1016/j.devcel.2009.01.008.Peer-Reviewed Original ResearchConceptsCadherin adhesionBlastocoel roofPlanar cell polarity signalingMatrix assemblyCell polarity signalingCell-cell adhesionFN fibril formationFN fibril assemblyPolarity signalingFocal adhesionsActin reorganizationXenopus embryosRegulatory pathwaysMyosin contractilityFibronectin matrixMatrix organizationSpatiotemporal localizationCultured cellsCell surfaceAnalogous roleFibril formationFibril assemblyFibrillar matrixMechanical tensionAssembly
2008
A manganese-dependent ribozyme in the 3′-untranslated region of Xenopus Vg1 mRNA
Kolev NG, Hartland EI, Huber PW. A manganese-dependent ribozyme in the 3′-untranslated region of Xenopus Vg1 mRNA. Nucleic Acids Research 2008, 36: 5530-5539. PMID: 18753150, PMCID: PMC2553595, DOI: 10.1093/nar/gkn530.Peer-Reviewed Original Research
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