2025
Precision 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 technologyGenome
2024
Increasing the Level of Knock-In of the MT-C34-Encoding Construct into the <i>CXCR4</i> Locus by Modifying Donor DNA with Cas9 Target Sites
Shepelev M, Komkov D, Golubev D, Borovikova S, Mazurov D, Kruglova N. Increasing the Level of Knock-In of the MT-C34-Encoding Construct into the CXCR4 Locus by Modifying Donor DNA with Cas9 Target Sites. Молекулярная Биология 2024, 58 DOI: 10.31857/s0026898424040058.Peer-Reviewed Original ResearchKnock-in efficiencyDonor DNADonor plasmidGenetic constructsKnock-inApplication of genome editing technologiesCleavage in vitroDonor plasmid DNACas9 target sitesDouble-strand breaksInduction of double-strand breaksGenome editing technologyPAM sitesDonor sequenceTruncated targetsCell genomeDNA modificationsInduced cleavageIncreased knock-in efficiencyCRISPR/Cas9 systemCas9LociDNAEditing technologyPlasmid DNADonor DNA Modification with Cas9 Targeting Sites Improves the Efficiency of MTC34 Knock-in into the CXCR4 Locus
Shepelev M, Komkov D, Golubev D, Borovikova S, Mazurov D, Kruglova N. Donor DNA Modification with Cas9 Targeting Sites Improves the Efficiency of MTC34 Knock-in into the CXCR4 Locus. Molecular Biology 2024, 58: 672-682. DOI: 10.1134/s0026893324700250.Peer-Reviewed Original ResearchCas9 target sitesDouble-strand breaksKnock-inCell genomeGenetic constructsDNA modificationsDonor DNADonor plasmid DNATarget siteKnock-in efficiencyGenome editing technologyInduce double-strand breaksProximal nucleotidesPAM sitesDonor plasmidDonor sequenceCXCR4 locusGenomeIn vitroInduced cleavageCRISPR/Cas9 systemCas9LociEditing technologyDNAConserved genes regulating human sex differentiation, gametogenesis and fertilization
Fakhro K, Awwad J, Garibova S, Saraiva L, Avella M. Conserved genes regulating human sex differentiation, gametogenesis and fertilization. Journal Of Translational Medicine 2024, 22: 473. PMID: 38764035, PMCID: PMC11103854, DOI: 10.1186/s12967-024-05162-2.Peer-Reviewed Original ResearchConceptsFertility phenotypesReproductive biologyMechanisms of gene functionNewly-discovered genesHuman reproductive biologyCharacterization of genesLoss-of-function mutationsFundamental reproductive processesNext-generation sequencingGenome editing technologyConserved genesFunctional genomicsGene functionFunctional characterizationConsanguineous populationsSex differentiationGenesReproductive tissuesMonogenic causeMolecular mechanismsHuman reproductive tissuesEditing technologyReproductive processesPhenotypeFertility disorders[Donor DNA Modification with Cas9 Targeting Sites Improves the Efficiency of MTC34 Knock-in into the CXCR4 Locus].
Shepelev M, Komkov D, Golubev D, Borovikova S, Mazurov D, Kruglova N. [Donor DNA Modification with Cas9 Targeting Sites Improves the Efficiency of MTC34 Knock-in into the CXCR4 Locus]. Молекулярная Биология 2024, 58: 590-600. PMID: 39709563, DOI: 10.31857/s0026898424040058, edn: incoyt.Peer-Reviewed Original ResearchConceptsCas9 target sitesDouble-strand breaksCell genomeGenetic constructsDonor DNAKnock-inDonor plasmid DNAKnock-in efficiencyGenome editing technologyInduce double-strand breaksProximal nucleotidesPAM sitesDonor plasmidDonor sequenceDNA modificationsGenomeIn vitroInduced cleavageCRISPR/Cas9 systemCas9Editing technologyDNAPlasmid DNAT cell linesTarget cell genome
2021
Mouse Embryonic Fibroblasts Isolated From Nthl1 D227Y Knockin Mice Exhibit Defective DNA Repair and Increased Genome Instability
Marsden CG, Das L, Nottoli TP, Kathe SD, Doublié S, Wallace SS, Sweasy JB. Mouse Embryonic Fibroblasts Isolated From Nthl1 D227Y Knockin Mice Exhibit Defective DNA Repair and Increased Genome Instability. DNA Repair 2021, 109: 103247. PMID: 34826736, PMCID: PMC8787541, DOI: 10.1016/j.dnarep.2021.103247.Peer-Reviewed Original ResearchConceptsGenomic instabilityEmbryonic fibroblastsExogenous DNA damaging agentsBifunctional DNA glycosylaseIncreased genome instabilityGenome editing technologyMurine embryonic fibroblastsDNA damaging agentsMouse embryonic fibroblastsNormal cellular metabolismDefective DNA repairHomozygous stateDNA glycosylase 1Genome instabilityMutant MEFsReplication stressDNA repairCellular phenotypesDNA glycosylaseEditing technologyCellular metabolismDamaging agentsWT proteinOxidative DNA damagePyrimidine lesions
2020
Antibody reactivity with new antigens revealed in multi‐transgenic triple knockout pigs may cause early loss of pig kidneys in baboons
Ariyoshi Y, Takeuchi K, Pomposelli T, Ekanayake‐Alper D, Shimizu A, Boyd L, Estime E, Ohta M, Asfour A, Arn J, Ayares D, Lorber M, Sykes M, Sachs D, Yamada K. Antibody reactivity with new antigens revealed in multi‐transgenic triple knockout pigs may cause early loss of pig kidneys in baboons. Xenotransplantation 2020, 28: e12642. PMID: 32909301, PMCID: PMC8957702, DOI: 10.1111/xen.12642.Peer-Reviewed Original ResearchConceptsPeripheral blood mononuclear cellsCytidine monophospho-N-acetylneuraminic acid hydroxylaseEndothelial protein C receptorTransgenic pigsMulti-transgenesPigsPre-screening assayPig kidneyGene editing technologyPig-to-baboonRenal functionKO pigsEditing technologyVascularized thymic graftsBaboon seraKnockout pigsStable renal functionGalT-KOHuman thrombomodulinMaintained renal functionBlood mononuclear cellsAcute xenograft rejectionProtein C receptorGenetic manipulationNatural antibodies
2019
APOBEC3A Loop 1 Is a Determinant for Single-Stranded DNA Binding and Deamination
Ziegler SJ, Hu Y, Devarkar SC, Xiong Y. APOBEC3A Loop 1 Is a Determinant for Single-Stranded DNA Binding and Deamination. Biochemistry 2019, 58: 3838-3847. PMID: 31448897, PMCID: PMC7211764, DOI: 10.1021/acs.biochem.9b00394.Peer-Reviewed Original ResearchConceptsSubstrate specificityLoop 1A3 proteinsRecent structural studiesBase editing technologyEnzyme catalytic polypeptideProtein functionSubstrate recognitionDNA bindingEditing technologySsDNA recognitionSubstrate selectionNovel CRISPRDeamination activityApolipoprotein B mRNACatalytic polypeptideBiochemical levelBase editorsLoop regionInnate immune systemProteinA3ADeaminase activityA3GA3 family
2018
CRISPR/Cas9 F0 Screening of Congenital Heart Disease Genes in Xenopus tropicalis
Deniz E, Mis EK, Lane M, Khokha MK. CRISPR/Cas9 F0 Screening of Congenital Heart Disease Genes in Xenopus tropicalis. Methods In Molecular Biology 2018, 1865: 163-174. PMID: 30151766, DOI: 10.1007/978-1-4939-8784-9_12.Peer-Reviewed Original ResearchConceptsCardiac developmentCRISPR/Candidate genesHigh-density SNP arrayCRISPR/Cas9 systemGenome editing technologyCongenital heart disease genesNew genomic technologiesHeart disease genesCopy number variationsRapid functional assayXenopus tropicalisCas9 systemGenetic basisDevelopmental systemsEditing technologyGenomic technologiesSequence variationDisease genesDifferent genesGenetic analysisSNP arrayDevelopmental mechanismsMolecular mechanismsWhole-exome sequencingDebugging the genetic code: non-viral in vivo delivery of therapeutic genome editing technologies
Piotrowski-Daspit AS, Glazer P, Saltzman WM. Debugging the genetic code: non-viral in vivo delivery of therapeutic genome editing technologies. Current Opinion In Biomedical Engineering 2018, 7: 24-32. PMID: 30984891, PMCID: PMC6456264, DOI: 10.1016/j.cobme.2018.08.002.Peer-Reviewed Original ResearchGenome editingNon-viral delivery methodsCRISPR/Cas9 systemGenome engineering technologiesGenome editing technologyTherapeutic genome editingPeptide nucleic acidSpecific cell typesGenetic codeVivo deliveryCas9 systemEditing technologyEfficient deliveryGenomic mutationsCell typesPolymeric vehiclesFuture outlookDisease phenotypePrecise technologyEngineering technologyDelivery methodsNucleic acidsCell culturesEditingHereditary disease
2017
Diverse Class 2 CRISPR-Cas Effector Proteins for Genome Engineering Applications
Pyzocha NK, Chen S. Diverse Class 2 CRISPR-Cas Effector Proteins for Genome Engineering Applications. ACS Chemical Biology 2017, 13: 347-356. PMID: 29121460, PMCID: PMC6768076, DOI: 10.1021/acschembio.7b00800.Peer-Reviewed Original ResearchConceptsGenome engineering applicationsCRISPR-Cas genome editing technologiesMicrobial adaptive immune systemGenome editing technologyEffector enzymeNucleic acid cleavageEditing technologyUnique propertiesModern molecular biologyEngineering applicationsEffector proteinsMammalian cellsMolecular biologyAdaptive immune systemWide diversityTechnologyEnzymeApplicationsFunctionalityAcid cleavageImmune systemBiologyProteinDNADiversity
2015
Using hiPSCs to model neuropsychiatric copy number variations (CNVs) has potential to reveal underlying disease mechanisms
Flaherty E, Brennand K. Using hiPSCs to model neuropsychiatric copy number variations (CNVs) has potential to reveal underlying disease mechanisms. Brain Research 2015, 1655: 283-293. PMID: 26581337, PMCID: PMC4865445, DOI: 10.1016/j.brainres.2015.11.009.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsCopy number variationsIsogenic hiPSC linesRare variantsFull genetic architectureGenome editing technologyPluripotent stem cellsStrong heritable componentPatient-derived humanGenetic architectureEditing technologyHeritable componentBehavioral defectsNumber variationsNew therapeutic targetsHiPSC linesGenetic backgroundStem cellsCommon variantsFunctional contributionDisease mechanismsSingle variantMouse modelHigh penetranceHiPSCsTherapeutic target
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