A supervised learning framework for chromatin loop detection in genome-wide contact maps

• Published in: Nature communications 2020-07, Vol.11 (1), p.3428-12, Article 3428
• Main Authors: Salameh, Tarik J., Wang, Xiaotao, Song, Fan, Zhang, Bo, Wright, Sage M., Khunsriraksakul, Chachrit, Ruan, Yijun, Yue, Feng
• Format: Article
• Language: English
• Subjects: 38/15; 38/23; 45; 631/114/2114; 631/114/2785; 631/337/100/101; Chromatin; Chromatin - chemistry; Classification; Databases, Genetic; Datasets; Gene mapping; Gene regulation; Genome; Genomes; Humanities and Social Sciences; Humans; K562 Cells; multidisciplinary; Organ Specificity; Positron emission; Science; Science (multidisciplinary); Sequence Analysis, DNA; Species Specificity; Supervised learning; Supervised Machine Learning; Tomography
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-020-17239-9

Accurately predicting chromatin loops from genome-wide interaction matrices such as Hi-C data is critical to deepening our understanding of proper gene regulation. Current approaches are mainly focused on searching for statistically enriched dots on a genome-wide map. However, given the availability of orthogonal data types such as ChIA-PET, HiChIP, Capture Hi-C, and high-throughput imaging, a supervised learning approach could facilitate the discovery of a comprehensive set of chromatin interactions. Here, we present Peakachu, a Random Forest classification framework that predicts chromatin loops from genome-wide contact maps. We compare Peakachu with current enrichment-based approaches, and find that Peakachu identifies a unique set of short-range interactions. We show that our models perform well in different platforms, across different sequencing depths, and across different species. We apply this framework to predict chromatin loops in 56 Hi-C datasets, and release the results at the 3D Genome Browser. Predicting chromatin loops from genome-wide interaction matrices such as Hi-C data provides insight into gene regulation events. Here, the authors present Peakachu, a Random Forest classification framework that predicts chromatin loops from genome-wide contact maps, and apply it to systematically predict chromatin loops in 56 Hi-C datasets, with results available at the 3D Genome Browser.