Genetic sharing is extensively observed for many autoimmune diseases, but the causal variants and their underlying molecular mechanisms remain largely unknown. Through systematic investigation of known autoimmune disease pleiotropic loci, we find most of these genetic effects are transmitted from regulatory code and colocalize with hematopoietic lineage-specific expression quantitative trait loci. We leverage evidence-based strategy to functionally prioritize known pleiotropic variants and identify their target genes. A top-ranked pleiotropic variant, rs4728142, obtains many lines of evidence to be causal and regulates IRF5 transcript expression. Mechanistically, the rs4728142-containing region interacts with IRF5 downstream alternative promoter in an allele-specific manner and orchestrates its upstream enhancer to regulate IRF5 alternative promoter usage through chromatin looping. A putative structural regulator, ZBTB3, mediates the allele-specific chromatin looping to promote IRF5-short transcript expression at rs4728142 risk allele, resulting in IRF5 overactivation and M1 macrophage polarization. Together, our findings establish a causal mechanism between regulatory variant and fine-scale molecular phenotype underlying dysfunction of pleiotropic gene in human autoimmunity.
The high mutation burden of melanoma genome raises a major challenge for identifying true driver events from the background mutations genome-widely. Many noncoding recurrent events, such as those occurred in enhancer, can shape the tumor evolution, emphasizing the necessity of systematic deciphering enhancer disruptions in melanoma. Here, we leveraged 297 melanoma whole-genome sequencing (WGS) samples to prioritize highly recurrent regions (HRRs). By performing a genome-scale CRISPR interference (CRISPRi) screening on HRR-associated enhancers in melanoma cells, we identified 66 significant hits which could play tumor-suppressive roles. These functional enhancers show unique mutational patterns independent of classical significantly mutated genes in melanoma. Target gene analysis for the essential enhancers revealed many known and hidden mechanisms underlying melanoma development. We demonstrated that an enhancer could modulate melanoma cell proliferation by targeting MEF2A and another distal enhancer is able to sustain PTEN tumor-suppressive potential via long-range interaction. Our study established a catalogue of crucial enhancers and their target genes in melanoma development and progression.