Capture Hi-C reveals novel candidate genes and complex long-range interactions with related autoimmune risk loci

Abstract

Genome-wide association studies have been tremendously successful in identifying genetic variants associated with complex diseases. The majority of association signals are intergenic and evidence is accumulating that a high proportion of signals lie in enhancer regions. We use Capture Hi-C to investigate, for the first time, the interactions between associated variants for four autoimmune diseases and their functional targets in B- and T-cell lines. Here we report numerous looping interactions and provide evidence that only a minority of interactions are common to both B- and T-cell lines, suggesting interactions may be highly cell-type specific; some disease-associated SNPs do not interact with the nearest gene but with more compelling candidate genes (for example, FOXO1, AZI2) often situated several megabases away; and finally, regions associated with different autoimmune diseases interact with each other and the same promoter suggesting common autoimmune gene targets (for example, PTPRC, DEXI and ZFP36L1).

Capture Hi-C identifies a novel causal gene, IL20RA, in the pan-autoimmune genetic susceptibility region 6q23

“…Investigation of chromatin interactions at the 6q23 locus was carried out as part of a larger study that included all known risk loci for RA, JIA, PsA and T1D [21]. We selected four target regions mapping to 6q23 for enrichment in two different CHi-C experiments: first, the Region Capture Hi-C targeted the LD blocks (r 2  > 0.8) for three SNPs associated with the diseases under study: rs6920220 (RA, T1D, JIA), rs7752903 (RA) and rs610604 (Ps, PsA) (Fig.…”

“…However, the functional impact of the remaining disease-associated SNPs at the locus, such as the intergenic rs6920220 nominally assigned to TNFAIP3 , had remained unexplored. Our CHi-C study, supplemented by confirmatory 3C, eQTL and ChIP evidence, offers for the first time a firm indication that autoimmune-associated regions in general [21], and this region in particular, can demonstrate complex regulatory interactions with a number of plausible candidate genes, potentially functional lncRNA genes and, importantly, each other. The complexity of the interactions is magnified when considering the differences observed in cell types (here, in B and T-cell lines and synovial fibroblasts).…”

“…Recently, a new method that incorporates a targeted sequence capture step into Hi-C, Capture Hi-C (CHi-C), has been developed [13, 18–20]. The method has facilitated the identification of interactions between non-coding SNPs associated with cancer and autoimmunity with their targets [18, 19, 21]. …”

Genome-wide mapping and analysis of chromosome architecture

“…Second, Hi-C has recently been combined with target enrichment and sequencing (Capture-HiC) to reveal chromatin contacts of mammalian gene promoters 49,53–57 and other specific genomic loci 29,53,58–60 . Unlike 4C and 5C, Capture-HiC involves first generating a library of proximity-ligated DNA fragments using one of several published Hi-C methods.…”

“…b | Hi-C includes the sequencing of all biotin-labelled ligation products, which are enriched by biotin-affinity purification and subsequent library preparation 22,69,70 . In Capture-HiC, sequences of interest can be enriched from a Hi-C DNA library to obtain highly multiplexed, targeted interaction profiles 29,53–60 . This involves the hybridization of biotinylated capture-probes to DNA sequences of interest (step 1), the immobilization of this library of probe–target sequence duplexes on streptavidin beads (step 2) and the washing away of unbound DNA, leaving only the captured probe–library duplexes (step 3).…”