2021
Spatial transcriptome profiling by MERFISH reveals fetal liver hematopoietic stem cell niche architecture
Lu Y, Liu M, Yang J, Weissman SM, Pan X, Katz SG, Wang S. Spatial transcriptome profiling by MERFISH reveals fetal liver hematopoietic stem cell niche architecture. Cell Discovery 2021, 7: 47. PMID: 34183665, PMCID: PMC8238952, DOI: 10.1038/s41421-021-00266-1.Peer-Reviewed Original ResearchWild typeCell typesHSC nicheMultiplexed error-robust fluorescenceStem cell niche architectureFetal liverHematopoietic stem cell nicheStem cell nicheLoss of TET2Endothelial cellsBioinformatic foundationNumber of HSCsNiche architectureTranscriptome profilingSpatial regulationTranscriptional profilesCell nicheArterial endothelial cellsIndividual cellsNicheSitu hybridizationSpatial organizationLiver cell typesMicroenvironment regulationRobust fluorescence
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 studiesSpatial organization shapes the turnover of a bacterial transcriptome
Moffitt JR, Pandey S, Boettiger AN, Wang S, Zhuang X. Spatial organization shapes the turnover of a bacterial transcriptome. ELife 2016, 5: e13065. PMID: 27198188, PMCID: PMC4874777, DOI: 10.7554/elife.13065.Peer-Reviewed Original ResearchConceptsBacterial transcriptomesSpatial organizationE. coli transcriptomeCo-translational insertionInner membrane proteinProtein mRNASignal recognition particlePost-transcriptional fatePost-transcriptional regulationSuper-resolution microscopyRNA degradosomePeriplasmic proteinsSignal peptideRNA sequencingTranscriptomeMembrane enrichmentSelective destabilizationMRNARNAProteinDegradosomeEukaryotesMembraneProkaryotesPowerful meansSuper-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
2013
Cell Shape Can Mediate the Spatial Organization of the Bacterial Cytoskeleton
Wang S, Wingreen NS. Cell Shape Can Mediate the Spatial Organization of the Bacterial Cytoskeleton. Biophysical Journal 2013, 104: 541-552. PMID: 23442905, PMCID: PMC3566457, DOI: 10.1016/j.bpj.2012.12.027.Peer-Reviewed Original ResearchConceptsBacterial cytoskeletonCell shapeCytoskeletal filamentsBacterial cytoskeletal proteinsRod-shaped cellsCytoskeletal proteinsCell wallCytoskeletal polymerizationCytoskeletonSpatial patterningMreBConformational transitionSpatial organizationFilament lengthSame membraneFilamentsMembraneFtsZSpatial patternsChemical energyFilament bendingProteinPatterningProper controlMicrofluidic approach