coiTAD: Detection of Topologically Associating Domains Based on Clustering of Circular Influence Features from Hi-C Data

• Published in: Genes Vol. 15; no. 10; p. 1293
• Main Authors: Houchens, Drew, Chowdhury, H M A Mohit, Oluwadare, Oluwatosin
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 30.09.2024; MDPI
• Subjects: Algorithms; Biomarkers; Chromatin; Chromatin - genetics; Chromatin Assembly and Disassembly; Cluster Analysis; Clustering; Computational Biology - methods; Gene regulation; Genetic disorders; Genomes; Genomic analysis; Humans; Identification; Proteins; features; clustering; topologically associating domain; TAD caller; principal component analysis
• ISSN: 2073-4425; 2073-4425
• DOI: 10.3390/genes15101293

Topologically associating domains (TADs) are key structural units of the genome, playing a crucial role in gene regulation. TAD boundaries are enriched with specific biological markers and have been linked to genetic diseases, making consistent TAD detection essential. However, accurately identifying TADs remains challenging due to the lack of a definitive validation method. This study aims to develop a novel algorithm, termed coiTAD, which introduces an innovative approach for preprocessing Hi-C data to improve TAD prediction. This method employs a proposed "circle of influence" (COI) approach derived from Hi-C contact matrices. The coiTAD algorithm is based on the creation of novel features derived from the circle of influence in input contact matrices, which are subsequently clustered using the HDBSCAN clustering algorithm. The TADs are extracted from the clustered features based on intra-cluster interactions, thereby providing a more accurate method for identifying TADs. Rigorous tests were conducted using both simulated and real Hi-C datasets. The algorithm's validation included analysis of boundary proteins such as H3K4me1, RNAPII, and CTCF. coiTAD consistently matched other TAD prediction methods. The coiTAD algorithm represents a novel approach for detecting TADs. At its core, the circle-of-influence methodology introduces an innovative strategy for preparing Hi-C data, enabling the assessment of interaction strengths between genomic regions. This approach facilitates a nuanced analysis that effectively captures structural variations within chromatin. Ultimately, the coiTAD algorithm enhances our understanding of chromatin organization and offers a robust tool for genomic research. The source code for coiTAD is publicly available, and the URL can be found in the Data Availability Statement section.