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Related Experiment Video

Updated: Nov 4, 2025

Mapping Mammalian 3D Genome Interactions with Micro-C-XL
11:41

Mapping Mammalian 3D Genome Interactions with Micro-C-XL

Published on: November 3, 2023

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The two waves in single-cell 3D genomics.

Sergey V Ulianov1, Sergey V Razin1

  • 1Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia.

Seminars in Cell & Developmental Biology
|May 25, 2021
PubMed
Summary

Advanced microscopy and biochemical techniques now enable detailed study of 3D genome organization in single cells. This allows researchers to understand genome folding and cell-to-cell variations in 3D genome structure.

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Biomolecular Condensates in the Regulation of Transcription and Chromatin Architecture.

Biochemistry. Biokhimiia·2025

Area of Science:

  • Genomics
  • Cell Biology
  • Biophysics

Background:

  • Traditional biochemical methods yielded averaged genome data, lacking single-cell resolution.
  • Previous microscopy lacked the spatial resolution for detailed 3D genome folding analysis.
  • Single-cell studies indicated significant variability in genome organization between cells.

Purpose of the Study:

  • To review the current state of 3D genome organization studies at the single-cell level.
  • To analyze technical challenges in single-cell genomics.
  • To outline future perspectives in the field of 3D genomics.

Main Methods:

  • Integration of advanced biochemical techniques and super-resolution microscopy.
  • Generation of 3D genome maps from combined C-data and microscopy.
Keywords:
Chromatin compartmentsGenome spatial organizationLoop extrusionNucleosome interactionsOligopaintSingle-cell Hi-CTAD

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Last Updated: Nov 4, 2025

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  • Application of 3D modeling for investigating genome folding mechanisms.

    • Main Results:

    • High consistency between C-data and super-resolution microscopy-based 3D genome maps.
    • Resolution of internal chromosome structures, loci, and topologically associating domains (TADs).
    • Observation of cell-cycle dynamics in genome organization.

    Conclusions:

    • Current technologies enable comprehensive single-cell 3D genome studies.
    • 3D genome organization is highly variable between cells.
    • Future 3D genomics will integrate topology with epigenetic features to address cell heterogeneity.