2025
A Multi-Modal and Generalizable Nanogold Tag for Cryo-Electron Tomography in Intact Cells
Young L, Sherrard A, Shaikh F, Zhou H, Hutchings J, Rosen M, Giraldez A, Villa E. A Multi-Modal and Generalizable Nanogold Tag for Cryo-Electron Tomography in Intact Cells. Structural Dynamics 2025, 12: a166-a166. DOI: 10.1063/4.0000475.Peer-Reviewed Original ResearchCryo-electron tomographyPer-particle basisSpatial resolutionSubtomogram analysisCryo-electronAssociated with heterochromatinHistone variantsStructure-function-relationshipsRibosomal targetMinimal perturbationIntact cellsTagging methodHomologous moleculesHeterochromatinTarget macromoleculesNative environmentGold nanoparticlesSubtomogramPerturbation
2024
Genetic and epigenetic determinants of non-alcoholic fatty liver disease (NAFLD) in lean individuals: a systematic review
Njei B, Al-Ajlouni Y, Ugwendum D, Abdu M, Forjindam A, Mohamed M. Genetic and epigenetic determinants of non-alcoholic fatty liver disease (NAFLD) in lean individuals: a systematic review. Translational Gastroenterology And Hepatology 2024, 9: 11-11. PMID: 38317742, PMCID: PMC10838615, DOI: 10.21037/tgh-23-31.Peer-Reviewed Original ResearchNewcastle Ottawa ScaleLean non-alcoholic fatty liver diseaseNon-alcoholic fatty liver diseaseSystematic reviewDeterminants of non-alcoholic fatty liver diseaseAscertainment of exposureLean individualsEpigenetic factorsModerate overall qualityFatty liver diseaseRisk of biasGene variantsPeer-reviewed studiesLiver diseaseQuality assessmentFrequent genetic risk factorGenetic risk factorsOttawa ScaleHistone variantsQualitative synthesisStudy designNAFLD riskPRISMA guidelinesEpigenetic determinantsEpigenetic contributions
2022
Postmitotic accumulation of histone variant H3.3 in new cortical neurons establishes neuronal chromatin, transcriptome, and identity
Funk O, Qalieh Y, Doyle D, Lam M, Kwan K. Postmitotic accumulation of histone variant H3.3 in new cortical neurons establishes neuronal chromatin, transcriptome, and identity. Proceedings Of The National Academy Of Sciences Of The United States Of America 2022, 119: e2116956119. PMID: 35930666, PMCID: PMC9371731, DOI: 10.1073/pnas.2116956119.Peer-Reviewed Original ResearchConceptsNeuronal chromatinHistone variantsVariant H3.3Histone H3 variant H3.3Replication-coupled depositionHistone variant H3.3Replication-dependent histonesKey developmental roleNucleosome turnoverNeural progenitor cellsChromatin stateHistone replacementNeuronal transcriptomeModification landscapeDevelopmental phenotypesGene regulationTranscriptional disruptionH3.3Neuronal lifespanCellular phenotypesHistone H3 levelsNeuronal identityDevelopmental roleTranscriptomePostmitotic cells
2021
Loss of ATRX confers DNA repair defects and PARP inhibitor sensitivity
Garbarino J, Eckroate J, Sundaram RK, Jensen RB, Bindra RS. Loss of ATRX confers DNA repair defects and PARP inhibitor sensitivity. Translational Oncology 2021, 14: 101147. PMID: 34118569, PMCID: PMC8203843, DOI: 10.1016/j.tranon.2021.101147.Peer-Reviewed Original ResearchPARP inhibitor sensitivityInhibitor sensitivityKey DNA damage response pathwaysDNA damage response pathwayFunction of ATRXHR-defective cellsDamage response pathwayAlpha thalassemia/mental retardation syndrome XDNA repair defectsLoss of ATRXHistone chaperonesHistone variantsReplication stressMental retardation syndrome XModel cell lineResponse pathwaysEpistatic interactionsDNA repairGene targetingAtaxia telangiectasiaKO cellsIsocitrate dehydrogenase 1DDR defectsMolecular markersRepair defects
2014
Using Native Chromatin Immunoprecipitation to Interrogate Histone Variant Protein Deposition in Embryonic Stem Cells
Tseng Z, Wu T, Liu Y, Zhong M, Xiao A. Using Native Chromatin Immunoprecipitation to Interrogate Histone Variant Protein Deposition in Embryonic Stem Cells. Methods In Molecular Biology 2014, 1176: 11-22. PMID: 25030915, DOI: 10.1007/978-1-4939-0992-6_2.Peer-Reviewed Original ResearchConceptsNative chromatin immunoprecipitationHigh-throughput sequencingEmbryonic stem cellsChromatin immunoprecipitationHistone variantsMouse embryonic stem cellsGenome-wide localizationChromatin-associated factorsStem cellsProtein of interestMassive parallel sequencingHistone modificationsChromatin regionsChromatin pelletEpigenetic techniquesDNA fragmentsParallel sequencingImmunoprecipitationLibrary constructionSequencingEnzymatic digestionProtein depositionCellsH2A.XSpecific antibodiesSelective Methylation of Histone H3 Variant H3.1 Regulates Heterochromatin Replication
Jacob Y, Bergamin E, Donoghue MT, Mongeon V, LeBlanc C, Voigt P, Underwood CJ, Brunzelle JS, Michaels SD, Reinberg D, Couture JF, Martienssen RA. Selective Methylation of Histone H3 Variant H3.1 Regulates Heterochromatin Replication. Science 2014, 343: 1249-1253. PMID: 24626927, PMCID: PMC4049228, DOI: 10.1126/science.1248357.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceArabidopsisArabidopsis ProteinsCatalytic DomainConserved SequenceCrystallography, X-RayDNA ReplicationEpigenesis, GeneticGene Expression Regulation, PlantHeterochromatinHistonesMethylationMethyltransferasesMitosisMolecular Sequence DataProtein Processing, Post-TranslationalThreonineConceptsHistone H3 variantWidespread regulatory functionsHistone-modifying enzymesARABIDOPSIS TRITHORAXMitotic inheritanceH3 variantHistone variantsHeterochromatin replicationSET domainDNA replicationPosttranslational modificationsCatalytic domainRegulatory functionsPosition 31Protein 5ATXR5H3.3Selective methylationReplicationATXR6TrithoraxH3K27me1ParalogsHeterochromatizationH3.1
2012
Modeling gene expression using chromatin features in various cellular contexts
Dong X, Greven MC, Kundaje A, Djebali S, Brown JB, Cheng C, Gingeras TR, Gerstein M, Guigó R, Birney E, Weng Z. Modeling gene expression using chromatin features in various cellular contexts. Genome Biology 2012, 13: r53. PMID: 22950368, PMCID: PMC3491397, DOI: 10.1186/gb-2012-13-9-r53.Peer-Reviewed Original ResearchConceptsChromatin featuresRNA-seqExpression levelsGene expressionPolyA RNADNase I hypersensitivity sitesGenome-wide mappingCell linesDifferent cellular contextsDifferent cellular compartmentsDifferent cell compartmentsGene expression levelsHigh-throughput techniquesHistone variantsHistone marksTranscriptional regulationHuman cell linesRNA-PETENCODE projectCellular contextCellular compartmentsCytosolic RNANuclear RNAHypersensitivity sitesRNA
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