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Nuclear protein sorting regulates nucleus composition and gene expression, crucial for determining the fate of a eukaryotic cell. Hence, the entry and exit of molecules across the nuclear envelope is a tightly controlled process. Nuclear protein sorting can be inhibited by one of the following ways: 1) masking cargo signal sequences, 2) modifying the nuclear receptor's affinity for cargo, 3) controlling the nuclear pore size, 4) retaining the cargo during its transit to the cytosol or the...
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Spatial multi-omics reveals cell-type-specific nuclear compartments.

Yodai Takei1, Yujing Yang2, Jonathan White2

  • 1Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA. ytakei@caltech.edu.

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Summary
This summary is machine-generated.

This study introduces two-layer DNA seqFISH+ for mapping genomic loci, transcriptome, and nuclear structures in single cells. It reveals cell-type specific chromatin organization and gene regulation in the mouse cerebellum.

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Area of Science:

  • Cell Biology
  • Genomics
  • Epigenetics

Background:

  • The mammalian nucleus contains diverse, cell-type specific subnuclear structures influencing gene regulation and genome organization.
  • Understanding these structures requires mapping their molecular components, genomic associations, and transcriptional effects in single cells within complex tissues.

Purpose of the Study:

  • To develop and apply a novel high-resolution multi-omics method for simultaneous mapping of genomic loci, nascent transcriptome, and subnuclear structures in single cells.
  • To investigate cell-type specific chromatin organization, gene regulation, and the role of subnuclear structures in complex tissues.

Main Methods:

  • Development of two-layer DNA seqFISH+ for simultaneous mapping of 100,049 genomic loci, 17,856 genes' nascent transcriptome, and subnuclear structures in single cells.
  • Application of the method to adult mouse cerebellum multi-omics datasets.
  • Analysis of imaging-based chromatin profiling data at genomic scales from 100-200 kilobases to ~1 megabase.

Main Results:

  • Repressive chromatin regions exhibit greater cell-type variability than active regions across the genome.
  • RNA polymerase II foci associate with long, cell-type specific genes, distinct from nuclear speckles.
  • Cell-type specific heterochromatin (H3K27me3, H4K20me3) enriches at genes/clusters, influencing chromosomal positioning and interactions in neurons and glial cells.

Conclusions:

  • Two-layer DNA seqFISH+ provides a single-cell, high-resolution multi-omics view of subnuclear structures and their genomic associations.
  • The findings offer insights into the effects of subnuclear structures on gene regulation and 3D genome organization within complex tissues.