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 technologyDNA[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
2020
Analysis of Cell and Nucleus Genome by Next-Generation Sequencing
Oh J, Abyzov A. Analysis of Cell and Nucleus Genome by Next-Generation Sequencing. 2020, 35-65. DOI: 10.1007/978-3-030-62532-0_3.Peer-Reviewed Original ResearchSingle-cell genomesBulk of cellsNext-generation sequencing technologiesMosaic variantsNuclear genomeNucleus genomeGenomic mosaicismAnalysis of cellsGenome analysisNext-generation sequencingCell genomeSequencing technologiesGenomeGenomic variantsSingle cellsCellsVariantsMosaicismDiscoverySequencingValuable insightsEnvironmental exposures
2019
Approaches and Methods for Variant Analysis in the Genome of a Single Cell
Abyzov A, Vaccarino F, Urban A, Sarangi V. Approaches and Methods for Variant Analysis in the Genome of a Single Cell. Healthy Ageing And Longevity 2019, 10: 203-228. DOI: 10.1007/978-3-030-24970-0_14.Chapters
2017
Different mutational rates and mechanisms in human cells at pregastrulation and neurogenesis
Bae T, Tomasini L, Mariani J, Zhou B, Roychowdhury T, Franjic D, Pletikos M, Pattni R, Chen BJ, Venturini E, Riley-Gillis B, Sestan N, Urban AE, Abyzov A, Vaccarino FM. Different mutational rates and mechanisms in human cells at pregastrulation and neurogenesis. Science 2017, 359: 550-555. PMID: 29217587, PMCID: PMC6311130, DOI: 10.1126/science.aan8690.Peer-Reviewed Original ResearchConceptsSingle nucleotide variationsMutation rateCancer cell genomeClonal cell populationsCell genomeCell lineagesBackground mutagenesisHuman cellsMutational rateSomatic mosaicismSingle cellsOxidative damageGenomeMutagenesisCell populationsMutation spectrumNeurogenesisCellsHuman fetusesIndividual neuronsLineagesPregastrulationHuman brainBrainMutations
2008
Two levels of protection for the B cell genome during somatic hypermutation
Liu M, Duke JL, Richter DJ, Vinuesa CG, Goodnow CC, Kleinstein SH, Schatz DG. Two levels of protection for the B cell genome during somatic hypermutation. Nature 2008, 451: 841-845. PMID: 18273020, DOI: 10.1038/nature06547.Peer-Reviewed Original ResearchConceptsError-free DNA repairB cell genomeGenomic stabilityNumerous oncogenesDNA repairCell genomeBase excisionGenomeMismatch repairImmunoglobulin genesSomatic hypermutationWidespread mutationsHypermutationB-cell tumorsB-cell malignanciesHigh-affinity antibodiesB cellsGenesOncogeneLarge fractionDiversityVital roleMutationsEnzymeRepairCftr gene targeting in mouse embryonic stem cells mediated by Small Fragment Homologous Replacement (SFHR).
Sangiuolo F, Scaldaferri ML, Filareto A, Spitalieri P, Guerra L, Favia M, Caroppo R, Mango R, Bruscia E, Gruenert DC, Casavola V, De Felici M, Novelli G. Cftr gene targeting in mouse embryonic stem cells mediated by Small Fragment Homologous Replacement (SFHR). Frontiers In Bioscience-Landmark 2008, 13: 2989-99. PMID: 17981772, PMCID: PMC3725395, DOI: 10.2741/2904.Peer-Reviewed Original ResearchConceptsSmall fragment homologous replacementES cellsSmall DNA fragmentsGene functionHomologous replacementEmbryonic stem cell genomeMouse embryonic stem cell genomeGenomic DNAMurine ES cellsTissue-specific gene functionEndogenous genomic DNAMouse embryonic stem cellsSpecific genomic lociStem cell genomeNormal gene functionCFTR-dependent chloride effluxEmbryonic stem cellsDifferent cell lineagesGene correctionGenomic lociGenomic sequencesCFTR locusCell genomeDifferent genesCell lineages
1986
Nonsense mutation in open reading frame E2 of bovine papillomavirus DNA
DiMaio D. Nonsense mutation in open reading frame E2 of bovine papillomavirus DNA. Journal Of Virology 1986, 57: 475-480. PMID: 3003380, PMCID: PMC252759, DOI: 10.1128/jvi.57.2.475-480.1986.Peer-Reviewed Original ResearchConceptsMutant viral DNAOpen reading frame E2C127 cellsBovine papillomavirus DNAViral DNAGenetic mapping experimentsNonsense mutationMouse C127 cellsSingle base substitution mutationsHost cell genomeFull-length viral DNAFocus-forming activityBase substitution mutationsWild-type DNAAmber mutationCell genomeOncogenic transformationViral ORFsSubstitution mutationsORF E2Mapping experimentsMutant DNATransformation assaysDNABovine papillomavirus
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