Disease-Associated Single-Nucleotide Polymorphisms From Noncoding Regions in Juvenile Idiopathic Arthritis Are Located Within or Adjacent to Functional Genomic Elements of Human Neutrophils and CD4+ T Cells.

Both clinical and experimental evidence supports the hypothesis that juvenile idiopathic arthritis (JIA) is a complex trait mediated by gene-environment interactions. While the past 20 years have been marked by advances in understanding genetic risk using candidate gene approaches (e.g., [(1)], the contribution of any single genetic polymorphism is small, particularly for those genes outside of the major histocompatibility complex (MHC). Thus, the recent publication of a genome-wide association study (GWAS) identifying multiple new genomic regions conferring risk for JIA (2) was appropriately received with enthusiasm from geneticists and pediatric rheumatologists. However, the results of the GWAS left many unanswered questions. Most interestingly, Hinks et al found that most genetic risk for JIA resides not within coding regions of genes, but, rather, in intergenic regions and introns. This finding is not unique to JIA. Indeed, most GWAS for complex traits have revealed genetic risk resides predominantly in non-coding regions of the genome (3). The question must inevitably arise, therefore, “What’s in those regions?” After the initial sequencing of the human genome, there was some surprise at the relatively small numbers of genes and the vast regions of the genome that seemed to be devoid of anything informative. However, NIH projects like ENCODE (the Encyclopedia of Functional DNA Elements) and Roadmap Epigenomics have given us a much clearer picture of the non-coding genome and its functions. For example, we are now learning that multiple classes of RNA transcripts are expressed in regions of the genome that do not encode proteins, and that many of these non-coding transcripts serve specific functions, such as regulating transcript stability (e.g., miRNA (4)) or chromatin accessibility (e.g., some long non-coding RNA (5, 6)). In addition to ncRNA, we have learned that the non-coding regions of the genome contain many other functional sites that serve to regulate and coordinate transcription. These functional sites include transcriptional enhancers. Enhancers are cis-acting DNA regions that promote gene transcription. These DNA elements represent an important component of the non-coding genome; recent studies in mouse and human genomes demonstrated that about half of the highly conserved regions had enhancer activity (7, 8). Enhancers may be considerable distance (in genomic terms) from the promoters they regulate, and may not regulate the genes that are most proximal. In some cases (most notably in the immune system), enhancers may regulate more than one gene (9). Enhancers can’t be predicted with accuracy from DNA sequence. However, both ENCODE and Roadmap Epigenomics have shown that identification of enhancers can be facilitated using chromatin immunoprecipitation-sequencing (ChIP-seq) techniques for specific histone marks (10–12), including histone H3 acetylated at lysine 27 (H3K27ac) and histone H3 monomethylated at lysine 4 (H3K4me1) (13). Over the past 10 years, we have published a series of papers demonstrating the importance of neutrophils in the pathogenesis of JIA (14, 15) and its response to therapy (16). These findings led us to question whether the genomic regions associated with genetic risk in JIA might correspond to functional elements in human neutrophils (17). In this paper, we demonstrate that the majority of the non-coding regions identified by Hinks et al contain such elements.