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A Comprehensive Benchmark of Chromatin Loop Detection Methods

Katharina E. Hayer, PhD candidate, DBHi at CHOP and School of Biomedical Engineering, Science & Health Systems, Drexel University, Philadelphia Brittney Allyn, Phd candidate, Department of Pathology and Laboratory Medicine, UPenn, Philadelphia Craig Bassing, PhD, Department of Pathology and Laboratory Medicin, UPenn, Philadelphia Ahmet Sacan, PhD, School of Biomedical Engineering, Science & Health Systems, Drexel University, Philadelphia

Poster # 55

Chromatin looping plays a vital role in shaping the three-dimensional structure of chromatin and thereby orchestrating enhancer-promoter interactions. Specialized software tools, such as HiCCUPS, SIP, and MUSTACHE, have been developed to analyze chromatin conformation data, particularly from Hi-C assays. In this study, we conduct a comprehensive benchmarking analysis to evaluate and compare the performance of these tools and other state-of-the-art loop detection algorithms. The benchmarking assessment involved utilization of full-resolution and down-sampled Hi-C datasets to evaluate loop recovery, computational efficiency, and user-friendliness. Furthermore, we correlated the identified loops with ChIP-seq data targeting some of the known players in loop formation, notably the CTCF protein, its target sequences, and cohesin complex members. Integration of these elements enhance the likelihood of a loop being a true positive and biologically meaningful. To further assess the loop detection methods, we benchmarked them on a genetically modified chromosomal locus with cell type-specific loop formation and disruption of this looping through precise mutations in mice. Algorithms that accurately detect these genetically induced differences are preferred for their potential to unveil such important changes in less controlled, but more common experimental conditions. Our research aims to advance the understanding of the capabilities and limitations of chromatin looping detection methods. The insights gained from this study will contribute to unraveling the complexities of gene regulation and chromatin dynamics, aiding researchers in making informed choices when investigating chromatin interaction, such as between enhancers and promoters, that govern the complex 3D chromatin organization.

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