2025
Energetics of Whole Genome Doubling and Genomic Instability
Beck R, Tagal V, Amin S, Bakhoum S, Maley C, Verhaak R, Gomes A, Andor N. Energetics of Whole Genome Doubling and Genomic Instability. Cancer Letters 2025, 217878. PMID: 40517938, DOI: 10.1016/j.canlet.2025.217878.Peer-Reviewed Original ResearchWhole-genome doublingGenome doublingBuffering deleterious mutationsDeleterious mutationsHaploinsufficient genesGenomic instabilityGenomic alterationsEnergetic constraintsTime of diagnosisCancer cellsMutationsPloidyCancer researchTissue sitesCancerAneuploidyTime of detectionGenomeCellsGenesShed lightNew tsetse (Glossina fuscipes fuscipes) genomes generated from wild and laboratory‐reared specimens
Bruzzese D, Weiss B, Echodu R, Mireji P, Abd‐Alla A, Aksoy S. New tsetse (Glossina fuscipes fuscipes) genomes generated from wild and laboratory‐reared specimens. Insect Science 2025 PMID: 40509668, DOI: 10.1111/1744-7917.70085.Peer-Reviewed Original ResearchHigh-quality genomesVectors of African trypanosomesSingle-copy homologsPopulation-level variationBUSCO scoreUnique orthologsAssembled genomeAnimal African trypanosomiasesGenetic diversityNatural wild populationsNanopore sequencingGenomeWild populationsLong-term captivityAfrican trypanosomesLaboratory linesGlossina fuscipes fuscipesGeographical originOrthologsLaboratory-reared specimensQV scoreVector biologyCentral African RepublicNorthwestern UgandaFliesSeparation of telomere protection from length regulation by two different point mutations at amino acid 492 of RTEL1
Smoom R, May C, Lichtental D, Bar-Ness K, Rangel R, Khoury J, Nachmani D, Avrahami D, Ahangari F, Skordalakes E, Kaminski N, Kaestner K, Tzfati Y. Separation of telomere protection from length regulation by two different point mutations at amino acid 492 of RTEL1. Nucleic Acids Research 2025, 53: gkaf507. PMID: 40530700, PMCID: PMC12203905, DOI: 10.1093/nar/gkaf507.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SubstitutionAnimalsDisease Models, AnimalDNA DamageDNA HelicasesDyskeratosis CongenitaFetal Growth RetardationGrowth DisordersHematopoiesisHumansIntellectual DisabilityLimb Deformities, CongenitalLungMiceMicrocephalyPoint MutationTelomereTelomere HomeostasisX-Linked Intellectual DisabilityConceptsHoyeraal-Hreidarsson syndromeTelomere protectionLength regulationTelomere length regulationTelomere-related diseasesTelomere biology disordersDNA helicaseMouse genomeGenome stabilityMouse modelMouse telomeresAberrant hematopoiesisGenomic instabilityPoint mutationsHouse miceTelomeric DNA damageAnaphase bridgesRTEL1Amino acidsTelomereMechanistic rolesDNA damageMutationsIsoleucine mutationGenomePrecision multiplexed base editing in human cells using Cas12a-derived base editors
Schweitzer A, Adams E, Nguyen M, Lek M, Isaacs F. Precision multiplexed base editing in human cells using Cas12a-derived base editors. Nature Communications 2025, 16: 5061. PMID: 40449999, PMCID: PMC12126522, DOI: 10.1038/s41467-025-59653-x.Peer-Reviewed Original ResearchConceptsMultiplex base editingBase editingBase editorsBase editor variantsMammalian genome engineeringBase editing technologyGenome engineering technologiesDNA double strand breaksBase editing systemMammalian genomesDouble strand breaksMultiple lociPolygenic phenotypesHuman cell linesHuman genomeGenome engineeringTarget nucleotideEditing outcomesMutation rateMultiplex editingMultiple gRNAsHuman cellsExpression cassetteEditing technologyGenomeCell-type specific global reprogramming of the transcriptome and epigenome in induced neurons with the 16p11.2 neuropsychiatric CNVs
Ward T, Qu P, Leung L, Zhou B, Muench K, Khechaduri A, Plastini M, Charlton C, Pattni R, Ho S, Ho M, Huang Y, Zhou P, Hallmayer J, Mourrain P, Palmer T, Zhang X, Urban A. Cell-type specific global reprogramming of the transcriptome and epigenome in induced neurons with the 16p11.2 neuropsychiatric CNVs. European Journal Of Human Genetics 2025, 1-10. PMID: 40374944, DOI: 10.1038/s41431-025-01856-3.Peer-Reviewed Original ResearchCopy number variantsDNA methylation patternsGlobal reprogrammingMethylation patternsInduced pluripotent stem cellsNeuropsychiatric copy number variantsGene expressionDifferentially expressed genesInduced neuronsCell-type specific alterationsGenome-wideDNA methylomeDuplicate genotypingHuman genomeGene familyLocal genomesDNA methylationInduced pluripotent stem cell lineGenesMolecular etiologyDNAGenomePluripotent stem cellsProtocadherinTranscriptomeDevelopmental Biology of the Placenta
Hui P. Developmental Biology of the Placenta. 2025, 15-30. DOI: 10.1007/978-3-031-83545-2_2.Peer-Reviewed Original ResearchUnique to eutherian mammalsParental gene expressionMammalian biologyPathogenesis of gestational trophoblastic diseasesEutherian mammalsGene expressionDevelopmental biologyGestational trophoblastic diseaseMaternal immunological rejectionTrophoblastic diseaseGas exchangeCell disordersMaternal uterusImmunological rejectionProliferative disordersPlacentaImplantation sitesImmunological characteristicsTissue remodelingHormone productionImmunological interactionsBiologyTransient organGenomeBiological changesStructural study on human microbiome-derived polyketide synthases that assemble genotoxic colibactin
Kim M, Kim J, Lee G, Olinares P, Airan Y, Chow J, Park J, Jeong Y, Park J, Chait B, Herzon S, Kim C, Kang J. Structural study on human microbiome-derived polyketide synthases that assemble genotoxic colibactin. Structure 2025 PMID: 40381618, DOI: 10.1016/j.str.2025.04.017.Peer-Reviewed Original ResearchNRPS-PKSCarrier proteinCryo-EM structurePKS enzymesPolyketide synthaseBiosynthesis mechanismBiosynthetic enzymesUpstream enzymesDimer interfaceColibactinBinding sitesDocking interactionsKetosynthasePromote colorectal cancerEnzymeStructural studiesGenomeBiosynthesisStructural detailsStructural analysisProteinGenotoxinsSynthaseHostCLBIThe application of irreversible genomic states to define and trace ancient cell type homologies
Simakov O, Wagner G. The application of irreversible genomic states to define and trace ancient cell type homologies. EvoDevo 2025, 16: 5. PMID: 40319312, PMCID: PMC12049793, DOI: 10.1186/s13227-025-00242-w.Peer-Reviewed Original ResearchImpact gene expressionGenomic stateCell typesGene expressionGene regulatory networksHomologous cell typesBranching animalsGenomic charactersRegulatory elementsRegulatory networksRegulatory signaturesMorphological traitsHomologyPhenotypic levelMolecular signaturesOntogenetic originGenesMorphological featuresNon-functionalCellsHypothesis articleGenomeExpressionTraitsTypeAdvancing translational exposomics: bridging genome, exposome and personalized medicine
Sarigiannis D, Karakitsios S, Anesti O, Stem A, Valvi D, Sumner S, Chatzi L, Snyder M, Thompson D, Vasiliou V. Advancing translational exposomics: bridging genome, exposome and personalized medicine. Human Genomics 2025, 19: 48. PMID: 40307849, PMCID: PMC12044731, DOI: 10.1186/s40246-025-00761-6.Peer-Reviewed Original ResearchConceptsExposome-wide association studyBridge genomicsLifestyle exposuresEnhancing causal inferencePublic health decision-makingEnvironmental health researchHealth decision-makingMulti-omics technologiesGenomic variationGenomic dataAssociation studiesHealth outcomesBioinformatics approachHealth researchPrecision preventionGenetic variabilityExposome dataExposure-response relationshipMulti-omicsGenomeInternal exposomeVulnerable populationsComplex diseasesDisease phenotypePublic healthSynteny Enabled Upgrade of the Galapagos Giant Tortoise Genome Improves Inferences of Runs of Homozygosity
Jensen E, Marchisio C, Ochoa A, Gray R, Parra V, Miller J, Çilingir F, Caccone A. Synteny Enabled Upgrade of the Galapagos Giant Tortoise Genome Improves Inferences of Runs of Homozygosity. Ecology And Evolution 2025, 15: e71358. PMID: 40290375, PMCID: PMC12032190, DOI: 10.1002/ece3.71358.Peer-Reviewed Original ResearchContiguous genomeGiant tortoisesGenome assemblyGalapagos giant tortoisesChromosome-level genome assemblySynteny-based methodsGenome resequencing dataEstimates of inbreedingWhole-genome sequencingHigh-quality DNAAldabra giant tortoiseReference genomeResequencing dataComplete genomeImproved genomeSpecies groupsExtinct speciesGenomeTortoisesHomozygositySpeciesSequenceAssemblyImprove inferenceGalapagosThe retrotransposon-derived capsid genes PNMA1 and PNMA4 maintain reproductive capacity
Wood T, Henriques W, Cullen H, Romero M, Blengini C, Sarathy S, Sorkin J, Bekele H, Jin C, Kim S, Wang X, Laureau R, Chemiakine A, Khondker R, Isola J, Stout M, Gennarino V, Mogessie B, Jain D, Schindler K, Suh Y, Wiedenheft B, Berchowitz L. The retrotransposon-derived capsid genes PNMA1 and PNMA4 maintain reproductive capacity. Nature Aging 2025, 5: 765-779. PMID: 40263616, PMCID: PMC12180178, DOI: 10.1038/s43587-025-00852-y.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesTranscription factor MYBL1Gonadal tissueMale gonadal tissueRNA intermediateEvolutionary innovationHuman genomeAssociation studiesHost genomeProtein self-assemblyDevelopmental regulationCapsid geneCapsid-like structuresHuman cellsCapsid formationYears ago4,5RetrotransposonsGenomeSequenceGenesRNAReproductive capacityPNMA1Reproductive functionMouse modelEukaryotic Microproteins
Jaunbocus N, Ebenki V, Su H, Slavoff S. Eukaryotic Microproteins. Annual Review Of Biochemistry 2025, 94: 1-28. PMID: 40245354, PMCID: PMC12207985, DOI: 10.1146/annurev-biochem-080124-012840.Peer-Reviewed Original ResearchA genetically informed brain atlas for enhancing brain imaging genomics
Bao J, Wen J, Chang C, Mu S, Chen J, Shivakumar M, Cui Y, Erus G, Yang Z, Yang S, Wen Z, Zhao Y, Kim D, Duong-Tran D, Saykin A, Zhao B, Davatzikos C, Long Q, Shen L. A genetically informed brain atlas for enhancing brain imaging genomics. Nature Communications 2025, 16: 3524. PMID: 40229250, PMCID: PMC11997130, DOI: 10.1038/s41467-025-57636-6.Peer-Reviewed Original ResearchConceptsBrain imaging genomicsImaging genomicsComplex traits/diseasesSNP heritabilityFunctional annotationGenetic architecturePolygenic risk scoresGenomic investigationsGenetic ancestryDiscovery powerBrain atlasesHuman brain structureGenetic determinantsNeuroanatomical heterogeneityGenomeNeuroanatomical variationImaging endophenotypesBrain structuresMolecular levelBrain voxelsHeritabilityPhenotypic correlationsGiant regionGeneticsBrain conditionsH3.1K27M-induced misregulation of the TONSOKU-H3.1 pathway causes genomic instability
Yuan W, Huang Y, LeBlanc C, Poulet A, De Luna Vitorino F, Valsakumar D, Dean R, Garcia B, van Wolfswinkel J, Voigt P, Jacob Y. H3.1K27M-induced misregulation of the TONSOKU-H3.1 pathway causes genomic instability. Nature Communications 2025, 16: 3547. PMID: 40229276, PMCID: PMC11997104, DOI: 10.1038/s41467-025-58892-2.Peer-Reviewed Original ResearchConceptsGenomic instabilityChromatin-based mechanismsHistone mark H3K27me3DNA damageH3K27MChromatin maturityGenome integrityNascent chromatinCell identityHistone H3Transcriptional programsH3.1 variantsGenomic alterationsDNAGenomeHistoneH3K27M expressionTumors of patientsEctopic activityATXR5ATXR6ExpressionCellsChromatinIntegrating genomic and spatial analyses to describe tuberculosis transmission: a scoping review
Lan Y, Rancu I, Chitwood M, Sobkowiak B, Nyhan K, Lin H, Wu C, Mathema B, Brown T, Colijn C, Warren J, Cohen T. Integrating genomic and spatial analyses to describe tuberculosis transmission: a scoping review. The Lancet Microbe 2025, 101094. PMID: 40228509, DOI: 10.1016/j.lanmic.2025.101094.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsGenome sequencing approachGenetic similarityGenomic dataSequencing approachGenotyping methodsPathogen geneticsGenetic methodsPathogen sequencesSampling completenessTuberculosis isolatesTransmission patternsTuberculosis casesPathogensTuberculosis transmissionM tuberculosis isolatesInfection-related mortalityEnvironmental factorsTuberculosis transmission dynamicsSpatial proximityTransmission clustersGenomeSpatial patternsTuberculosisTransmission dynamicsGeneticsTwo chromosomal reference genome sequences for the malaria mosquito, Anopheles (Nyssorhynchus) darlingi, Root, 1926 from French Guiana and Peru
Gendrin M, Heu K, Moreno M, Gamboa D, Vinetz J, Tong C, Conn J, Johnson H, Heaton H, Wagah M, Collins J, Krasheninnikova K, Pelan S, Pointon D, Torrance J, Tracey A, Uliano-Silva M, Wood J, von Wyschetzki K, McCarthy S, Lawniczak M, Neafsey D, Makunin A. Two chromosomal reference genome sequences for the malaria mosquito, Anopheles (Nyssorhynchus) darlingi, Root, 1926 from French Guiana and Peru. Wellcome Open Research 2025, 10: 187. DOI: 10.12688/wellcomeopenres.23989.1.Peer-Reviewed Original ResearchGenome sequenceChromosome arm 2RReference genome sequenceX sex chromosomeFrench GuianaChromosomal pseudomoleculesGenome assemblyMitochondrial genomeWild populationsGenomeMalaria mosquitoesNyssorhynchusChromosomeSequenceGuianaAssemblyAnophelesFemale AnophelesPseudomoleculesMegabasesKilobasesDarlingiPeruMosquitoesIntegrated Genomic, Proteomic, and Transcriptomic Profiling Support Cathepsin-B as a Drug Repurposing Target in Cerebral Small Vessel Disease (S2.001)
Rivier C, Huo S, Clocchiatti-Tuozzo S, Renedo D, Sharma R, Payabvash S, Rangaraju S, Dong X, Sheth K, Sansing L, Falcone G. Integrated Genomic, Proteomic, and Transcriptomic Profiling Support Cathepsin-B as a Drug Repurposing Target in Cerebral Small Vessel Disease (S2.001). Neurology 2025, 104 DOI: 10.1212/wnl.0000000000211788.Peer-Reviewed Original ResearchPsychiatric genetics in the diverse landscape of Latin American populations
Bruxel E, Rovaris D, Belangero S, Chavarría-Soley G, Cuellar-Barboza A, Martínez-Magaña J, Nagamatsu S, Nievergelt C, Núñez-Ríos D, Ota V, Peterson R, Sloofman L, Adams A, Albino E, Alvarado A, Andrade-Brito D, Arguello-Pascualli P, Bandeira C, Bau C, Bulik C, Buxbaum J, Cappi C, Corral-Frias N, Corrales A, Corsi-Zuelli F, Crowley J, Cupertino R, da Silva B, De Almeida S, De la Hoz J, Forero D, Fries G, Gelernter J, González-Giraldo Y, Grevet E, Grice D, Hernández-Garayua A, Hettema J, Ibáñez A, Ionita-Laza I, Lattig M, Lima Y, Lin Y, López-León S, Loureiro C, Martínez-Cerdeño V, Martínez-Levy G, Melin K, Moreno-De-Luca D, Muniz Carvalho C, Olivares A, Oliveira V, Ormond R, Palmer A, Panzenhagen A, Passos-Bueno M, Peng Q, Pérez-Palma E, Prieto M, Roussos P, Sanchez-Roige S, Santamaría-García H, Shansis F, Sharp R, Storch E, Tavares M, Tietz G, Torres-Hernández B, Tovo-Rodrigues L, Trelles P, Trujillo-ChiVacuan E, Velásquez M, Vera-Urbina F, Voloudakis G, Wegman-Ostrosky T, Zhen-Duan J, Zhou H, Santoro M, Nicolini H, Atkinson E, Giusti-Rodríguez P, Montalvo-Ortiz J. Psychiatric genetics in the diverse landscape of Latin American populations. Nature Genetics 2025, 57: 1074-1088. PMID: 40175716, PMCID: PMC12133068, DOI: 10.1038/s41588-025-02127-z.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesPsychiatric genomicsPsychiatric genome-wide association studiesLarge-scale genome-wide association studiesGenetic risk lociNon-European populationsGenetic diversityRisk lociGenetic admixtureBurden of psychiatric disordersAssociation studiesPsychiatric disordersEuropean ancestryPsychiatric geneticsGenomeHealthcare disparitiesConsortium effortLatin American populationsPromote equityEnvironmental factorsDiversityAmerican populationDiverse landscapeLociAncestryPlant graph-based pangenomics: techniques, applications, and challenges
Du Z, He J, Jiao W. Plant graph-based pangenomics: techniques, applications, and challenges. ABIOTECH 2025, 1-16. DOI: 10.1007/s42994-025-00206-7.Peer-Reviewed Original ResearchNovo-assembled genomeMolecular breeding of cropsDNA sequencing technologiesInvestigate population diversityAgronomically important genesBreeding of cropsPangenome graphsGenetic mapSmall variantsGenomic regionsGenetic diversityGraph pangenomeSequencing technologiesGenomic analysisPangenomic studiesGenomic studiesGenetic variationImportant genesMolecular breedingStructural variantsPangenomeGenomeCrop breedingPlantsVariantsSynthetic Genetic Elements Enable Rapid Characterization of Inorganic Carbon Uptake Systems in Cupriavidus necator H16
Nakamura A, Fulk E, Johnson C, Isaacs F. Synthetic Genetic Elements Enable Rapid Characterization of Inorganic Carbon Uptake Systems in Cupriavidus necator H16. ACS Synthetic Biology 2025, 14: 943-953. PMID: 40048245, PMCID: PMC11934965, DOI: 10.1021/acssynbio.4c00869.Peer-Reviewed Original ResearchConceptsSynthetic genetic elementsExpression of heterologous pathwaysUptake systemCupriavidus necator H16Genome engineering technologiesHeterologous pathwaysHeterotrophic conditionsGenetic elementsChromosomal expressionTunable expressionInducible promoterGenetic engineering technologyModel microbesCarbon sourceGene expressionFacultative chemolithotrophsUptake pathwayH16PathwayLanding padExpressionGenomeGenesMicrobesChemolithotrophs
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