HLA-DRB1 May Be Antagonistically Regulated by the Coordinately Evolved Promoter and 3′-UTR under Stabilizing Selection

HLA-DRB1 is the most polymorphic MHC (major histocompatibility complex) class II gene in human, and plays a crucial role in the development and function of the immune system. Extensive polymorphisms exist in the promoter and 3′-UTR of HLA-DRB1, especially a LTR (Long terminal repeat) element in the promoter, which may be involved in the expression regulation. However, it remains unknown how the polymorphisms in the whole promoter region and 3′-UTR to regulate the gene expression. In this study, we investigated the extensive polymorphisms in the HLA-DRB1 promoter and 3′-UTR, and how these polymorphisms affect the gene expression in both independent and jointly manners. It was observed that most of the haplotypes in the DRB1 promoter and 3′-UTR were clustered into 4 conserved lineages (H1, H2, H3 and H4), and showed high linkage disequilibrium. Compared with H1 and H2 lineage, a LTR element in the promoter of H3 and H4 lineage significantly suppressed the promoter activity, whereas the activity of the linked 3′-UTR increased, leading to no apparent difference in the final expression product between H1/H2 and H3/H4 lineage. Nevertheless, compared with the plasmid with a promoter and 3′-UTR from the same lineage, the recombinant plasmid with a promoter from H2 and a 3′-UTR from H3 showed about double fold increased luciferase activity, Conversely, the recombinant plasmid with a promoter from H3 and a 3′-UTR from H2 resulted in about 2-fold decreased luciferase activity. These results indicate that the promoter and 3′-UTR of HLA-DRB1 may antagonistically regulate the gene expression, which may be subjected to stabilizing selection. These findings may provide a novel insight into the mechanisms of the diseases associated with HLA-DRB1 genes.

HLA-DRB1是人类中多态性最高的主要组织相容性复合体（major histocompatibility complex, MHC）II类基因，在免疫系统的发育与功能调控中发挥关键作用。HLA-DRB1的启动子区域与3′-UTR存在广泛的多态性，尤其是启动子中的长末端重复序列（Long terminal repeat, LTR）元件，该元件可能参与基因表达的调控过程。然而，目前仍不清楚整个启动子区域与3′-UTR内的多态性如何调控基因表达。本研究围绕HLA-DRB1启动子与3′-UTR的广泛多态性，以及这些多态性以独立与联合方式影响基因表达的机制开展了系统性探究。研究结果显示，DRB1启动子与3′-UTR的绝大多数单倍型可聚类为4个保守谱系（H1、H2、H3与H4），且呈现出高度的连锁不平衡（linkage disequilibrium）。相较于H1与H2谱系，H3与H4谱系启动子内的LTR元件可显著抑制启动子活性，但与之相连的3′-UTR活性却有所升高，最终使得H1/H2与H3/H4谱系的基因表达终产物无明显差异。不过，与携带同一谱系启动子和3′-UTR的对照质粒相比，携带H2启动子与H3 3′-UTR的重组质粒的荧光素酶活性提升至原水平的约2倍；反之，携带H3启动子与H2 3′-UTR的重组质粒的荧光素酶活性则降至原水平的约1/2。上述结果表明，HLA-DRB1的启动子与3′-UTR可能通过拮抗作用共同调控基因表达，这一调控过程可能受到稳定选择的作用。本研究发现可为与HLA-DRB1基因相关疾病的发病机制研究提供全新的研究视角。