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

• 批准号: 10456124
• 负责人: Long Cai
• 金额: $ 113.62万
• 依托单位: CALIFORNIA INSTITUTE OF TECHNOLOGY
• 依托单位国家: 美国
• 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: https://reporter.nih.gov/project-details/10456124
• 关键词: Address; Adopted; Antibodies; Biological; Biological Models; CRISPR imaging; Cell Nucleus; Cells; Chromatin; Chromosome Structures; Chromosomes; Color; Coupled; DNA; Data; Elements; Engineering; Epigenetic Process; Event; Fluorescent in Situ Hybridization; Gene Expression; Gene Expression Profile; Genes; Genetic Transcription; Genomics; Heterochromatin; Heterogeneity; Human Cell Line; Image; Imaging Device; Imaging technology; Immunofluorescence Immunologic; In Situ; Individual; Introns; Kinetics; Label; Lamins; Link; Measurement; Measures; Messenger RNA; Methods; Molecular Conformation; Mus; Mutagenesis; Nature; Nuclear; Optics; Phase; Positioning Attribute; Process; Protein Dynamics; Proteins; RNA; RNA analysis; Sister; Site; Structure; System; Techniques; Technology; Time; Transcript; Trees; Visualization software; Work; X Chromosome; X Inactivation; base; chromatin modification; chromosomal location; embryonic stem cell; fluorophore; genome-wide; genomic locus; genomic tools; human disease; insight; memory encoding; microscopic imaging; preservation; reconstruction; red fluorescent protein; sample fixation; scale up; spatiotemporal; telomere; tool; whole genome

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.

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