2025
Guidelines to Analyze ChIP-Seq Data: Journey Through QC and Analysis Considerations
De Kumar B, Krishnan J. Guidelines to Analyze ChIP-Seq Data: Journey Through QC and Analysis Considerations. Methods In Molecular Biology 2025, 2889: 193-206. PMID: 39745614, DOI: 10.1007/978-1-0716-4322-8_14.Peer-Reviewed Original ResearchConceptsChIP-seqChIP-seq analysisQC metricsProperties of transcription factorsNext-generation sequencing approachChIP-seq experimentsStudy DNA-protein interactionsGene regulatory propertiesDNA-protein interactionsENCODE consortiumChromatin stateSequencing approachTranscription factorsChromatinGenesNext-generationImmunoprecipitationSequence
2024
DNA-Assisted Assays for Studying Lipid Transfer Between Membranes
Wang Y, Shi Q, Yang Q, Yang Y, Bian X. DNA-Assisted Assays for Studying Lipid Transfer Between Membranes. Methods In Molecular Biology 2024, 2888: 221-236. PMID: 39699734, DOI: 10.1007/978-1-0716-4318-1_15.Peer-Reviewed Original ResearchConceptsSynaptotagmin-like mitochondrial lipid-binding proteinLipid transfer assaysFluorescence resonance energy transferEndoplasmic reticulumLipid transferPlasma membraneLipid-binding proteinsLipid transfer proteinsTransfer assayE-SytsExtended-synaptotagminsResonance energy transferLipid homeostasisReleased lipidsTransfer proteinProteinAssayMembraneLipidTransfer signalsReticulumHomeostasisEnergy transferChannel width modulates the permeability of DNA origami–based nuclear pore mimics
Feng Q, Saladin M, Wu C, Cao E, Zheng W, Zhang A, Bhardwaj P, Li X, Shen Q, Kapinos L, Kozai T, Mariappan M, Lusk C, Xiong Y, Lim R, Lin C. Channel width modulates the permeability of DNA origami–based nuclear pore mimics. Science Advances 2024, 10: eadq8773. PMID: 39536094, PMCID: PMC11559598, DOI: 10.1126/sciadv.adq8773.Peer-Reviewed Original ResearchAn RNA-centric view of transcription and genome organization
Henninger J, Young R. An RNA-centric view of transcription and genome organization. Molecular Cell 2024, 84: 3627-3643. PMID: 39366351, PMCID: PMC11495847, DOI: 10.1016/j.molcel.2024.08.021.Peer-Reviewed Original ResearchConceptsGene regulationGenome architectureTranscriptional regulationModel of transcriptional regulationAssembly of protein complexesAssembly of transcription complexesLocal genome architectureSilencing of genesGenomic compartmentsGenome organizationGenomic structureRNA polymeraseChromatin regulationTranscription complexActive genesProtein complexesRNA moleculesTranscription factorsGenomeProtein kinaseSpecific genesGenesFeedback regulationRNASpatial compartmentsDNA-Based Molecular Clamp for Probing Protein Interactions and Structure under Force
Chung M, Zhou K, Powell J, Lin C, Schwartz M. DNA-Based Molecular Clamp for Probing Protein Interactions and Structure under Force. ACS Nano 2024, 18: 27590-27596. PMID: 39344156, PMCID: PMC11518680, DOI: 10.1021/acsnano.4c08663.Peer-Reviewed Original ResearchConceptsTalin rod domainNegative-stain electron microscopyDouble-stranded DNADNA clampProtein functionRod domainCryptic sitesProtein interactionsMolecular clampCellular mechanotransductionStudy proteinsBiochemical studiesCell biologyAdult physiologyProtein conformationTalinProteinBiochemical scaleMultiple diseasesDNAARPC5LVinculinStructural analysisEmbryogenesisDNA-based devicesBeyond the “spine of hydration”: Chiral SFG spectroscopy detects DNA first hydration shell and base pair structures
Perets E, Konstantinovsky D, Santiago T, Videla P, Tremblay M, Velarde L, Batista V, Hammes-Schiffer S, Yan E. Beyond the “spine of hydration”: Chiral SFG spectroscopy detects DNA first hydration shell and base pair structures. The Journal Of Chemical Physics 2024, 161: 095104. PMID: 39230381, PMCID: PMC11377083, DOI: 10.1063/5.0220479.Peer-Reviewed Original ResearchConceptsChiral SFG spectraProbe water moleculeWater moleculesChiral SFG spectroscopyHydration shellSFG spectraMinor grooveSFG spectroscopyHydration shell water moleculesWater structureO-H stretching of waterSum frequency generation spectroscopyShell water moleculesPhosphate backboneN-H stretchingO-H stretchingDNA base pairsDNA minor grooveSpine of hydrationSpectra of DNAN-HVibrational spectroscopyO-HSFG responseSFG signalStrand-resolved mutagenicity of DNA damage and repair
Anderson C, Talmane L, Luft J, Connelly J, Nicholson M, Verburg J, Pich O, Campbell S, Giaisi M, Wei P, Sundaram V, Connor F, Ginno P, Sasaki T, Gilbert D, López-Bigas N, Semple C, Odom D, Aitken S, Taylor M. Strand-resolved mutagenicity of DNA damage and repair. Nature 2024, 630: 744-751. PMID: 38867042, PMCID: PMC11186772, DOI: 10.1038/s41586-024-07490-1.Peer-Reviewed Original ResearchConceptsDNA damageDNA damage-induced mutationsSingle-base resolutionCancer genome evolutionDamage-induced mutationsRepair of DNA damageNucleotide excision repairGenome evolutionMultiple distinct mutationsDNA accessibilityGenomic conditionsReplicative strandProcess genomesDNA base damageTranslesion polymerasesExcision repairDNAMutation patternsMutationsBase damageRepair efficiencyStrandsAlkyl adductsReplicationIdentity fidelityDNA lesion bypass and the stochastic dynamics of transcription-coupled repair
Nicholson M, Anderson C, Odom D, Aitken S, Taylor M. DNA lesion bypass and the stochastic dynamics of transcription-coupled repair. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2403871121. PMID: 38717857, PMCID: PMC11098089, DOI: 10.1073/pnas.2403871121.Peer-Reviewed Original ResearchConceptsTranscription-coupled repairRNA polymerase IIDistribution of mutationsStalling of RNA polymerase IITranscription-coupled repair (TCRDNA damageGene expressionBarriers to gene expressionSites of DNA damageGenome-wide distributionBarrier to transcriptionDamaged DNA strandMammalian model systemsDNA lesion bypassGene bodiesPolymerase IIRNA polymeraseGenetic integrityGene productsDNA base damageLesion bypassAlkylation damageDNA strandsBypass lesionsMutationsUnraveling cellular complexity with transient adapters in highly multiplexed super-resolution imaging
Schueder F, Rivera-Molina F, Su M, Marin Z, Kidd P, Rothman J, Toomre D, Bewersdorf J. Unraveling cellular complexity with transient adapters in highly multiplexed super-resolution imaging. Cell 2024, 187: 1769-1784.e18. PMID: 38552613, DOI: 10.1016/j.cell.2024.02.033.Peer-Reviewed Original ResearchConceptsInter-organelle contactsSuper-resolutionMultiplexed super-resolution microscopyIntricate spatial relationshipsGolgi stacksMammalian cellsCellular functionsSuper-resolution microscopyPrimary ciliaSuper-resolution fluorescence microscopyCellular complexityTransient adaptationFluorescence microscopyDNA-PAINTFluorogenic labelingMolecular targetsSpatial relationshipsImagesThroughputPeri-Transplant Inflammation and Long-Term Diabetes Outcomes Were Not Impacted by Either Etanercept or Alpha-1-Antitrypsin Treatment in Islet Autotransplant Recipients
Abdel-Karim T, Hodges J, Herold K, Pruett T, Ramanathan K, Hering B, Dunn T, Kirchner V, Beilman G, Bellin M. Peri-Transplant Inflammation and Long-Term Diabetes Outcomes Were Not Impacted by Either Etanercept or Alpha-1-Antitrypsin Treatment in Islet Autotransplant Recipients. Transplant International 2024, 37: 12320. PMID: 38357216, PMCID: PMC10864605, DOI: 10.3389/ti.2024.12320.Peer-Reviewed Original ResearchConceptsAlpha 1-antitrypsinTolerance testPerioperative periodAlpha-1 antitrypsin treatmentMixed meal tolerance testBenefit of etanerceptMeal tolerance testTrial of etanerceptGlucose tolerance testMonths post-TPIATIntravenous glucose tolerance testIslet autotransplant recipientsLong-term diabetes outcomesSerum A1ATEtanercept groupAdministered etanerceptAutotransplant recipientsDiabetes outcomesInflammatory profileEtanerceptIL-10Endogenous upregulationMCP-1Randomized trialsInflammatory cytokinesscENCORE: leveraging single-cell epigenetic data to predict chromatin conformation using graph embedding
Duan Z, Xu S, Srinivasan S, Hwang A, Lee C, Yue F, Gerstein M, Luan Y, Girgenti M, Zhang J. scENCORE: leveraging single-cell epigenetic data to predict chromatin conformation using graph embedding. Briefings In Bioinformatics 2024, 25: bbae096. PMID: 38493342, PMCID: PMC10944576, DOI: 10.1093/bib/bbae096.Peer-Reviewed Original ResearchConceptsA/B compartmentsEpigenetic dataChromatin interaction frequenciesCell type-specific mannerChromatin conformational changesGenome binsGenomic regionsChromatin conformationEukaryotic DNAChromatin compartmentsDynamic compartmentalizationRepressed stateGenetic blueprintTranscriptional programsTranscriptional changesChromatinConformational changesComplex tissuesInteraction frequencyCompartmentGenomeChromosomeStructural heterogeneityDNAA/BA synthetic agent ameliorates polycystic kidney disease by promoting apoptosis of cystic cells through increased oxidative stress
Fedeles B, Bhardwaj R, Ishikawa Y, Khumsubdee S, Krappitz M, Gubina N, Volpe I, Andrade D, Westergerling P, Staudner T, Campolo J, Liu S, Dong K, Cai Y, Rehman M, Gallagher A, Ruchirawat S, Croy R, Essigmann J, Fedeles S, Somlo S. A synthetic agent ameliorates polycystic kidney disease by promoting apoptosis of cystic cells through increased oxidative stress. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2317344121. PMID: 38241440, PMCID: PMC10823221, DOI: 10.1073/pnas.2317344121.Peer-Reviewed Original ResearchConceptsCyst cellsAutosomal dominant polycystic kidney diseaseMouse models of autosomal dominant polycystic kidney diseasePolycystic kidney diseaseModel of autosomal dominant polycystic kidney diseaseKidney diseaseDeveloped primersMitochondrial oxidative stressPathophysiology of autosomal dominant polycystic kidney diseaseOxidative stressInduce apoptosisMitochondrial respirationCystic cellsUp-regulating aerobic glycolysisHomozygous inactivationMonogenic causeDominant polycystic kidney diseaseAerobic glycolysisRenal replacement therapyApoptosisEnd-stage kidney diseaseAnti-tumor agentsAdult mouse modelChronic kidney diseaseAlkylate DNAThe HER2-directed antibody-drug conjugate DHES0815A in advanced and/or metastatic breast cancer: preclinical characterization and phase 1 trial results
Lewis G, Li G, Guo J, Yu S, Fields C, Lee G, Zhang D, Dragovich P, Pillow T, Wei B, Sadowsky J, Leipold D, Wilson T, Kamath A, Mamounas M, Lee M, Saad O, Choeurng V, Ungewickell A, Monemi S, Crocker L, Kalinsky K, Modi S, Jung K, Hamilton E, LoRusso P, Krop I, Schutten M, Commerford R, Sliwkowski M, Cho E. The HER2-directed antibody-drug conjugate DHES0815A in advanced and/or metastatic breast cancer: preclinical characterization and phase 1 trial results. Nature Communications 2024, 15: 466. PMID: 38212321, PMCID: PMC10784567, DOI: 10.1038/s41467-023-44533-z.Peer-Reviewed Original ResearchConceptsHER2 antibody-drug conjugatesAntibody-drug conjugatesMetastatic breast cancerPhase 1 trialBreast cancerHER2-positive metastatic breast cancerHER2-positive breast cancerObjective response rateDose-escalation studyDuration of responseModel of HER2Anti-tumor activityMechanism of actionTrastuzumab deruxtecanPulmonary toxicityTrastuzumab emtansinePreclinical characterizationResponse rateHigh dosesVivo efficacySecondary objectiveEarly signsPotent cytotoxic agentCytotoxic agentsCancerOuter membrane vesicles and the outer membrane protein OmpU govern Vibrio cholerae biofilm matrix assembly
Potapova A, Garvey W, Dahl P, Guo S, Chang Y, Schwechheimer C, Trebino M, Floyd K, Phinney B, Liu J, Malvankar N, Yildiz F. Outer membrane vesicles and the outer membrane protein OmpU govern Vibrio cholerae biofilm matrix assembly. MBio 2024, 15: e03304-23. PMID: 38206049, PMCID: PMC10865864, DOI: 10.1128/mbio.03304-23.Peer-Reviewed Original ResearchConceptsBiofilm matrix assemblyOuter membrane proteinsOuter membrane protein OmpUOuter membrane vesiclesBiofilm formationBiofilm matrixMatrix assemblyMatrix proteinsBiofilm architectureExtracellular DNAPresence of outer membrane proteinsCausative agent of choleraMembrane vesiclesAgent of choleraBiofilm matrix proteinsBiofilm matrix componentsVibrio cholerae</i>Single-cell force spectroscopyCell surface adhesion forceMatrix proteomeVibrio cholerae</i>.OmpUHuman pathogensMicrobial communitiesEnvironmental survivalAntitumor efficacy of a sequence-specific DNA-targeted γPNA-based c-Myc inhibitor
Malik S, Pradeep S, Kumar V, Xiao Y, Deng Y, Fan R, Vasquez J, Singh V, Bahal R. Antitumor efficacy of a sequence-specific DNA-targeted γPNA-based c-Myc inhibitor. Cell Reports Medicine 2024, 5: 101354. PMID: 38183981, PMCID: PMC10829792, DOI: 10.1016/j.xcrm.2023.101354.Peer-Reviewed Original ResearchConceptsTarget genomic DNAGenomic DNASequencing of genomic DNAGenomic DNA levelInhibit c-myc transcriptionC-myc transcriptionGenomic DNA targetsTarget oncogenesMultiple cell linesC-Myc inhibitorCancer therapyHistone deacetylase inhibitorsRNA targetsDNA targetsPatient-derived xenograftsPre-clinical modelsDNADeacetylase inhibitorsCell linesOncogeneInhibiting oncogenesDNA levelsAntitumor efficacyPrecision medicineChemotherapeutic drugsMutant p53 gains oncogenic functions through a chromosomal instability-induced cytosolic DNA response
Zhao M, Wang T, Gleber-Netto F, Chen Z, McGrail D, Gomez J, Ju W, Gadhikar M, Ma W, Shen L, Wang Q, Tang X, Pathak S, Raso M, Burks J, Lin S, Wang J, Multani A, Pickering C, Chen J, Myers J, Zhou G. Mutant p53 gains oncogenic functions through a chromosomal instability-induced cytosolic DNA response. Nature Communications 2024, 15: 180. PMID: 38167338, PMCID: PMC10761733, DOI: 10.1038/s41467-023-44239-2.Peer-Reviewed Original Research[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
2023
Primary complex motor stereotypies are associated with de novo damaging DNA coding mutations that identify KDM5B as a risk gene
Fernandez T, Williams Z, Kline T, Rajendran S, Augustine F, Wright N, Sullivan C, Olfson E, Abdallah S, Liu W, Hoffman E, Gupta A, Singer H. Primary complex motor stereotypies are associated with de novo damaging DNA coding mutations that identify KDM5B as a risk gene. PLOS ONE 2023, 18: e0291978. PMID: 37788244, PMCID: PMC10547198, DOI: 10.1371/journal.pone.0291978.Peer-Reviewed Original ResearchConceptsRisk genesDe novo damaging variantsGene expression patternsWhole-exome DNA sequencingMid-fetal developmentAdditional risk genesHigh-confidence risk genesParent-child triosGene OntologyCell signalingExpression patternsCalcium ion transportFunctional convergenceCell cycleDamaging variantsGenesDNA sequencingDe novoASD probandsGenetic etiologyBiological mechanismsSequencingDNANetwork analysisIon transportATR promotes clearance of damaged DNA and damaged cells by rupturing micronuclei
Joo Y, Black E, Trier I, Haakma W, Zou L, Kabeche L. ATR promotes clearance of damaged DNA and damaged cells by rupturing micronuclei. Molecular Cell 2023, 83: 3642-3658.e4. PMID: 37788673, PMCID: PMC10599252, DOI: 10.1016/j.molcel.2023.09.003.Peer-Reviewed Original ResearchConceptsATR inhibitorsLamin A/CCytoplasmic DNA sensor cGASHuman ataxia telangiectasiaDNA sensor cGASCdk1 phosphorylationGenomic integrityKinase functionMicronuclear DNAAtaxia telangiectasiaCDK1 inhibitionChromosomal instabilityS phaseAutonomous mechanismsAutophagosome accumulationATRCancer cellsDNACell populationsCGASCellsMicronucleiRad3GenomeChromothripsisDigital assay for rapid electronic quantification of clinical pathogens using DNA nanoballs
Tayyab M, Barrett D, van Riel G, Liu S, Reinius B, Scharfe C, Griffin P, Steinmetz L, Javanmard M, Pelechano V. Digital assay for rapid electronic quantification of clinical pathogens using DNA nanoballs. Science Advances 2023, 9: eadi4997. PMID: 37672583, PMCID: PMC10482329, DOI: 10.1126/sciadv.adi4997.Peer-Reviewed Original ResearchConceptsMicrofluidic impedance cytometerDNA nanoballsLabel-free assayColorimetric readoutImpedance cytometerDigital assaysLoop-mediated isothermal amplificationCapillary-driven flowNanoballsDNA detectionStandalone deviceDNA/RNAIsothermal amplificationCompact systemNucleic acidsClinical pathogensPathogen identificationAccurate detectionRapid testReadoutDetectionNovel methodImpedance
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