ArticleMethods (San Diego, Calif.)2017
Comparative analysis of 2D and 3D distance measurements to study spatial genome organization.
Article in Methods (San Diego, Calif.), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
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- From survival of irradiated mice to modern molecular insights: a seventy-year journey in radiobiology at the institute of biophysics, Czech academy of sciences.European biophysics journal : EBJ · 2025Review
- High-throughput DNA repair monitoring in Saccharomyces cerevisiae suggests SSB- and DSB-induced chromatin reconfiguration.Scientific reports · 2025Article
- Distinguishing individual photobodies using Oligopaints reveals thermo-sensitive and -insensitive phytochrome B condensation at distinct subnuclear locations.Nature communications · 2024Article
- Nuclear position modulates long-range chromatin interactions.PLoS genetics · 2022Article
- A guide for single-particle chromatin tracking in live cell nuclei.Cell biology international · 2022Review
- High-Throughput DNA FISH (hiFISH).Methods in molecular biology (Clifton, N.J.) · 2022Article
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- A high-throughput DNA FISH protocol to visualize genome regions in human cells.STAR protocols · 2021Article
- Performance of deep learning restoration methods for the extraction of particle dynamics in noisy microscopy image sequences.Molecular biology of the cell · 2021Article
- A unified framework for inferring the multi-scale organization of chromatin domains from Hi-C.PLoS computational biology · 2021Article
- FISH Going Meso-Scale: A Microscopic Search for Chromatin Domains.Frontiers in cell and developmental biology · 2021Review
- Heterogeneous Loop Model to Infer 3D Chromosome Structures from Hi-C.Biophysical journal · 2019Article
- Article
- HiCTMap: Detection and analysis of chromosome territory structure and position by high-throughput imaging.Methods (San Diego, Calif.) · 2018Article
- Chromatin loops and causality loops: the influence of RNA upon spatial nuclear architecture.Chromosoma · 2017Review
- Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation.Molecular cell · 2017Article
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Authors and funding
4 authors.
Funding
Abstract
The spatial organization of genomes is non-random, cell-type specific, and has been linked to cellular function. The investigation of spatial organization has traditionally relied extensively on fluorescence microscopy. The validity of the imaging methods used to probe spatial genome organization often depends on the accuracy and precision of distance measurements. Imaging-based measurements may either use 2 dimensional datasets or 3D datasets which include the z-axis information in image stacks. Here we compare the suitability of 2D vs 3D distance measurements in the analysis of various features of spatial genome organization. We find in general good agreement between 2D and 3D analysis with higher convergence of measurements as the interrogated distance increases, especially in flat cells. Overall, 3D distance measurements are more accurate than 2D distances, but are also more susceptible to noise. In particular, z-stacks are prone to error due to imaging properties such as limited resolution along the z-axis and optical aberrations, and we also find significant deviations from unimodal distance distributions caused by low sampling frequency in z. These deviations are ameliorated by significantly higher sampling frequency in the z-direction. We conclude that 2D distances are preferred for comparative analyses between cells, but 3D distances are preferred when comparing to theoretical models in large samples of cells. In general and for practical purposes, 2D distance measurements are preferable for many applications of analysis of spatial genome organization.
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