Enhancer-gene regulatory interactions in colorectal cancer revealed through genome-wide CRISPRi perturbations

作者：Philip Law, Jayaram Vijayakrishnan, James Smith, Timothy Barry, Maria Mandelia, Eugene Katsevich, Richard S Houlston · 发表于：bioRxiv (Cold Spring Harbor Laboratory) · 年份：2026 · DOI：10.64898/2026.06.05.730086 · 研究领域：Genomics and Chromatin Dynamics、Bioinformatics and Genomic Networks、Single-cell and spatial transcriptomics

ABSTRACT Background Establishing functional relationships between distal enhancers and their target genes is a central challenge in genome biology and cancer genetics. CRISPR/dCas9-mediated perturbations followed by single-cell RNA sequencing (Perturb-seq) has emerged as an efficient means of establishing enhancer-target gene relationships. Results We used genome-wide CRISPRi Perturb-seq with 35,139 guide RNAs targeting 12,117 enhancers to create a functional enhancer-gene map of colorectal cancer (CRC), identifying 238 significant regulatory associations (FDR < 0.1). Integration of chromatin accessibility (ATAC-seq), histone modification profiling (ChIP-seq), and ultra-high resolution chromatin conformation capture (Micro-C) data revealed that enhancer regulation in CRC is constrained by topological domains and often targets the nearest gene, findings corroborated by Activity-by-Contact modelling. Conclusions We present here a comprehensive, genome-scale functional atlas of enhancer-gene associations in CRC. This resource should provide a foundation for studying gene regulation in colorectal tumorigenesis and for prioritising candidate non-coding drivers in cancer sequencing studies. PLAIN LANGUAGE SUMMARY Mapping the hidden DNA switches that control colon cancer genes The total amount of DNA in humans is vast, but only a tiny proportion of it is directly related to genes. While people may know that genes act as blueprints for the body, there are also short stretches of D...