Defining the regulatory landscape of the C4A/C4B immune risk locus with long-read sequencing

Abstract

The complement component 4 gene (C4) is highly associated with autoimmune risk and schizophrenia. C4 is the most polymorphic gene in the complement system due to copy number variation and an endogenous retrovirus (HERV-K(C4)) insertion which confers variable transcript sizes. From public epigenomics data we found 4 candidate liver specific and 2 astrocyte specific enhancers in a 500 kb region flanking the C4 locus. Additionally, a topological site was discovered in a region corresponding to the LTR of HERV-K(C4) suggesting that different haplotypes could confer distinct topologies. In future directions, we will apply Oxford Nanopore Technologies long read sequencing, a Cas9-based enrichment approach, and a GpC methyltransferase to mark accessible chromatin to validate these candidate regulatory elements in SNU-475 cells, a liver cell line that shows high expression of C4A and C4B. These methods can enhance the understanding of the transcriptional regulation of genes highly associated with disease risk and will enable future work to link structural variation to gene regulation, with broad implications for the understanding of immune-mediated diseases.