Spatial ChIP (ChIP-SP) as a New Bioinformatics Tool to Characterize Spatial Gene Regulation

Traditional ChIP-seq analysis is essential for identifying transcription factor (TF) binding sites, but it is constrained by its linear view of the genome. How TF-bound regions interact with distant genomic loci within the three-dimensional (3D) chromatin architecture often remains unclear, limiting our ability to interpret enhancer-promoter communication and long-range gene regulation. To address these limitations, we developed ChIP-SP, an R package that integrates ChIP-seq data with Hi-C chromatin loop interactions, enabling the study of TF-mediated regulatory regions within a 3D genomic context. In this study, we evaluated ChIP-SP using the androgen receptor (AR) as a model TF in LNCaP prostate cancer cells. By focusing on AR ChIP-seq peaks that participate in chromatin looping and examining a 25 kb radius around each peak in 3D genomic space, ChIP-SP identified 1,499 AR-spatially regulated genes, and many of them were confirmed to be androgen-responsive. We similarly applied ChIP-SP to glucocorticoid receptor (GR) ChIP-seq data in A549 lung cancer cells and successfully identified GR-spatially regulated genes. These results demonstrate that ChIP-SP extends traditional ChIP-seq annotation into a multidimensional framework and enables the construction of a spatial cistrome for transcription factors. The tool is flexible, customizable, and holds strong potential for uncovering novel regulatory target genes, particularly in cancer biology.