2023
De novo reconstruction of satellite repeat units from sequence data
Zhang Y, Chu J, Cheng H, Li H. De novo reconstruction of satellite repeat units from sequence data. Genome Research 2023, 33: 1994-2001. PMID: 37918962, PMCID: PMC10760446, DOI: 10.1101/gr.278005.123.Peer-Reviewed Original ResearchConceptsSatellite repeat unitSequence dataSatellite repeatsLong tandem repeated sequencesReal sequencing dataSatellite DNA evolutionTandem repeat sequencesDe novo reconstructionRepeat unitsGenomic contentGenome sequenceSatellite DNADNA evolutionModel organismsGenomeComplete assemblySequenceRepeatsCentromereAssemblyDNASpeciesAnnotationRegulation of gene editing using T-DNA concatenation
Dickinson L, Yuan W, LeBlanc C, Thomson G, Wang S, Jacob Y. Regulation of gene editing using T-DNA concatenation. Nature Plants 2023, 9: 1398-1408. PMID: 37653336, PMCID: PMC11193869, DOI: 10.1038/s41477-023-01495-w.Peer-Reviewed Original ResearchConceptsT-DNA copy numberLong terminal repeatGene editingCopy numberT-DNA copiesPlant gene editingT-DNA structureTransfer DNAT-DNADNA repeatsAgrobacterium tumefaciensDNA repairSingle copyGene targetingExogenous DNATerminal repeatMolecular determinantsArabidopsisLarge concatemersRepeatsDNAEditingCopiesRad17RetrotransposonsPooled screening with next-generation gene editing tools
Zhou L, Yang L, Feng Y, Chen S. Pooled screening with next-generation gene editing tools. Current Opinion In Biomedical Engineering 2023, 28: 100479. PMID: 38222973, PMCID: PMC10786633, DOI: 10.1016/j.cobme.2023.100479.Peer-Reviewed Original ResearchGene editing toolsEditing toolsFunction of genesShort palindromic repeatsPooled screensPalindromic repeatsGenetic elementsPool of cellsBiological processesPooled screeningGenetic variantsPotential targetRecent advancesGenesRepeatsPlantsSequencingMutationsAgricultural researchTherapeutic interventionsSimultaneous examinationExpressionPotential future directionsCellsPoolEvolutionary constraint and innovation across hundreds of placental mammals
Christmas M, Kaplow I, Genereux D, Dong M, Hughes G, Li X, Sullivan P, Hindle A, Andrews G, Armstrong J, Bianchi M, Breit A, Diekhans M, Fanter C, Foley N, Goodman D, Goodman L, Keough K, Kirilenko B, Kowalczyk A, Lawless C, Lind A, Meadows J, Moreira L, Redlich R, Ryan L, Swofford R, Valenzuela A, Wagner F, Wallerman O, Brown A, Damas J, Fan K, Gatesy J, Grimshaw J, Johnson J, Kozyrev S, Lawler A, Marinescu V, Morrill K, Osmanski A, Paulat N, Phan B, Reilly S, Schäffer D, Steiner C, Supple M, Wilder A, Wirthlin M, Xue J, Birren B, Gazal S, Hubley R, Koepfli K, Marques-Bonet T, Meyer W, Nweeia M, Sabeti P, Shapiro B, Smit A, Springer M, Teeling E, Weng Z, Hiller M, Levesque D, Lewin H, Murphy W, Navarro A, Paten B, Pollard K, Ray D, Ruf I, Ryder O, Pfenning A, Lindblad-Toh K, Karlsson E, 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. Evolutionary constraint and innovation across hundreds of placental mammals. Science 2023, 380: eabn3943. PMID: 37104599, PMCID: PMC10250106, DOI: 10.1126/science.abn3943.Peer-Reviewed Original ResearchConceptsEncyclopedia of DNA ElementsProtein-coding exonsUltraconserved elementsGenome functionGenomic resourcesOrganismal phenotypesDNA elementsFunctional annotationEvolutionary constraintsHuman genomeRegulatory elementsMammalian traitsGenomeGenetic variantsPlacental mammalsTherapeutic developmentMammalsSpeciesDisease riskExonGenesBiodiversityPhenotypeTraitsRepeats
2022
Phenome-wide association study of loci harboring de novo tandem repeat mutations in UK Biobank exomes
Wendt F, Pathak G, Polimanti R. Phenome-wide association study of loci harboring de novo tandem repeat mutations in UK Biobank exomes. Nature Communications 2022, 13: 7682. PMID: 36509785, PMCID: PMC9744822, DOI: 10.1038/s41467-022-35423-x.Peer-Reviewed Original ResearchConceptsProtein structureTandem repeatsTandem repeat mutationsPhenome-wide association studyAlters protein structureGenetic variationAssociation studiesEuropean ancestry participantsUK BiobankCarotid intima-media thicknessTR mutationsIntima-media thicknessMicroRNA-184Repeat mutationsFamily-based designsTestable hypothesesLociPopulation levelRespiratory outcomesMutationsDisease outcomeFAN1FNBP4RepeatsSystematic generation and imaging of tandem repeats reveal base-pairing properties that promote RNA aggregation
Isiktas A, Eshov A, Yang S, Guo J. Systematic generation and imaging of tandem repeats reveal base-pairing properties that promote RNA aggregation. Cell Reports Methods 2022, 2: 100334. PMID: 36452875, PMCID: PMC9701603, DOI: 10.1016/j.crmeth.2022.100334.Peer-Reviewed Original ResearchConceptsBase pairsRNA aggregationRNA-RNA interactionsLive-cell imagingConsecutive base pairsNoncanonical base pairsRNA aggregatesRepeat RNARepeat DNAMolecular basisRepeat sequencesMolecular mechanismsTandem repeatsRNAHexanucleotide repeatsStructural determinantsGGGGCC hexanucleotide repeatBase-pairing propertiesCommon pathological featureRepeatsSequenceUnifying modelGeneralizable approachDistinct propertiesEnhanced aggregationMitochondrial dysfunction caused by targeted deletion of Mfn1 does not result in telomere shortening in oocytes.
Cozzolino M, Seli E. Mitochondrial dysfunction caused by targeted deletion of Mfn1 does not result in telomere shortening in oocytes. Zygote 2022, 30: 735-737. PMID: 35730364, DOI: 10.1017/s0967199422000089.Peer-Reviewed Original ResearchConceptsMitochondrial dysfunctionMaintenance of telomeresTargeted deletionEnd-protection functionTTAGGG repeatsMitochondrial fusionTelomeric repeatsSomatic cellsMitofusin 1Reactive oxygen speciesEnzyme complexWild-type miceOocyte growthDNA damageMouse oocytesTelomerase activityOocyte maturationDeletionFollicular depletionOxygen speciesTelomere lengthTelomeresFollicular developmentOocytesRepeatsSingle particle cryo-EM structure of the outer hair cell motor protein prestin
Butan C, Song Q, Bai JP, Tan WJT, Navaratnam D, Santos-Sacchi J. Single particle cryo-EM structure of the outer hair cell motor protein prestin. Nature Communications 2022, 13: 290. PMID: 35022426, PMCID: PMC8755724, DOI: 10.1038/s41467-021-27915-z.Peer-Reviewed Original ResearchConceptsTransmembrane domainProtein prestinSingle-particle cryo-EM structuresAnti-sigma factor antagonist domainOuter hair cell motor protein prestinCryo-EM structureCryo-electron microscopyMotor protein prestinSLC26 family membersSulfate transportersTransmembrane segmentsPrestin functionÅ resolutionPrestinOHC electromotilityOpen stateCochlear amplificationPutative mechanismsFamily membersDomainRepeatsSLC26A9TransportersMutationsElectromotility
2021
Retrospective cell lineage reconstruction in humans by using short tandem repeats
Tao L, Raz O, Marx Z, Ghosh MS, Huber S, Greindl-Junghans J, Biezuner T, Amir S, Milo L, Adar R, Levy R, Onn A, Chapal-Ilani N, Berman V, Arie A, Rom G, Oron B, Halaban R, Czyz ZT, Werner-Klein M, Klein CA, Shapiro E. Retrospective cell lineage reconstruction in humans by using short tandem repeats. Cell Reports Methods 2021, 1: 100054. PMID: 34341783, PMCID: PMC8313865, DOI: 10.1016/j.crmeth.2021.100054.Peer-Reviewed Original ResearchConceptsLineage reconstructionShort tandem repeatsCell lineagesTandem repeatsCell lineage reconstructionCell lineage analysisSingle cellsLineage tracing methodHuman cell lineagesGenome editingLineage analysisMolecular inversion probesReconstructed lineagesLineagesDU145 cellsSomatic mutationsDiscovery platformCell of originRepeatsHealthy cellsCellsImportant insightsTissue formationOrganismsDevelopmental historyWhat is the role of synaptic protein TRIO's spectrin repeats?
Corcoran E, Bircher J, Koleske A. What is the role of synaptic protein TRIO's spectrin repeats? The FASEB Journal 2021, 35 DOI: 10.1096/fasebj.2021.35.s1.01837.Peer-Reviewed Original ResearchSpectrin repeatsProper neuronal developmentSpectrin repeat domainRare damaging variantsDisease-associated mutationsAccessory domainsCatalytic domainRepeat domainRegulatory proteinsRepeat functionDe novo missense mutationsSignaling mechanismDamaging mutationsNeuronal developmentDamaging variantsDisease mutationsBiochemical eventsNovo missense mutationNeurodevelopmental disordersMissense mutationsSpectrinRepeatsMutationsDomainTherapeutic strategiesStructural insights into the cause of human RSPH4A primary ciliary dyskinesia
Zhao Y, Pinskey J, Lin J, Yin W, Sears P, Daniels L, Zariwala M, Knowles M, Ostrowski L, Nicastro D. Structural insights into the cause of human RSPH4A primary ciliary dyskinesia. Molecular Biology Of The Cell 2021, 32: 1202-1209. PMID: 33852348, PMCID: PMC8351563, DOI: 10.1091/mbc.e20-12-0806.Peer-Reviewed Original ResearchConceptsStructural basisCryo-electron tomographyRadial spokesCentral pair complexUnderlying structural basisAxonemal repeatEukaryotic organellesArch domainThree-dimensional structureSubtomogram averagingOrgan positioningCell motilityStructural insightsPrimary ciliary dyskinesiaCiliaHuman ciliaHuman respiratory ciliaRS1Primary defectStructure determinationCiliary dyskinesiaHuman healthOrganellesFlagellaRepeatsForensic Ancestry Inference: Data Requirements, Analysis Methods, and Interpretation of Results
Bulbul O, Kidd K. Forensic Ancestry Inference: Data Requirements, Analysis Methods, and Interpretation of Results. 2021, 225-240. DOI: 10.1201/9781003043027-12.Peer-Reviewed Original ResearchStandard DNA markersSingle nucleotide polymorphismsInformative single nucleotide polymorphismsAncestry informative single nucleotide polymorphismsDNA markersShort tandem repeatsTandem repeatsBiogeographic ancestryDNA profilesCrime scene DNANucleotide polymorphismsParallel sequencing technologiesAncestry informative SNPsShort tandem repeat polymorphismsDifferent populationsSequencing technologiesFuture forensic studiesMost populationsForensic geneticsAncestry assignmentTandem repeat polymorphismDNA samplesRepeatsAncestryDNA
2020
C9orf72 arginine-rich dipeptide repeats inhibit UPF1-mediated RNA decay via translational repression
Sun Y, Eshov A, Zhou J, Isiktas AU, Guo JU. C9orf72 arginine-rich dipeptide repeats inhibit UPF1-mediated RNA decay via translational repression. Nature Communications 2020, 11: 3354. PMID: 32620797, PMCID: PMC7335171, DOI: 10.1038/s41467-020-17129-0.Peer-Reviewed Original ResearchMeSH KeywordsAmyotrophic Lateral SclerosisAnimalsC9orf72 ProteinCell Line, TumorCell SurvivalDatasets as TopicDNA Repeat ExpansionEmbryo, MammalianFemaleFrontal LobeFrontotemporal DementiaHumansIntronsMiceNeuronsNonsense Mediated mRNA DecayPrimary Cell CultureProtein BiosynthesisRNA HelicasesRNA-SeqRNA, MessengerTrans-ActivatorsConceptsArginine-rich dipeptide repeatsNonsense-mediated decayRNA surveillanceTranslational repressionNMD inhibitionDipeptide repeatsRNA Decay mechanismsGlobal translational repressionStress granule formationC9ALS/FTDRNA decayFrameshift 1Repeat regionFamilial amyotrophic lateral sclerosisGranule formationCultured cellsFTD brainC9orf72 geneRepressionSurvival of neuronsRepeatsAmyotrophic lateral sclerosisMutantsGenesLateral sclerosisA satellite repeat-derived piRNA controls embryonic development of Aedes
Halbach R, Miesen P, Joosten J, Taşköprü E, Rondeel I, Pennings B, Vogels C, Merkling S, Koenraadt C, Lambrechts L, van Rij R. A satellite repeat-derived piRNA controls embryonic development of Aedes. Nature 2020, 580: 274-277. PMID: 32269344, PMCID: PMC7145458, DOI: 10.1038/s41586-020-2159-2.Peer-Reviewed Original ResearchConceptsPIWI-interacting RNAsSatellite repeatsEmbryonic developmentGene expressionAbundant piwi-interacting RNAsLocal chromatin structureGlobal gene expressionTandem repeat elementsSequence-specific geneMosquito Aedes aegyptiPiRNA productionEukaryotic chromosomesChromatin structureEuchromatic regionsPiRNA sequencesMosquito biologyRepeat elementsDevelopmental arrestRepeatsDiverse classAedes aegyptiGenesTranscriptsCentral functionExpression
2017
The repeat region of cortactin is intrinsically disordered in solution
Li X, Tao Y, Murphy JW, Scherer AN, Lam TT, Marshall AG, Koleske AJ, Boggon TJ. The repeat region of cortactin is intrinsically disordered in solution. Scientific Reports 2017, 7: 16696. PMID: 29196701, PMCID: PMC5711941, DOI: 10.1038/s41598-017-16959-1.Peer-Reviewed Original ResearchConceptsCortactin repeatsRepeat regionActin filamentsHydrogen-deuterium exchange mass spectrometryAdjacent helical regionsMulti-domain proteinsExchange mass spectrometryExtensive biophysical analysisCircular dichroismHydrophobic core regionSmall-angle X-ray scatteringBiophysical analysisHelical regionCortactinRepeatsSimilar copiesUnfolded peptidesProteinMotifSize exclusion chromatographyMass spectrometryFilamentsExclusion chromatographyX-ray scatteringRegionBRCA2's Role in Homologous Recombination Through Interaction with RAD51
D'Ausilio M, Beckman A, Brown G, Emeghara U, Ho F, Malzberg E, Spellman B, Tavan K, Xiao J, Jensen R. BRCA2's Role in Homologous Recombination Through Interaction with RAD51. The FASEB Journal 2017, 31 DOI: 10.1096/fasebj.31.1_supplement.lb261.Peer-Reviewed Original ResearchHomologous recombinationBRC repeatsSites of DNA damageNucleoprotein filament formationPortion of DNARAD51 moleculesProcess of HRNucleoprotein filamentStructure-function relationshipsFilamentous growthSister chromatidsGenomic instabilityDNA repairRAD51Damaged DNABRCA2Filament formationDNA damageDNARepeatsRecombinationRecombinaseBiomolecular modelingChromatidSsDNA
2016
Distinct binding of BRCA2 BRC repeats to RAD51 generates differential DNA damage sensitivity
Chatterjee G, Jimenez-Sainz J, Presti T, Nguyen T, Jensen RB. Distinct binding of BRCA2 BRC repeats to RAD51 generates differential DNA damage sensitivity. Nucleic Acids Research 2016, 44: 5256-5270. PMID: 27084934, PMCID: PMC4914107, DOI: 10.1093/nar/gkw242.Peer-Reviewed Original ResearchConceptsDNA double-strand breaksDomain of BRCA2Homology-directed repairDouble-strand breaksBRC repeatsDNA damageDNA damage sensitivityPatient-derived mutationsRegulation of RAD51Cellular DNA damageComplementation functionRepair complexRAD51 bindingRad51 filamentsDNA substratesHomologous recombinationFaceted proteinProper regulationStrand pairingRAD51Damage sensitivityCellular propertiesRepeatsCellular featuresRepeat units
2015
Recruitment of RAG1 and RAG2 to Chromatinized DNA during V(D)J Recombination
Shetty K, Schatz DG. Recruitment of RAG1 and RAG2 to Chromatinized DNA during V(D)J Recombination. Molecular And Cellular Biology 2015, 35: 3701-3713. PMID: 26303526, PMCID: PMC4589606, DOI: 10.1128/mcb.00219-15.Peer-Reviewed Original ResearchConceptsConserved heptamerRAG2 proteinsChromatin immunoprecipitationNonamer elementsRecombination substratesSignal sequenceNonamer sequencesMutant formsCryptic RSSsRAG1DNA cleavageGene segmentsChromatinCell linesRAG2ProteinRecruitmentRecombinationSequenceMajor roleMutagenesisImmunoprecipitationRepeatsRSSsRAGMonitoring the DNA Damage Response at Dysfunctional Telomeres
Rai R, Chang S. Monitoring the DNA Damage Response at Dysfunctional Telomeres. Methods In Molecular Biology 2015, 1343: 175-180. PMID: 26420717, DOI: 10.1007/978-1-4939-2963-4_14.Peer-Reviewed Original ResearchConceptsDysfunctional telomeresDNA damage sensorDNA damage responseDNA damage fociSitu hybridization approachEukaryotic chromosomesShelterin componentsDNA repeatsGenomic stabilityDDR proteinsDamage responseTelomeric DNADDR pathwaysDamage fociChromosomal endsTelomere dysfunctionDamage sensorTelomeresDNA damageHybridization approachCellular viabilityPathwayProper maintenanceChromosomesRepeats
2014
Nonenzymatic domains of Kalirin7 contribute to spine morphogenesis through interactions with phosphoinositides and Abl
Ma XM, Miller MB, Vishwanatha KS, Gross MJ, Wang Y, Abbott T, Lam TT, Mains RE, Eipper BA. Nonenzymatic domains of Kalirin7 contribute to spine morphogenesis through interactions with phosphoinositides and Abl. Molecular Biology Of The Cell 2014, 25: 1458-1471. PMID: 24600045, PMCID: PMC4004595, DOI: 10.1091/mbc.e13-04-0215.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCalpainCells, CulturedDendritic SpinesGuanine Nucleotide Exchange FactorsHippocampusMice, KnockoutNeuronsOncogene Proteins v-ablPeptide FragmentsPhosphatidylinositolsPhosphorylationProtein Processing, Post-TranslationalProtein Structure, TertiaryProteolysisRats, Sprague-DawleySynapsesTransferrinConceptsGDP/GTP exchange factorSec14 domainSpectrin repeatsSpine morphogenesisNon-receptor tyrosine kinaseGTP exchange factorSpine formationNatural splice variantSpectrin repeat domainReceptor-mediated endocytosisRho GDP/GTP exchange factorDrosophila orthologueMembrane traffickingPhosphomimetic mutationExchange factorCalpain-mediated degradationRepeat domainTruncation mutantsTyrosine kinaseGenetic studiesCellular membranesSplice variantsRepeatsNonneuronal cellsMorphogenesis
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