2020
Transcriptomic responses to hypoxia in endometrial and decidual stromal cells
Rytkönen KT, Heinosalo T, Mahmoudian M, Ma X, Perheentupa A, Elo LL, Poutanen M, Wagner G. Transcriptomic responses to hypoxia in endometrial and decidual stromal cells. Reproduction 2020, 160: 39-51. PMID: 32272449, DOI: 10.1530/rep-19-0615.Peer-Reviewed Original ResearchConceptsDecidual stromal cellsEndometrial stromal fibroblastsEndometriotic stromal cellsStromal cellsInflammatory transcription factorsEpithelial-mesenchymal transitionExpression of JunDCEBP transcription factorsCell typesHealthy endometriumEndometriosis lesionsProgesterone receptorDecidualization processUterine endometriumStromal fibroblastsMesenchymal transitionProgesterone signalingEndometriumHypoxiaHypoxia pathwayTranscription factorsHuman reproductive successDistinct transcriptional statesExpression of genesJun/Fos
2009
Measuring Transcription Factor–Binding Site Turnover: A Maximum Likelihood Approach Using Phylogenies
Otto W, Stadler PF, López-Giraldéz F, Townsend JP, Lynch VJ, Wagner GP. Measuring Transcription Factor–Binding Site Turnover: A Maximum Likelihood Approach Using Phylogenies. Genome Biology And Evolution 2009, 1: 85-98. PMID: 20333180, PMCID: PMC2817405, DOI: 10.1093/gbe/evp010.Peer-Reviewed Original ResearchTranscription factor-binding sitesCis-regulatory elementsHOXA clusterSelective pressureGene expression evolutionMethionine biosynthesis pathwayLow sequence similarityFactor-binding sitesClade-specific differencesTurnover rateExpression evolutionSpecies treeBiosynthesis pathwayRelated speciesSequence similaritySite turnoverDifferent organismsSequence evolutionTranscription factorsDifferent cladesFungal dataProgesterone response elementMaximum likelihood modelVertebratesTurnover
2008
Adaptive changes in the transcription factor HoxA-11 are essential for the evolution of pregnancy in mammals
Lynch VJ, Tanzer A, Wang Y, Leung FC, Gellersen B, Emera D, Wagner GP. Adaptive changes in the transcription factor HoxA-11 are essential for the evolution of pregnancy in mammals. Proceedings Of The National Academy Of Sciences Of The United States Of America 2008, 105: 14928-14933. PMID: 18809929, PMCID: PMC2567470, DOI: 10.1073/pnas.0802355105.Peer-Reviewed Original ResearchConceptsCis-regulatory elementsHoxa-11Evolutionary changePlacental mammalsEutherian mammalsTranscription factorsCis-regulatory evolutionDirect regulatory targetsGene expression domainsStrong positive selectionNovel developmental pathwayPRL expressionTherian ancestorGene regulationExpression domainsPositive selectionRegulatory targetsNovel functionDevelopmental pathwaysMammalsSpatial expressionProlactin expressionGenesExpressionAdaptive changes
2004
Adaptive evolution of HoxA11 and HoxA13 at the origin of the uterus in mammals
Lynch V, Roth J, Takahashi K, Dunn C, Nonaka D, Stopper G, Wagner G. Adaptive evolution of HoxA11 and HoxA13 at the origin of the uterus in mammals. Proceedings Of The Royal Society B 2004, 271: 2201-2207. PMID: 15539344, PMCID: PMC1691855, DOI: 10.1098/rspb.2004.2848.Peer-Reviewed Original ResearchConceptsAdaptive evolutionTranscription factorsMolecular evolutionHoxa-11Hoxa-13Cis-regulatory evolutionAdaptive molecular evolutionEvolution of developmentMammalian female reproductive systemStrong positive selectionCis-regulatory elementsAmniote taxaDevelopmental genesStem lineageDevelopmental evolutionEvolutionary changeEutherian mammalsSpatial regulationPositive selectionMorphological charactersFemale reproductive organsGenesFemale reproductive systemReproductive organsMammals
2000
Evolution of Hoxa-11 in Lineages Phylogenetically Positioned along the Fin–Limb Transition
Chiu C, Nonaka D, Xue L, Amemiya C, Wagner G. Evolution of Hoxa-11 in Lineages Phylogenetically Positioned along the Fin–Limb Transition. Molecular Phylogenetics And Evolution 2000, 17: 305-316. PMID: 11083943, DOI: 10.1006/mpev.2000.0837.Peer-Reviewed Original ResearchMeSH KeywordsAlanineAmino Acid SequenceAnimalsBinding SitesCell LineConserved SequenceDNAEvolution, MolecularExtremitiesFishesHeLa CellsHomeodomain ProteinsHumansIntronsMolecular Sequence DataPhylogenyProtein IsoformsSequence AlignmentSequence Analysis, DNASequence Homology, Amino AcidXenopusXenopus ProteinsZebrafishZebrafish ProteinsConceptsFin-limb transitionSequence evolutionAmino acid sequence comparisonsHoxa-11Domain IElectrophoretic mobility shift assaysMobility shift assaysAmino acid sequencePatterns of evolutionConsecutive alanine residuesWhole cell extractsEvolutionary timeAppendage developmentCharacter reconstructionEvolutionary changeTranscription factorsSequence comparisonIntron sequencesNucleotide conservationShift assaysAcid sequenceAlanine residuesLineagesAccelerated rateCoelacanth