Ultra-Structural Imaging Provides 3D Organization of 46 Chromosomes of a Human Lymphocyte Prophase Nucleus
Abstract
:1. Introduction
2. Results
2.1. Segmentation and Reconstruction of Chromosomes
2.2. Identification of All Individual 46 Chromosomes
2.3. Validation of Chromosomes
2.4. Building the 3D Human Genome
2.5. Radial Organization of Chromosomes in the Prophase Nucleus
2.6. 3D Chromosome Neighborhood Analysis
3. Discussion
4. Materials and Methods
4.1. Cell Culture and Nuclei Preparation
4.2. Multicolor Fluorescence In Situ Hybridization
4.3. Sample Fixation, Staining, and Embedding for SBFSEM
4.4. SBFSEM Sample Block Preparation and Imaging
4.5. 3D Reconstruction and Modeling of Prophase Chromosomes
4.6. Identification and Validation of Chromosomes
4.7. Diameter Measurements of Chromosomes
4.8. Assessment of 3D Spatial Positioning of Chromosomes
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
Base pairs (bp) |
Chromosomal territories (CT) |
Chromosome conformation capture (3C) |
Electron microscopy (EM) |
Fluorescence in situ hybridization (FISH) |
Mega base pairs (Mbp) |
Multicolor fluorescence in-situ hybridization (mFISH) |
Nanometer (nm) |
Serial block-face scanning electron microscopy (SBFSEM) |
Three dimensional (3D) |
Topologically associating domains (TADS) |
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Sajid, A.; Lalani, E.-N.; Chen, B.; Hashimoto, T.; Griffin, D.K.; Bhartiya, A.; Thompson, G.; Robinson, I.K.; Yusuf, M. Ultra-Structural Imaging Provides 3D Organization of 46 Chromosomes of a Human Lymphocyte Prophase Nucleus. Int. J. Mol. Sci. 2021, 22, 5987. https://doi.org/10.3390/ijms22115987
Sajid A, Lalani E-N, Chen B, Hashimoto T, Griffin DK, Bhartiya A, Thompson G, Robinson IK, Yusuf M. Ultra-Structural Imaging Provides 3D Organization of 46 Chromosomes of a Human Lymphocyte Prophase Nucleus. International Journal of Molecular Sciences. 2021; 22(11):5987. https://doi.org/10.3390/ijms22115987
Chicago/Turabian StyleSajid, Atiqa, El-Nasir Lalani, Bo Chen, Teruo Hashimoto, Darren K. Griffin, Archana Bhartiya, George Thompson, Ian K. Robinson, and Mohammed Yusuf. 2021. "Ultra-Structural Imaging Provides 3D Organization of 46 Chromosomes of a Human Lymphocyte Prophase Nucleus" International Journal of Molecular Sciences 22, no. 11: 5987. https://doi.org/10.3390/ijms22115987