2025
A genetic modifier links integrin α5 to the phenotypic variation in fibronectin 1a mutant zebrafish.
Capon S, Maroufidou A, Feltes M, Xu Y, Matharoo D, Jülich D, Holley S, Farber S, Stainier D. A genetic modifier links integrin α5 to the phenotypic variation in fibronectin 1a mutant zebrafish. PLOS Genetics 2025, 21: e1011747. PMID: 40549824, PMCID: PMC12212883, DOI: 10.1371/journal.pgen.1011747.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCodon, NonsenseFibronectinsGene Expression Regulation, DevelopmentalGenes, ModifierIntegrin alpha5MutationPhenotypeZebrafishZebrafish ProteinsConceptsMutant phenotypePhenotypic variationNonsense mutationGenetic modifiersDouble mutant analysisWhole-genome sequencingITGA5 expressionSevere phenotypeIntegrin alpha 5Mutant analysisMutant larvaeProximal promoterMutantsMutant zebrafishCardia bifidaGene expressionIntegrin A5Genetic backgroundAlpha 5PhenotypeMutationsExpression levelsFibronectinFunctional cardiovascular systemZebrafishOrchestrating Neural Development Through mRNA Translation Regulation
Rodrigue B, Sajish M, Salmaso N, Aguilar‐Valles A. Orchestrating Neural Development Through mRNA Translation Regulation. Journal Of Neurochemistry 2025, 169: e70128. PMID: 40509688, PMCID: PMC12163303, DOI: 10.1111/jnc.70128.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBrainGene Expression Regulation, DevelopmentalHumansNeurogenesisProtein BiosynthesisRNA, MessengerConceptsMRNA translation regulationRegulation of mRNA translationMammalian/mechanistic target of rapamycin complex 1MRNA translationTranslational regulationFragile X Messenger Ribonucleoprotein 1Neural developmentGene expressionRegulation of gene expressionCell fate decisionsControlling gene expressionControl of brain developmentTarget of rapamycin complex 1Integrated stress responseNeuronal growth conesDysregulation of mRNA translationRapamycin complex 1Fate decisionsSubcellular compartmentsTranscriptional controlSignaling cascadesFragile X syndromeAxon guidanceMammalian/mechanistic targetStem cell proliferationRates of Evolution of Developmental Changes in Gene Expression in Sordariomycetes
Wang Y, Wang F, Meng G, Lopez-Giraldez F, Dong C, Wang Z, Townsend J. Rates of Evolution of Developmental Changes in Gene Expression in Sordariomycetes. Molecular Biology And Evolution 2025, 42: msaf131. PMID: 40452442, PMCID: PMC12203517, DOI: 10.1093/molbev/msaf131.Peer-Reviewed Original ResearchMeSH KeywordsBiological EvolutionEvolution, MolecularGene Expression Regulation, DevelopmentalGene Expression Regulation, FungalMeiosisReproduction, AsexualConceptsRate of gene expression evolutionGene expression evolutionExpression evolutionGene expressionPhenotypic evolutionHeterogeneous rates of evolutionNonsynonymous to synonymous substitution ratesRates of phenotypic evolutionDevelopmental stagesSingle-copy orthologsGene sequence evolutionSynonymous substitution ratesRate of evolutionExpression of genesFunctional pathway analysisCarbon metabolismEvolutionary forcesConsequent phenotypesSexual reproductionSequence evolutionConserved pathwaysMeiosis pathwaysSubstitution ratesCell cyclePathway analysisTblncRNA-23, a long non-coding RNA transcribed by RNA polymerase I, regulates developmental changes in Trypanosoma brucei
Galili-Kostin B, Rajan K, Ida Ashkenazi Y, Freedman A, Doniger T, Cohen-Chalamish S, Waldman Ben-Asher H, Unger R, Roditi I, Tschudi C, Michaeli S. TblncRNA-23, a long non-coding RNA transcribed by RNA polymerase I, regulates developmental changes in Trypanosoma brucei. Nature Communications 2025, 16: 3697. PMID: 40251171, PMCID: PMC12008373, DOI: 10.1038/s41467-025-58979-w.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsGene Expression Regulation, DevelopmentalLife Cycle StagesPolyribosomesProtozoan ProteinsRNA InterferenceRNA Polymerase IRNA, Long NoncodingRNA, MessengerRNA, ProtozoanTranscription, GeneticTrypanosoma brucei bruceiConceptsProcyclic formsNon-coding RNAsLong non-coding RNAsPolycistronic transcription unitsRNA polymerase I.RNA polymerase IProtozoan parasite Trypanosoma bruceiRegulate gene expressionParasite Trypanosoma bruceiTsetse fly vectorComplex life cycleInsect midgutProcyclin genesSocial motilityLate procyclic formsRegulating developmental changesTranscription unitPolymerase I.Polymerase IBase pairsMammalian hostsTrypanosoma bruceiChanging abundanceInsect hostsTarget mRNAsCACNA1G, 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 ResearchMeSH KeywordsAnimalsBody PatterningCalcium Channels, T-TypeCiliaGene Expression Regulation, DevelopmentalHeterotaxy SyndromeXenopusXenopus ProteinsConceptsCongenital 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 developmentResolving the three-dimensional interactome of human accelerated regions during human and chimpanzee neurodevelopment
Pal A, Noble M, Morales M, Pal R, Baumgartner M, Yang J, Yim K, Uebbing S, Noonan J. Resolving the three-dimensional interactome of human accelerated regions during human and chimpanzee neurodevelopment. Cell 2025, 188: 1504-1523.e27. PMID: 39889695, PMCID: PMC11928272, DOI: 10.1016/j.cell.2025.01.007.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBrainGene Expression Regulation, DevelopmentalHumansNeural Stem CellsNeurogenesisPan troglodytesSpecies SpecificityNup107 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 ResearchMeSH KeywordsActive Transport, Cell NucleusAnimalsEctodermFemaleGastrulaGastrulationGene Expression Regulation, DevelopmentalMicroRNAsNuclear Pore Complex ProteinsXenopus laevisXenopus ProteinsZygoteConceptsMaternal 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 courseThe human and non-human primate developmental GTEx projects
Bell T, Blanchard T, Hernandez R, Linn R, Taylor D, VonDran M, Ahooyi T, Beitra D, Bernieh A, Delaney M, Faith M, Fattahi E, Footer D, Gilbert M, Guambaña S, Gulino S, Hanson J, Hattrell E, Heinemann C, Kreeb J, Leino D, Mcdevitt L, Palmieri A, Pfeiffer M, Pryhuber G, Rossi C, Rasool I, Roberts R, Salehi A, Savannah E, Stachowicz K, Stokes D, Suplee L, Van Hoose P, Wilkins B, Williams-Taylor S, Zhang S, Ardlie K, Getz G, Lappalainen T, Montgomery S, Aguet F, Anderson L, Bernstein B, Choudhary A, Domenech L, Gaskell E, Johnson M, Liu Q, Marderstein A, Nedzel J, Okonda J, Padhi E, Rosano M, Russell A, Walker B, Sestan N, Gerstein M, Milosavljevic A, Borsari B, Cho H, Clarke D, Deveau A, Galeev T, Gobeske K, Hameed I, Huttner A, Jensen M, Jiang Y, Li J, Liu J, Liu Y, Ma J, Mane S, Meng R, Nadkarni A, Ni P, Park S, Petrosyan V, Pochareddy S, Salamon I, Xia Y, Yates C, Zhang M, Zhao H, Conrad D, Feng G, Brady F, Boucher M, Carbone L, Castro J, del Rosario R, Held M, Hennebold J, Lacey A, Lewis A, Lima A, Mahyari E, Moore S, Okhovat M, Roberts V, de Castro S, Wessel B, Zaniewski H, Zhang Q, Arguello A, Baroch J, Dayal J, Felsenfeld A, Ilekis J, Jose S, Lockhart N, Miller D, Minear M, Parisi M, Price A, Ramos E, Zou S. The human and non-human primate developmental GTEx projects. Nature 2025, 637: 557-564. PMID: 39815096, PMCID: PMC12013525, DOI: 10.1038/s41586-024-08244-9.Peer-Reviewed Original ResearchConceptsChromatin accessibility dataFunctional genomic studiesWhole-genome sequencingEffects of genetic variationSpatial gene expression profilesNon-human primatesGenotype-Tissue ExpressionGene expression profilesGenomic studiesGene regulationGenetic dataGenetic variationGenomic researchDonor diversityCommunity engagementHuman evolutionEarly developmental defectsGene expressionCell statesDevelopmental programmeHuman diseasesExpression profilesAdult tissuesDevelopmental defectsSingle-cellBiology of Hox Genes: Questions and Technological Challenges
Parambil S, De Kumar B. Biology of Hox Genes: Questions and Technological Challenges. Methods In Molecular Biology 2025, 2889: 1-10. PMID: 39745601, DOI: 10.1007/978-1-0716-4322-8_1.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBody PatterningGene Expression Regulation, DevelopmentalGenes, HomeoboxHomeodomain ProteinsHumans
2024
NaP-TRAP reveals the regulatory grammar in 5’UTR-mediated translation regulation during zebrafish development
Strayer E, Krishna S, Lee H, Vejnar C, Neuenkirchen N, Gupta A, Beaudoin J, Giraldez A. NaP-TRAP reveals the regulatory grammar in 5’UTR-mediated translation regulation during zebrafish development. Nature Communications 2024, 15: 10898. PMID: 39738051, PMCID: PMC11685710, DOI: 10.1038/s41467-024-55274-y.Peer-Reviewed Original ResearchMeSH Keywords5' Untranslated RegionsAnimalsEmbryo, NonmammalianGene Expression Regulation, DevelopmentalHumansMicroRNAsPolyribosomesProtein BiosynthesisRibosomesRNA, MessengerZebrafishZebrafish ProteinsConceptsMassively parallel reporter assaysCis-regulatory elementsMaternal-to-zygotic transitionGC-rich motifsU-rich motifsTrans-acting proteinsRepressor of translationRibosome affinity purificationRegulatory grammarUpstream ORFsZygotic expressionTranslational switchReporter mRNATranslational controlTranslational regulationNascent peptideAffinity purificationMicroRNA sitesPolysome profilingMRNA translationZebrafish developmentMRNA stabilityExpression of miR-430MiR-430Regulatory functionsThe search to understand the development of the chicken immune system: Differences in expression of MHC class I loci and waves of thymocytes as evolutionary relics?
Halabi S, Rocos N, Kaufman J. The search to understand the development of the chicken immune system: Differences in expression of MHC class I loci and waves of thymocytes as evolutionary relics? Developmental Biology 2024, 519: 38-45. PMID: 39694171, DOI: 10.1016/j.ydbio.2024.12.006.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBiological EvolutionChickensGene Expression Regulation, DevelopmentalGenes, MHC Class IHistocompatibility Antigens Class IImmune SystemThymocytesConceptsClass I genesI geneEvolutionary relicMHC class I lociClass I lociPoultry industryResistance to infectious diseasesChicken immune systemClass I expressionCytotoxic T lymphocytesGenetic lociNon-polymorphicI lociGlobal poultry industryChicken MHCClass I moleculesImmune defenceLociNatural killerT cellsDay-old chicksI expressionXenopus frogsAvian immunologyWell-expressedEffects of gestational hypothyroidism on mouse brain development: Gabaergic systems and oxidative stress
da Cunha Menezes E, de Abreu F, Davis J, Maurer S, Roshko V, Richardson A, Dowell J, Cassella S, Stevens H. Effects of gestational hypothyroidism on mouse brain development: Gabaergic systems and oxidative stress. Developmental Biology 2024, 515: 112-120. PMID: 39048051, PMCID: PMC11330572, DOI: 10.1016/j.ydbio.2024.07.010.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBrainCell MovementFemaleGABAergic NeuronsGene Expression Regulation, DevelopmentalGlutamate DecarboxylaseGlutathione PeroxidaseGlutathione Peroxidase GPX1HypothyroidismMaleMethimazoleMiceNF-E2-Related Factor 2Oxidative StressPlacentaPregnancyPrenatal Exposure Delayed EffectsThyroid HormonesConceptsGestational hypothyroidismGABAergic system developmentMaternal thyroid hormone supplyThyroid hormone supplyCortical GABAergic interneuronsMaternal thyroid hormonesGene expressionCD-1 miceCentral nervous system developmentEmbryonic day 9Central nervous systemIntrauterine restrictionGABAergic interneuronsGABAergic systemGPx1 gene expressionBrain gene expressionMouse brain developmentCD-1HypothyroidismEmbryonic dayNervous system developmentThyroid hormonesRisk factorsNeural system developmentHormonal imbalanceAccelerated evolution in the human lineage led to gain and loss of transcriptional enhancers in the RBFOX1 locus
Berasain L, Beati P, Trigila A, Rubinstein M, Franchini L. Accelerated evolution in the human lineage led to gain and loss of transcriptional enhancers in the RBFOX1 locus. Science Advances 2024, 10: eadl1049. PMID: 38924416, PMCID: PMC11204294, DOI: 10.1126/sciadv.adl1049.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAnimals, Genetically ModifiedEnhancer Elements, GeneticEvolution, MolecularGene Expression Regulation, DevelopmentalGene Regulatory NetworksGenetic LociHumansMiceMice, KnockoutPan troglodytesRNA Splicing FactorsZebrafishConceptsTranscriptional enhancersGoal of evolutionary biologyHuman lineageZebrafish reporter assayGene regulatory networksPotential regulatory elementsHuman-specific traitsChimpanzee sequencesRBFOX1 locusRegulatory elementsRegulatory networksRegulatory modificationsEvolutionary biologyAccelerated evolutionTarget genesGene expressionGenesDevelopmental stagesLociLineagesReporter assayExpressionRBFOX1SplicingTemporal changesRbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios
Wilson M, Romano S, Khatri N, Aharon D, Liu Y, Kaufman O, Draper B, Marlow F. Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios. Nature Communications 2024, 15: 5248. PMID: 38898112, PMCID: PMC11187175, DOI: 10.1038/s41467-024-49613-2.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsFemaleGene Expression Regulation, DevelopmentalMaleMechanistic Target of Rapamycin Complex 1Nuclear Pore Complex ProteinsNutrientsOocytesOogenesisOvaryRNA-Binding ProteinsSignal TransductionTestisZebrafishZebrafish ProteinsConceptsRibosome biogenesis factorsRNA-binding proteinsMTORC1 signaling pathwayBipotential stateBiogenesis factorsGAP activityFemale fateTranslational regulationReproductive successGenetic analysisFate switchZebrafish oogenesisBinding proteinSignaling pathwayRBPMS2Oocyte progressionRAG-2Oocyte factorsZebrafishPrimary gonadsDifferentiation factorPathwayFateRNAbpsRibosomeMassively parallel characterization of regulatory elements in the developing human cortex
Deng C, Whalen S, Steyert M, Ziffra R, Przytycki P, Inoue F, Pereira D, Capauto D, Norton S, Vaccarino F, Pollen A, Nowakowski T, Ahituv N, Pollard K, Akbarian S, Abyzov A, Ahituv N, Arasappan D, Almagro Armenteros J, Beliveau B, Bendl J, Berretta S, Bharadwaj R, Bhattacharya A, Bicks L, Brennand K, Capauto D, Champagne F, Chatterjee T, Chatzinakos C, Chen Y, Chen H, Cheng Y, Cheng L, Chess A, Chien J, Chu Z, Clarke D, Clement A, Collado-Torres L, Cooper G, Crawford G, Dai R, Daskalakis N, Davila-Velderrain J, Deep-Soboslay A, Deng C, DiPietro C, Dracheva S, Drusinsky S, Duan Z, Duong D, Dursun C, Eagles N, Edelstein J, Emani P, Fullard J, Galani K, Galeev T, Gandal M, Gaynor S, Gerstein M, Geschwind D, Girdhar K, Goes F, Greenleaf W, Grundman J, Guo H, Guo Q, Gupta C, Hadas Y, Hallmayer J, Han X, Haroutunian V, Hawken N, He C, Henry E, Hicks S, Ho M, Ho L, Hoffman G, Huang Y, Huuki-Myers L, Hwang A, Hyde T, Iatrou A, Inoue F, Jajoo A, Jensen M, Jiang L, Jin P, Jin T, Jops C, Jourdon A, Kawaguchi R, Kellis M, Khullar S, Kleinman J, Kleopoulos S, Kozlenkov A, Kriegstein A, Kundaje A, Kundu S, Lee C, Lee D, Li J, Li M, Lin X, Liu S, Liu J, Liu J, Liu C, Liu S, Lou S, Loupe J, Lu D, Ma S, Ma L, Margolis M, Mariani J, Martinowich K, Maynard K, Mazariegos S, Meng R, Myers R, Micallef C, Mikhailova T, Ming G, Mohammadi S, Monte E, Montgomery K, Moore J, Moran J, Mukamel E, Nairn A, Nemeroff C, Ni P, Norton S, Nowakowski T, Omberg L, Page S, Park S, Patowary A, Pattni R, Pertea G, Peters M, Phalke N, Pinto D, Pjanic M, Pochareddy S, Pollard K, Pollen A, Pratt H, Przytycki P, Purmann C, Qin Z, Qu P, Quintero D, Raj T, Rajagopalan A, Reach S, Reimonn T, Ressler K, Ross D, Roussos P, Rozowsky J, Ruth M, Ruzicka W, Sanders S, Schneider J, Scuderi S, Sebra R, Sestan N, Seyfried N, Shao Z, Shedd N, Shieh A, Shin J, Skarica M, Snijders C, Song H, State M, Stein J, Steyert M, Subburaju S, Sudhof T, Snyder M, Tao R, Therrien K, Tsai L, Urban A, Vaccarino F, van Bakel H, Vo D, Voloudakis G, Wamsley B, Wang T, Wang S, Wang D, Wang Y, Warrell J, Wei Y, Weimer A, Weinberger D, Wen C, Weng Z, Whalen S, White K, Willsey A, Won H, Wong W, Wu H, Wu F, Wuchty S, Wylie D, Xu S, Yap C, Zeng B, Zhang P, Zhang C, Zhang B, Zhang J, Zhang Y, Zhou X, Ziffra R, Zeier Z, Zintel T. Massively parallel characterization of regulatory elements in the developing human cortex. Science 2024, 384: eadh0559. PMID: 38781390, PMCID: PMC12085231, DOI: 10.1126/science.adh0559.Peer-Reviewed Original ResearchMeSH KeywordsCerebral CortexChromatinDeep LearningEnhancer Elements, GeneticGene Expression Regulation, DevelopmentalHumansNeurogenesisNeuronsOrganoidsRegulatory Sequences, Nucleic AcidConceptsGene regulatory elementsRegulatory elementsRegulation of enhancer activityCharacterization of regulatory elementsCis-regulatory activityNeuronal developmentPrimary cellsEnhanced activityGene regulationHuman neuronal developmentNucleotide changesEnhancer sequencesSequence basisUpstream regulatorComprehensive catalogHuman cellsDeveloping cortexSequenceVariantsOrganoidsCellsCerebral organoidsCortexHuman cortexNucleotideCross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain
Wen C, Margolis M, Dai R, Zhang P, Przytycki P, Vo D, Bhattacharya A, Matoba N, Tang M, Jiao C, Kim M, Tsai E, Hoh C, Aygün N, Walker R, Chatzinakos C, Clarke D, Pratt H, Peters M, Gerstein M, Daskalakis N, Weng Z, Jaffe A, Kleinman J, Hyde T, Weinberger D, Bray N, Sestan N, Geschwind D, Roeder K, Gusev A, Pasaniuc B, Stein J, Love M, Pollard K, Liu C, Gandal M, Akbarian S, Abyzov A, Ahituv N, Arasappan D, Almagro Armenteros J, Beliveau B, Bendl J, Berretta S, Bharadwaj R, Bicks L, Brennand K, Capauto D, Champagne F, Chatterjee T, Chatzinakos C, Chen Y, Chen H, Cheng Y, Cheng L, Chess A, Chien J, Chu Z, Clement A, Collado-Torres L, Cooper G, Crawford G, Davila-Velderrain J, Deep-Soboslay A, Deng C, DiPietro C, Dracheva S, Drusinsky S, Duan Z, Duong D, Dursun C, Eagles N, Edelstein J, Emani P, Fullard J, Galani K, Galeev T, Gaynor S, Girdhar K, Goes F, Greenleaf W, Grundman J, Guo H, Guo Q, Gupta C, Hadas Y, Hallmayer J, Han X, Haroutunian V, Hawken N, He C, Henry E, Hicks S, Ho M, Ho L, Hoffman G, Huang Y, Huuki-Myers L, Hwang A, Iatrou A, Inoue F, Jajoo A, Jensen M, Jiang L, Jin P, Jin T, Jops C, Jourdon A, Kawaguchi R, Kellis M, Kleopoulos S, Kozlenkov A, Kriegstein A, Kundaje A, Kundu S, Lee C, Lee D, Li J, Li M, Lin X, Liu S, Liu J, Liu J, Liu S, Lou S, Loupe J, Lu D, Ma S, Ma L, Mariani J, Martinowich K, Maynard K, Mazariegos S, Meng R, Myers R, Micallef C, Mikhailova T, Ming G, Mohammadi S, Monte E, Montgomery K, Moore J, Moran J, Mukamel E, Nairn A, Nemeroff C, Ni P, Norton S, Nowakowski T, Omberg L, Page S, Park S, Patowary A, Pattni R, Pertea G, Phalke N, Pinto D, Pjanic M, Pochareddy S, Pollen A, Purmann C, Qin Z, Qu P, Quintero D, Raj T, Rajagopalan A, Reach S, Reimonn T, Ressler K, Ross D, Roussos P, Rozowsky J, Ruth M, Ruzicka W, Sanders S, Schneider J, Scuderi S, Sebra R, Seyfried N, Shao Z, Shedd N, Shieh A, Shin J, Skarica M, Snijders C, Song H, State M, Steyert M, Subburaju S, Sudhof T, Snyder M, Tao R, Therrien K, Tsai L, Urban A, Vaccarino F, van Bakel H, Voloudakis G, Wamsley B, Wang T, Wang S, Wang D, Wang Y, Warrell J, Wei Y, Weimer A, Whalen S, White K, Willsey A, Won H, Wong W, Wu H, Wu F, Wuchty S, Wylie D, Xu S, Yap C, Zeng B, Zhang C, Zhang B, Zhang J, Zhang Y, Zhou X, Ziffra R, Zeier Z, Zintel T. Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain. Science 2024, 384: eadh0829. PMID: 38781368, PMCID: PMC12147038, DOI: 10.1126/science.adh0829.Peer-Reviewed Original ResearchMeSH KeywordsAlternative SplicingAtlases as TopicAutism Spectrum DisorderBrainGene Expression Regulation, DevelopmentalGene Regulatory NetworksGenome-Wide Association StudyHumansProtein IsoformsQuantitative Trait LociRNA SplicingSchizophreniaTranscriptomeConceptsGenome-wide association studiesGenome-wide association study lociSplicing quantitative trait lociQuantitative trait lociSplicing regulationCross-ancestryTrait lociAssociation studiesRegulatory elementsCellular contextHuman brainTranscriptome regulationCoexpression networkRisk genesAutism spectrum disorderGenesCellular heterogeneityComprehensive landscapeSpectrum disorderIsoformsSplicingIncreased cellular heterogeneityLociNeuronal maturationRegulationMannose controls mesoderm specification and symmetry breaking in mouse gastruloids
Dingare C, Cao D, Yang J, Sozen B, Steventon B. Mannose controls mesoderm specification and symmetry breaking in mouse gastruloids. Developmental Cell 2024, 59: 1523-1537.e6. PMID: 38636516, DOI: 10.1016/j.devcel.2024.03.031.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBody PatterningCell DifferentiationDeoxyglucoseFrizzled ReceptorsGastrulaGene Expression Regulation, DevelopmentalGlycosylationMannoseMesodermMiceMouse Embryonic Stem CellsWnt Signaling PathwayConceptsMesoderm specificationFeatures of embryonic developmentWnt pathway regulationEarly mesoderm developmentProtein glycosylationPathway regulationProteomic analysisIntracellular recyclingMesoderm developmentEmbryonic developmentGlycolytic intermediatesMannoseGlucose transportCompetitive inhibitorGlycosylationGlucose removal
2023
Molecular programs of regional specification and neural stem cell fate progression in macaque telencephalon
Micali N, Ma S, Li M, Kim S, Mato-Blanco X, Sindhu S, Arellano J, Gao T, Shibata M, Gobeske K, Duque A, Santpere G, Sestan N, Rakic P. Molecular programs of regional specification and neural stem cell fate progression in macaque telencephalon. Science 2023, 382: eadf3786. PMID: 37824652, PMCID: PMC10705812, DOI: 10.1126/science.adf3786.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBrain NeoplasmsFemaleGalanin-Like PeptideGene Expression Regulation, DevelopmentalMacacaMental DisordersNervous System DiseasesNeural Stem CellsNeurogenesisNeuronsPregnancyTelencephalonThe functional and evolutionary impacts of human-specific deletions in conserved elements
Xue J, Mackay-Smith A, Mouri K, Garcia M, Dong M, Akers J, Noble M, Li X, Lindblad-Toh K, Karlsson E, Noonan J, Capellini T, Brennand K, Tewhey R, Sabeti P, Reilly S, Andrews G, Armstrong J, Bianchi M, Birren B, Bredemeyer K, Breit A, Christmas M, Clawson H, Damas J, Di Palma F, Diekhans M, Dong M, Eizirik E, Fan K, Fanter C, Foley N, Forsberg-Nilsson K, Garcia C, Gatesy J, Gazal S, Genereux D, Goodman L, Grimshaw J, Halsey M, Harris A, Hickey G, Hiller M, Hindle A, Hubley R, Hughes G, Johnson J, Juan D, Kaplow I, Karlsson E, Keough K, Kirilenko B, Koepfli K, Korstian J, Kowalczyk A, Kozyrev S, Lawler A, Lawless C, Lehmann T, Levesque D, Lewin H, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu V, Marques-Bonet T, Mason V, Meadows J, Meyer W, Moore J, Moreira L, Moreno-Santillan D, Morrill K, Muntané G, Murphy W, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat N, Pfenning A, Phan B, Pollard K, Pratt H, Ray D, Reilly S, Rosen J, Ruf I, Ryan L, Ryder O, Sabeti P, Schäffer D, Serres A, Shapiro B, Smit A, Springer M, Srinivasan C, Steiner C, Storer J, Sullivan K, Sullivan P, Sundström E, Supple M, Swofford R, Talbot J, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder A, Wirthlin M, Xue J, Zhang X. The functional and evolutionary impacts of human-specific deletions in conserved elements. Science 2023, 380: eabn2253. PMID: 37104592, PMCID: PMC10202372, DOI: 10.1126/science.abn2253.Peer-Reviewed Original ResearchMeSH KeywordsBrainConserved SequenceEvolution, MolecularGene Expression Regulation, DevelopmentalGenomeGenomicsHumansRNA-Binding ProteinsSequence DeletionConceptsHuman-specific deletionHuman phenotypic traitsParallel reporterEvolutionary impactDevelopmental genesPhenotypic traitsEvolutionary mechanismsGenomic sequencesNew traitsTranscriptomic datasetsSequence altersRegulatory functionsCell typesRegulatory activityRich resourceDeletionSynaptic functionTraitsBrain developmentGenesSpeciesReporterHumansSequenceExpression
2022
Gene regulatory divergence amongst echinoderms underlies appearance of pigment cells in sea urchin development
Spurrell M, Oulhen N, Foster S, Perillo M, Wessel G. Gene regulatory divergence amongst echinoderms underlies appearance of pigment cells in sea urchin development. Developmental Biology 2022, 494: 13-25. PMID: 36519720, PMCID: PMC9870932, DOI: 10.1016/j.ydbio.2022.11.008.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsGene Expression Regulation, DevelopmentalRNASea UrchinsStarfishTranscription FactorsConceptsPigment cell-specific genePigment gene expressionCell-specific genesSea starsSea urchinsGene expressionPigment cellsHomologous gene expressionGene regulatory divergenceSea urchin developmentTemporal expression profilesScRNA-seq analysisSitu RNA hybridizationPigment biosynthesisRegulatory divergenceGene activationPigment genesStrongylocentrotus purpuratusImmune related genesPatiria miniataCell lineagesExpression profilesRelated genesRNA hybridizationMigratory cells
This site is protected by hCaptcha and its Privacy Policy and Terms of Service apply