Boosting the detection of enhancer-promoter loops via novel normalization methods for chromatin interaction data

Abstract

Accurately detecting enhancer-promoter loops from genome-wide interaction data, such as Hi-C, is crucial for understanding gene regulation. Current normalization methods, such as Iterative Correction and Eigenvector decomposition (ICE), are commonly used to remove biases in Hi-C data prior to chromatin loop detection. However, while structural or CTCF-associated loop signals are retained, enhancer-promoter interaction signals are often greatly diminished after ICE normalization and similar methods, making these regulatory loops harder to detect. To address this limitation, we developed Raichu, a novel method for normalizing chromatin contact data. Raichu identifies nearly twice as many chromatin loops as ICE, recovering almost all loops detected by ICE and revealing thousands of additional enhancer-promoter loops missed by ICE. With its enhanced sensitivity for regulatory loops, Raichu detects more biologically meaningful differential loops between conditions in the same cell type. Furthermore, Raichu performs consistently across different sequencing depths and platforms, including Hi-C, HiChIP, and single-cell Hi-C, making it a versatile tool for uncovering new insights into three- dimensional (3D) genomic organization and transcriptional regulation.