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Related Concept Videos

Chromatin Position Affects Gene Expression02:35

Chromatin Position Affects Gene Expression

Chromatin is the massive complex of DNA and proteins packaged inside the nucleus. The complexity of chromatin folding and how it is packaged inside the nucleus greatly influences  access to genetic information. Generally, the nucleus' periphery is considered transcriptionally repressive, while the cell's interior is considered a transcriptionally active area. 
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Mapping Absolute DNA Density in Cell Nuclei using Single-molecule Localization Microscopy
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Published on: November 11, 2025

Spatial compartmentalization at the nuclear periphery characterized by genome-wide mapping.

Feinan Wu1, Jie Yao

  • 1Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA. yao.j@yale.edu.

BMC Genomics
|August 31, 2013
PubMed
Summary

Genomic regions near the nuclear lamina (NL) show fewer active histone modifications, impacting gene expression. This study maps lamina-associated domains (sLADs) genome-wide, revealing connections between nuclear positioning and gene regulation.

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Area of Science:

  • Cell Biology
  • Epigenetics
  • Genomics

Background:

  • Gene positioning at the nuclear periphery's role in transcription is poorly understood.
  • Previous cell imaging showed differential compartmentalization of factors and modifications at the nuclear periphery.
  • The study aimed to identify DNA sequences associated with the nuclear lamina (NL) and examine genome-wide compartmentalization.

Purpose of the Study:

  • To identify DNA sequences associated with the nuclear lamina (NL).
  • To examine genome-wide compartmentalization of DNA sequences.
  • To investigate the relationship between subnuclear gene positioning, histone modifications, and gene expression.

Main Methods:

  • Integrated high-throughput DNA sequencing with the DNA adenine methyltransferase identification (DamID) assay.
  • Identified approximately 15,000 sequencing-based Lamina-Associated Domains (sLADs) in mouse 3T3 fibroblasts and C2C12 myoblasts.
  • Analyzed the distribution of active histone modifications (H3K4me2/3, H3K9Ac, H3K36me3) in relation to sLADs.

Main Results:

  • Identified ~15,000 sLADs, covering ~30% of the genome, spatially proximal to the NL.
  • Active histone modifications were predominantly located outside sLADs, away from the nuclear periphery.
  • Expressed sLAD genes showed reduced NL association and lower levels of active histone modifications compared to non-sLAD genes.

Conclusions:

  • Genomic regions associated with the NL are characterized by a lack of active histone modifications in mammalian cells.
  • Revealed novel connections between subnuclear gene positioning, histone modifications, and gene expression.
  • Established genome-wide maps of lamina-associated domains (sLADs).