Dynamics of chromosome organization and chromatin states in single cells
单细胞染色体组织和染色质状态的动力学
基本信息
- 批准号:10456124
- 负责人:
- 金额:$ 113.62万
- 依托单位:
- 依托单位国家:美国
- 项目类别:
- 财政年份:2020
- 资助国家:美国
- 起止时间:2020-09-19 至 2025-06-30
- 项目状态:未结题
- 来源:
- 关键词:AddressAdoptedAntibodiesBiologicalBiological ModelsCRISPR imagingCell NucleusCellsChromatinChromosome StructuresChromosomesColorCoupledDNADataElementsEngineeringEpigenetic ProcessEventFluorescent in Situ HybridizationGene ExpressionGene Expression ProfileGenesGenetic TranscriptionGenomicsHeterochromatinHeterogeneityHuman Cell LineImageImaging DeviceImaging technologyImmunofluorescence ImmunologicIn SituIndividualIntronsKineticsLabelLaminsLinkMeasurementMeasuresMessenger RNAMethodsMolecular ConformationMusMutagenesisNatureNuclearOpticsPhasePositioning AttributeProcessProtein DynamicsProteinsRNARNA analysisSisterSiteStructureSystemTechniquesTechnologyTimeTranscriptTreesVisualization softwareWorkX ChromosomeX Inactivationbasechromatin modificationchromosomal locationembryonic stem cellfluorophoregenome-widegenomic locusgenomic toolshuman diseaseinsightmemory encodingmicroscopic imagingpreservationreconstructionred fluorescent proteinsample fixationscale upspatiotemporaltelomeretoolwhole genome
项目摘要
SUMMARY
Cellular differentiation involves tightly coupled changes in gene expression, chromatin state, and
sub-nuclear arrangements of chromosomes. Understanding and controlling differentiation
requires understanding how each of these processes occurs dynamically within the same cell and
how they influence one another. Existing techniques can provide genome scale analysis of
interactions or spatial organization of a few chromosomal positions. However, we have lacked a
generalizable framework for simultaneous reconstruction of the overall dynamics of the nucleus
across all three levels. Recent work from our labs has opened up the possibility of achieving such
coupled analysis. Our track first, identify later approach allows many DNA to be simultaneously
tracked in living cells. RNA and DNA seqFISH allows a large number of transcripts and DNA loci
to be imaged in single fixed cells and MEMOIR allows lineage information to be recovered from
endpoint measurements. In this project, we propose to combine live imaging, multiplexed RNA,
DNA, and immunofluorescence measurements, and MEMOIR lineage tracking to capture whole-
genome dynamics of chromosomal loci and chromatin states. Using mouse embryonic stem cells
(mESCs) as a model system, we will study the transition from the pluripotent state to an earlier 2-
cell (2C) like state which shows drastic chromosome re-arrangement and changes in nascent
gene expression patterns. In addition, we will study the chromosomal dynamics of X-inactivation
based on the initial observations that sister X chromosomes are in contact with each other during
early phases of the inactivation process. Both of these biological questions require tracking
chromosomal dynamics and chromatin state simultaneously in single cells. The “Track First and
ID later” approach allows a large number of loci to be tracked in living cells. The combined
MEMOIR approach with multiplex immunofluorescence allows us to infer the kinetics of chromatin
states transitions. Bringing these tools to study X inactivation and 2C state transition will
demonstrate the capability of this approach for addressing a broad range of cell fate decision
questions. We will also develop analysis and visualization tools to integrate genomics (SPRITE)
and imaging data. The technology developed in this project can be readily implemented in human
cell lines and adopted by other labs in the 4DN consortium.
总结
项目成果
期刊论文数量(0)
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Dynamics of chromosome organization and chromatin states in single cells
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