2023
Female naïve human pluripotent stem cells carry X chromosomes with Xa-like and Xi-like folding conformations
Patterson B, Yang B, Tanaka Y, Kim K, Cakir B, Xiang Y, Kim J, Wang S, Park I. Female naïve human pluripotent stem cells carry X chromosomes with Xa-like and Xi-like folding conformations. Science Advances 2023, 9: eadf2245. PMID: 37540754, PMCID: PMC10403202, DOI: 10.1126/sciadv.adf2245.Peer-Reviewed Original ResearchConceptsNaïve human pluripotent stem cellsHuman pluripotent stem cellsX-chromosome inactivationX chromosomePluripotent stem cellsStem cellsNaïve human embryonic stem cellsX chromosome stateX chromosome statusInactive X chromosomeActive X chromosomeHuman embryonic stem cellsEarly embryonic cellsEmbryonic stem cellsUnique epigenetic regulationChromatin compactionGenomic resolutionEpigenetic regulationChromosome inactivationChromosome stateSomatic cellsEmbryonic cellsChromosomesChromosome statusCellsLive 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
2022
New mechanism of chromatin compartmentalization by BRD2
Cheng Y, Wang S. New mechanism of chromatin compartmentalization by BRD2. Trends In Genetics 2022, 38: 1197-1198. PMID: 35811175, DOI: 10.1016/j.tig.2022.06.016.Peer-Reviewed Original Research
2021
TAD-like single-cell domain structures exist on both active and inactive X chromosomes and persist under epigenetic perturbations
Cheng Y, Liu M, Hu M, Wang S. TAD-like single-cell domain structures exist on both active and inactive X chromosomes and persist under epigenetic perturbations. Genome Biology 2021, 22: 309. PMID: 34749781, PMCID: PMC8574027, DOI: 10.1186/s13059-021-02523-8.Peer-Reviewed Original ResearchConceptsInactive X chromosomeActive X chromosomeMajor epigenetic componentsSingle-cell domainsX chromosomeEpigenetic componentsThree-dimensional genome architectureGlobal epigenetic landscapeFemale human cellsLoop extrusion mechanismSame genomic regionGenome architectureChromatin domainsTAD structureChromatin compactionEpigenetic landscapeTAD boundariesChromatin foldingGenomic regionsChromosome copiesGenomic techniquesEpigenetic perturbationsEpigenetic interactionsDistinct cell linesChromosomesChromatin 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 ResearchMeSH KeywordsAnimalsCell LineChromatinGene Expression ProfilingHumansMolecular ImagingRNASingle-Cell AnalysisConceptsSame 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
Chromatin Tracing: Imaging 3D Genome and Nucleome
Hu M, Wang S. Chromatin Tracing: Imaging 3D Genome and Nucleome. Trends In Cell Biology 2020, 31: 5-8. PMID: 33191055, PMCID: PMC8094612, DOI: 10.1016/j.tcb.2020.10.006.Peer-Reviewed Original ResearchMultiplexed 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
2016
Spatial organization of chromatin domains and compartments in single chromosomes
Wang S, Su JH, Beliveau BJ, Bintu B, Moffitt JR, Wu CT, Zhuang X. Spatial organization of chromatin domains and compartments in single chromosomes. Science 2016, 353: 598-602. PMID: 27445307, PMCID: PMC4991974, DOI: 10.1126/science.aaf8084.Peer-Reviewed Original ResearchConceptsIndividual chromosomesChromatin domainsX chromosomeNumerous genomic regionsSpatial organizationInactive X chromosomeGenome functionChromatin organizationGenomic regionsFractal globule modelSingle chromosomePolarized mannerChromosomesDifferent foldingTADCompartmentsAutosomesChromatinDomainTADsFoldingRegulationCapture studiesAn RNA-aptamer-based two-color CRISPR labeling system
Wang S, Su JH, Zhang F, Zhuang X. An RNA-aptamer-based two-color CRISPR labeling system. Scientific Reports 2016, 6: 26857. PMID: 27229896, PMCID: PMC4882555, DOI: 10.1038/srep26857.Peer-Reviewed Original ResearchConceptsSingle guide RNAsDifferent fluorescent proteinsGenomic lociFluorescent proteinSpecific chromatin lociEndogenous genomic lociDynamics of chromatinPP7 coat proteinTarget genomic lociStem loop 2Essential biological functionsSpecific DNA sequencesDifferent bacterial speciesChromatin imagingCRISPR single guide RNAsChromatin lociRepetitive sequencesDNA sequencesChromatin labelingCoat proteinBiological functionsHuman cellsLoop 2RNA aptamersBacterial speciesSuper-resolution imaging reveals distinct chromatin folding for different epigenetic states
Boettiger AN, Bintu B, Moffitt JR, Wang S, Beliveau BJ, Fudenberg G, Imakaev M, Mirny LA, Wu CT, Zhuang X. Super-resolution imaging reveals distinct chromatin folding for different epigenetic states. Nature 2016, 529: 418-422. PMID: 26760202, PMCID: PMC4905822, DOI: 10.1038/nature16496.Peer-Reviewed Original Research