Native in situ architecture of the human inactive X chromosome revealed by correlative light and electron microscopy
- 1Nanyang Technological University, Singapore
Abstract
Knowledge of the nuclear organization of specific chromatin domains at the ultrastructural level remains limited. To address this, we employed correlative light and electron microscopy (CLEM) approaches to investigate the inactive X chromosome (Xi) in female human RPE1cells. Tandem fusion of macroH2A (mH2A), a histone variant enriched on the Xi, to eGFP and APEX2 enabled direct labeling and identification of the Xi by light microscopy, transmission electron microscopy, and electron tomography using conventional CLEM. The eGFP tag further allowed us to visualize the Xi at single nucleosome resolution under close-to-native conditions using cryo-CLEM. We found that, although heterochromatin domains of the Xi are substantially larger than those of autosomal regions, their chromatin density was not significantly different. Furthermore, our data reveal the organization of the interchromatin compartment (IC) within the Xi, characterized by a network of larger lacunae and smaller channels. Overall, we provide an ultrastructural characterization of a specific heterochromatin domain at unprecedented resolution, advancing our understanding of 3D chromatin organization and nuclear architecture in situ.
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BibTeX
@misc{ludwig2026native,
title = {{Native in situ architecture of the human inactive X chromosome revealed by correlative light and electron microscopy}},
author = {A. Ludwig and B. Huebner and S. Sandin and M. L. Wee and H. Y. S. Chan},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.04.749547},
url = {https://www.biorxiv.org/content/10.64898/2026.09.04.749547v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Native in situ architecture of the human inactive X chromosome revealed by correlative light and electron microscopy
AU - A. Ludwig
AU - B. Huebner
AU - S. Sandin
AU - M. L. Wee
AU - H. Y. S. Chan
PY - 2026
DA - 2026/09/04
PB - bioRxiv
DO - 10.64898/2026.09.04.749547
UR - https://www.biorxiv.org/content/10.64898/2026.09.04.749547v1
AB - Knowledge of the nuclear organization of specific chromatin domains at the ultrastructural level remains limited. To address this, we employed correlative light and electron microscopy (CLEM) approaches to investigate the inactive X chromosome (Xi) in female human RPE1cells. Tandem fusion of macroH2A (mH2A), a histone variant enriched on the Xi, to eGFP and APEX2 enabled direct labeling and identification of the Xi by light microscopy, transmission electron microscopy, and electron tomography using conventional CLEM. The eGFP tag further allowed us to visualize the Xi at single nucleosome resolution under close-to-native conditions using cryo-CLEM. We found that, although heterochromatin domains of the Xi are substantially larger than those of autosomal regions, their chromatin density was not significantly different. Furthermore, our data reveal the organization of the interchromatin compartment (IC) within the Xi, characterized by a network of larger lacunae and smaller channels. Overall, we provide an ultrastructural characterization of a specific heterochromatin domain at unprecedented resolution, advancing our understanding of 3D chromatin organization and nuclear architecture in situ.
ER -