SnakeHichipTF reveals transcription factor logic underlying enhancer-promoter wiring in the human brain

Abstract

Enhancer-promoter interactions are a central feature of gene regulation, yet the regulatory logic that governs their selective formation in complex tissues remains poorly understood. To address this gap, we developed SnakeHichipTF, a reproducible and scalable framework that integrates multi-engine HiChIP analysis with AI-based footprinting to decode the transcription factor (TF) logic underlying enhancer-promoter wiring. Applying SnakeHichipTF to HiChIP datasets from the human Middle Frontal Gyrus (MFG) and Substantia Nigra (SN), we identified distinct region-biased enhancer interactions associated with differential gene expression. MFG-biased interactions were enriched for cognitive and psychiatric associated GWAS traits, whereas SN-biased interactions preferentially intersected lipid and metabolic trait architectures. Integration of TF footprinting revealed that these region-biased interaction networks are governed by distinct TF programs: MFG-biased interactions preferentially recruited TFs linked to neuronal signaling and transcriptional activation, whereas SN-biased interactions were associated with metabolic and stress-responsive regulators. Interestingly, MFG-biased regulatory interactions were significantly enriched for Human Accelerated Regions (HARs), and HAR-associated genes showed elevated expression in humans relative to non-human primates, indicating that cortical enhancer wiring is embedded within evolutionarily modified regulatory elements. Together, by linking 3D chromatin architecture, TF logic, genetic risk, and evolutionary regulatory elements, SnakeHichipTF provides a general framework for dissecting the mechanistic basis of spatial gene regulation.