Abstract 6308: Dory: a computational method for differential chromatin tracing analysis

Abstract The spatial organization of the genome plays a vital role in maintaining the cell type-specific chromatin structures and regulating gene expression. The three-dimensional (3D) genome structures can be measured by sequencing-based techniques such as Hi-C on the ensemble level or by imaging-based techniques such as chromatin tracing on the single-molecule level. Chromatin tracing is a multiplexed DNA fluorescence in situ hybridization (FISH) technique that can directly trace the 3D positions of genomic loci along individual chromosomes in single cells. By designing the primary probes targeting specific genomic regions and dye-labeled secondary probes to indicate their positions, chromatin tracing can construct the 3D trace of chromatin at high resolution using microscopy. However, few computational tools have been developed for differential analysis of chromatin tracing data. Major challenges include the high variability of chromatin traces and missing values in the 3D coordinates of some loci. Here, we present Dory, a statistical method for identifying differential patterns from two groups of chromatin traces without imputation of missing data. Dory measures the spatial distance between each pair of regions in each chromatin trace and employs multi-level statistical tests to quantify the distance difference between the two groups of chromatin traces. The output of Dory includes the differential score for each region pair comparing chromatin traces between two biological conditions. We applied Dory to chromatin tracing data from six cell types in mouse fetal liver and from a mouse lung cancer progression model. We found that the changes in chromatin structure are associated with A-B compartment alterations and promoter-enhancer interaction alterations that cause differential gene expression. Dory is a user-friendly computational tool that can be applied to multiple types of imaging-based 3D genome data analysis for studying genome functions and gene regulation. Citation Format: Zhaoxia Ma, Miao Liu, Mengwei Hu, Shengyuan Wang, Siyuan Wang, Chongzhi Zang. Dory: a computational method for differential chromatin tracing analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 6308.