2025
Single-cell transcriptomic and chromatin dynamics of the human brain in PTSD
Hwang A, Skarica M, Xu S, Coudriet J, Lee C, Lin L, Terwilliger R, Sliby A, Wang J, Nguyen T, Li H, Wu M, Dai Y, Duan Z, Srinivasan S, Zhang X, Lin Y, Cruz D, Deans P, Huber B, Levey D, Glausier J, Lewis D, Gelernter J, Holtzheimer P, Friedman M, Gerstein M, Sestan N, Brennand K, Xu K, Zhao H, Krystal J, Young K, Williamson D, Che A, Zhang J, Girgenti M. Single-cell transcriptomic and chromatin dynamics of the human brain in PTSD. Nature 2025, 643: 744-754. PMID: 40533550, PMCID: PMC12267058, DOI: 10.1038/s41586-025-09083-y.Peer-Reviewed Original ResearchPost-traumatic stress disorderPrefrontal cortexDorsolateral prefrontal cortexHuman prefrontal cortexTraumatic stress responseHuman brainDepressive disorderStress disorderTrauma exposureCell type-specific contextRegulatory mechanismsGABAergic transmissionCell-type clusteringCell type-specific mannerMolecular regulatory mechanismsGlucocorticoid signalingGene expression changesChromatin dynamicsCredible variantsDisordersTranscriptional regulationEpigenetic dataCortexPersistent effectsPolygenic disorderCoarse-grained chromatin dynamics by tracking multiple similarly labeled gene loci
Mader A, Rodriguez A, Yuan T, Surovtsev I, King M, Mochrie S. Coarse-grained chromatin dynamics by tracking multiple similarly labeled gene loci. Biophysical Journal 2025, 124: 2120-2132. PMID: 40369871, DOI: 10.1016/j.bpj.2025.05.008.Peer-Reviewed Original ResearchChromatin polymerChromatin configurationLocus identityGenomic positionsLabeled lociLiving cellsLocus configurationsChromatin dynamicsMultiple lociGene locusChromatin researchChromatinLociSingle-particle trackingFluorescent labelingCorrect assignmentDynamic loopTemporal dynamicsCellsGenesModel polymersLabelingIdentity
2024
Effect of loops on the mean-square displacement of Rouse-model chromatin
Yuan T, Yan H, Bailey M, Williams J, Surovtsev I, King M, Mochrie S. Effect of loops on the mean-square displacement of Rouse-model chromatin. Physical Review E 2024, 109: 044502. PMID: 38755928, DOI: 10.1103/physreve.109.044502.Peer-Reviewed Original ResearchConceptsStretching exponentConsistent with recent experimentsTopologically associating domainsMean square displacementRecent experimentsLoop extrusionExponent valuesTAD formationTree of lifeDynamics of chromatinExponentEffects of loopChromatin lociChromatin dynamicsRouse modelChromatin organizationChromatin mobilityGene locusContact mapsDynamicsChromatinLoopPolymer dynamicsLociPolymer simulations
2023
Loops and the activity of loop extrusion factors constrain chromatin dynamics
Bailey M, Surovtsev I, Williams J, Yan H, Yuan T, Li K, Duseau K, Mochrie S, King M. Loops and the activity of loop extrusion factors constrain chromatin dynamics. Molecular Biology Of The Cell 2023, 34: ar78. PMID: 37126401, PMCID: PMC10398873, DOI: 10.1091/mbc.e23-04-0119.Peer-Reviewed Original ResearchConceptsChromatin dynamicsChromatin mobilityChromatin conformation capture experimentsINO80 chromatin remodelerSystematic genetic perturbationsDynamics of chromatinSWI/SNFChromatin fluctuationsCondensin complexRSC complexChromatin remodelersFission yeastChromosome structureChromatin polymerExtrusion factorsChromatin motionGenetic perturbationsThree-dimensional structureDNA structureChromatinCohesinPolymer simulationsIntroduction of loopsKey roleActive process
2020
Preserving genome integrity in human cells via DNA double-strand break repair
Jensen RB, Rothenberg E. Preserving genome integrity in human cells via DNA double-strand break repair. Molecular Biology Of The Cell 2020, 31: 859-865. PMID: 32286930, PMCID: PMC7185975, DOI: 10.1091/mbc.e18-10-0668.Peer-Reviewed Original ResearchConceptsGenome integrityHuman cellsHuman diseasesRepair pathwaysDNA DSB repair pathwaysDNA double-strand break repairDNA double-strand break repair pathwayDouble-strand break repair pathwayDouble-strand break repairDSB repair pathwaysCell cycle checkpointsBreak repair pathwayFull tumorigenic potentialDNA repair failureChromatin dynamicsGenome stabilityNuclear architectureCellular signalingDNA replicationBreak repairCellular stressCycle checkpointsDNA repairCellular activitiesHomologous recombination-deficient tumors
2016
Setd1a and NURF mediate chromatin dynamics and gene regulation during erythroid lineage commitment and differentiation
Li Y, Schulz VP, Deng C, Li G, Shen Y, Tusi BK, Ma G, Stees J, Qiu Y, Steiner LA, Zhou L, Zhao K, Bungert J, Gallagher PG, Huang S. Setd1a and NURF mediate chromatin dynamics and gene regulation during erythroid lineage commitment and differentiation. Nucleic Acids Research 2016, 44: 7173-7188. PMID: 27141965, PMCID: PMC5009724, DOI: 10.1093/nar/gkw327.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAntigens, NuclearCell LineageCells, CulturedChromatinChromatin Assembly and DisassemblyChromatin ImmunoprecipitationErythroblastsErythrocyte CountErythrocytesErythropoiesisFemaleGene Expression RegulationHemoglobinsHistone-Lysine N-MethyltransferaseHistonesHumansLysineMaleMethylationMiceMice, KnockoutMicrococcal NucleaseMultiprotein ComplexesNerve Tissue ProteinsPromoter Regions, GeneticSpleenTranscription FactorsUpstream Stimulatory FactorsConceptsNURF complexChromatin dynamicsErythroid genesLineage commitmentAdult β-globin geneErythroid gene promotersErythroid lineage differentiationCell context-dependent mannerErythroid lineage commitmentChromatin structural alterationsContext-dependent mannerΒ-globin geneChromatin architectureEnhancer accessibilityChromatin accessibilityNucleosome repositioningTranscription regulationChromatin structureH3K4 methylationGene regulationComplex occupancyMammalian cellsGene activationGene transcriptionLineage differentiation
2015
High‐content imaging with micropatterned multiwell plates reveals influence of cell geometry and cytoskeleton on chromatin dynamics
Harkness T, McNulty J, Prestil R, Seymour S, Klann T, Murrell M, Ashton R, Saha K. High‐content imaging with micropatterned multiwell plates reveals influence of cell geometry and cytoskeleton on chromatin dynamics. Biotechnology Journal 2015, 10: 1555-1567. PMID: 26097126, PMCID: PMC6948850, DOI: 10.1002/biot.201400756.Peer-Reviewed Original ResearchConceptsChromatin dynamicsHigh-content imagingMicroenvironmental cuesHuman cellsCellular microenvironment influencesHuman cell biologySingle cell geometryCell-cell contactExtracellular matrix connectionsActin cytoskeletonHuman cell behaviorCytoskeletal organizationHigh-content screening technologyCell biologyBiophysical cuesCellular responsesCellular microenvironmentNuclear elongationCell behaviorCellular biophysicsSubcellular imagingComplex milieuCellular geometryHuman fibroblastsCytoskeleton
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