2024
Image-based 3D genomics through chromatin tracing
Yang T, Wang S. Image-based 3D genomics through chromatin tracing. Nature Reviews Methods Primers 2024, 4: 76. DOI: 10.1038/s43586-024-00354-y.Peer-Reviewed Original ResearchChromatin tracingChromatin organizationHigh-throughput sequencing-based methodsRegulation of gene expressionSequencing-based methodsSingle-cellGenetic screening technologiesGenome foldingGenomic scaleGenome functionChromatin labelingGenomic levelSpectrum of cell typesDNA replicationModel organismsChromatinGene expressionIntact cellsSystematic profilingSingle-molecule levelCell typesGenomeScreening technologiesFilling major gapsPrimers
2023
Live imaging reveals chromatin compaction transitions and dynamic transcriptional bursting during stem cell differentiation in vivo
May D, Yun S, Gonzalez D, Park S, Chen Y, Lathrop E, Cai B, Xin T, Zhao H, Wang S, Gonzalez L, Cockburn K, Greco V. Live imaging reveals chromatin compaction transitions and dynamic transcriptional bursting during stem cell differentiation in vivo. ELife 2023, 12: e83444. PMID: 36880644, PMCID: PMC10027315, DOI: 10.7554/elife.83444.Peer-Reviewed Original ResearchConceptsStem cell differentiationCell differentiationStem cell compartmentCompaction changesChromatin compaction statesDynamic transcriptional statesCell compartmentChromatin architectureCell cycle statusChromatin rearrangementNascent RNATranscriptional burstingTranscriptional statesLive imagingTissue contextGene expressionDifferentiating cellsGlobal remodelingIndividual cellsCycle statusStem cellsDifferentiation statusDifferentiationCellsMorphological changes
2021
Chromatin tracing and multiplexed imaging of nucleome architectures (MINA) and RNAs in single mammalian cells and tissue
Liu M, Yang B, Hu M, Radda JSD, Chen Y, Jin S, Cheng Y, Wang S. Chromatin tracing and multiplexed imaging of nucleome architectures (MINA) and RNAs in single mammalian cells and tissue. Nature Protocols 2021, 16: 2667-2697. PMID: 33903756, PMCID: PMC9007104, DOI: 10.1038/s41596-021-00518-0.Peer-Reviewed Original ResearchConceptsSame single cellNucleome architecturesGene expressionMammalian tissuesChromatin foldingNuclear laminaSingle cellsNumerous RNA speciesDifferent biological processesSingle mammalian cellsDifferent cell typesMultiplexed imagingGenomic organizationGenomic architectureChromatin loopsGenomic regionsRNA speciesIndividual chromosomesMammalian cellsGenomic techniquesBiological processesDetailed protocolCopy numberCell typesNormal development
2020
Multiplexed imaging of nucleome architectures in single cells of mammalian tissue
Liu M, Lu Y, Yang B, Chen Y, Radda JSD, Hu M, Katz SG, Wang S. Multiplexed imaging of nucleome architectures in single cells of mammalian tissue. Nature Communications 2020, 11: 2907. PMID: 32518300, PMCID: PMC7283333, DOI: 10.1038/s41467-020-16732-5.Peer-Reviewed Original ResearchConceptsNucleome architecturesChromatin organizationMammalian tissuesNumerous RNA speciesNumerous genomic regionsSpecific chromatin architectureSurface of chromosomesSingle cellsDifferent cell typesMouse fetal liverChromatin architectureMultiplexed imagingChromatin loopsChromatin foldingGenomic functionsNuclear laminaGenomic regionsRNA speciesMultiple genomesGene expressionCopy numberCell typesDe novoGenomeSame cells
2013
Probing Allostery Through DNA
Kim S, Broströmer E, Xing D, Jin J, Chong S, Ge H, Wang S, Gu C, Yang L, Gao YQ, Su XD, Sun Y, Xie XS. Probing Allostery Through DNA. Science 2013, 339: 816-819. PMID: 23413354, PMCID: PMC3586787, DOI: 10.1126/science.1229223.Peer-Reviewed Original ResearchMeSH KeywordsAllosteric RegulationBase SequenceBinding SitesDNA, B-FormDNA-Binding ProteinsDNA-Directed RNA PolymerasesEscherichia coliGene ExpressionGene Expression Regulation, BacterialLac RepressorsMolecular Dynamics SimulationNucleosomesProtein BindingProtein Structure, TertiaryReceptors, GlucocorticoidTranscription FactorsViral Proteins