TopoLoop: A new tool for chromatin loop detection in live cells via single-particle tracking

被引：1
|
作者：
Kokkanti, Aryan [1 ]
Atanasiu, Andrew [1 ]
Kolbin, Daniel [1 ]
Adalsteinsson, David [2 ]
Bloom, Kerry [1 ]
Vasquez, Paula A. [3 ]
机构：
[1] Univ North Carolina Chapel Hill, Dept Biol, 622 Fordham Hall, CB3280, Chapel Hill, NC 27599 USA
[2] Univ North Carolina Chapel Hill, Dept Math, 120 E Cameron Ave,CB3250, Chapel Hill, NC 27599 USA
[3] Univ South Carolina, Dept Math, 1523 Greene St, LC417, Columbia, SC 29208 USA
来源：
JOURNAL OF CHEMICAL PHYSICS | 2024年 / 161卷 / 20期
关键词：
Cell culture;
D O I：
10.1063/5.0236090
中图分类号：
O64 [物理化学（理论化学）、化学物理学];
学科分类号：
070304 ; 081704 ;
摘要：
We present a novel method for identifying topological features of chromatin domains in live cells using single-particle tracking and topological data analysis (TDA). By applying TDA to particle trajectories, we can effectively detect complex spatial patterns, such as loops, that are often missed by traditional time series analysis. Using simulations of polymer bead-spring chains, we have validated the accuracy of our method and determined its limitations for detecting loops. Our approach offers a promising avenue for exploring the topological complexity of chromatin in living cells using TDA techniques.
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页数：10
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