scholarly journals Comparative analysis of 2D and 3D distance measurements to study spatial genome organization

Methods ◽  
2017 ◽  
Vol 123 ◽  
pp. 47-55 ◽  
Author(s):  
Elizabeth H. Finn ◽  
Gianluca Pegoraro ◽  
Sigal Shachar ◽  
Tom Misteli
Keyword(s):  
Comparative Analysis ◽  
Genome Organization ◽  
Distance Measurements ◽  
Spatial Genome Organization ◽  
2D And 3D

scholarly journals Comparative analysis of 2D and 3D distance measurements to study spatial genome organization

2016 ◽  
Author(s):  
Elizabeth H. Finn ◽  
Gianluca Pegoraro ◽  
Sigal Shachar ◽  
Tom Misteli
Keyword(s):  
Genome Organization ◽  
Spatial Organization ◽  
Theoretical Models ◽  
3D Analysis ◽  
Distance Measurements ◽  
Accuracy And Precision ◽  
Distance Distributions ◽  
Cell Type Specific ◽  
Spatial Genome Organization ◽  
2D And 3D

ABSTRACTThe spatial organization of eukaryotic 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 including the z-axis information in image stacks. Here we compare the suitability of 2D versus 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 prone 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 can be ameliorated by sampling at much higher 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, 2D distance measurements remain preferable for many applications of analysis of spatial genome organization.

scholarly journals Understanding Spatial Genome Organization: Methods and Insights

2016 ◽  
Vol 14 (1) ◽  
pp. 7-20 ◽  
Author(s):  
Vijay Ramani ◽  
Jay Shendure ◽  
Zhijun Duan
Keyword(s):  
Genome Organization ◽  
Spatial Genome Organization

Comparative analysis of bilirubin glucuronidation activity in 2D- and 3D-cultured human hepatocellular carcinoma HepG2 cells

2020 ◽  
Vol 56 (4) ◽  
pp. 277-280
Author(s):  
Takayuki Hirano ◽  
Maki Hirata ◽  
Shigeyuki Fujimoto ◽  
Nhien Thi Nguyen ◽  
Quynh Anh Le ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Comparative Analysis ◽  
Hepg2 Cells ◽  
Human Hepatocellular Carcinoma ◽  
2D And 3D

scholarly journals Technologies to study spatial genome organization: beyond 3C

2019 ◽  
Author(s):  
Nadine Übelmesser ◽  
Argyris Papantonis
Keyword(s):  
Genome Organization ◽  
Nuclear Organization ◽  
Three Dimensional ◽  
Nuclear Space ◽  
Chromosome Conformation ◽  
Novel Variants ◽  
Cell Processes ◽  
Systematic Biases ◽  
And Function ◽  
Spatial Genome Organization

Abstract The way that chromatin is organized in three-dimensional nuclear space is now acknowledged as a factor critical for the major cell processes, like transcription, replication and cell division. Researchers have been armed with new molecular and imaging technologies to study this structure-to-function link of genomes, spearheaded by the introduction of the ‘chromosome conformation capture’ technology more than a decade ago. However, this technology is not without shortcomings, and novel variants and orthogonal approaches are being developed to overcome these. As a result, the field of nuclear organization is constantly fueled by methods of increasing resolution and/or throughput that strive to eliminate systematic biases and increase precision. In this review, we attempt to highlight the most recent advances in technology that promise to provide novel insights on how chromosomes fold and function.

scholarly journals An integrated 3-Dimensional Genome Modeling Engine for data-driven simulation of spatial genome organization

2016 ◽  
Vol 26 (12) ◽  
pp. 1697-1709 ◽  
Author(s):  
Przemysław Szałaj ◽  
Zhonghui Tang ◽  
Paul Michalski ◽  
Michal J. Pietal ◽  
Oscar J. Luo ◽  
...  
Keyword(s):  
Genome Organization ◽  
Data Driven ◽  
3 Dimensional ◽  
Spatial Genome Organization

Mapping and Visualizing Spatial Genome Organization

2016 ◽  
pp. 359-383
Author(s):  
Christopher J. F. Cameron ◽  
James Fraser ◽  
Mathieu Blanchette ◽  
Josée Dostie
Keyword(s):  
Genome Organization ◽  
Spatial Genome Organization

scholarly journals Spatial Genome Organization: From Development to Disease

2019 ◽  
Vol 7 ◽  
Author(s):  
Aishwarya Sivakumar ◽  
Jose I. de las Heras ◽  
Eric C. Schirmer
Keyword(s):  
Genome Organization ◽  
Spatial Genome Organization
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