Construction And Application Of Human Quantitative Trait Genetic Locus Database

Objective:Recent advances of genome sequencing and functional genomic profiling promote many large-scale molecular traits quantitative trait locus(x QTL)studies,which connect genotype with tissue/cell type-specific cellular functions from transcriptional to post-translational levels.However,there is no comprehensive resource can perform QTL lookup across multiple molecular phenotypes and investigate the potential cascade effect of functional variants.Here we developed a versatile resource QTLbase for interpreting possible molecular functions of genetic variants as well as their tissue/cell type specificity,as well as provide gene annotation information.We provided a new perspective and direction for exploring and investigation the function and the molecular mechanism of genetic variant.At the same time,genome-wide association studies(GWASs)have identified many genetics variants related to autoimmune diseases.However,causal variants and their function in the development of autoimmune diseases are still unclear.Therefore,we combined function annotation and QTL analysis to prioritize genetics variants of autoimmune disease and identify the causal variants.Then we focused a causal variant and explored its likely regulatory effect as an e QTL to regulate gene expression and integrate bioinformatics prediction analysis to further reveal the molecular mechanism in the development of autoimmune disease.Exploration the molecular mechanism of non-coding regulatory variants has deepened our understanding for diseases,and then proposed more effective treatment methods.Method:We manually curated QTL studies for human molecular phenotypes from literatures by searching Pub Med or Google Scholar using QTL-relevant key.In order to reduce heterogeneous among collected QTL data,we synchronized originally recorded db SNP ID with db SNP build 151,and then we normalized the molecular phenotypes according to different QTL type with different criteria.To ensure a recognized tissue/cell type naming,we mapped QTL-relevant tissues/cell types to commonly-used anatomogram which has been adopted in GTEx and Expression Atlas.We integrated 20 functional annotations into QTLbase form other database or website,which could be divided into four major categories according to different usages,including variant information,functional prediction,functional evidence and disease association.We stored the QTL summary statistics and annotation information in My SQL,and then built human molecular phenotype database named QTLbase.We curated and prioritized pleiotropic SNPs for autoimmune disease though gene annotation analysis and then selected potential regulatory variant rs4728142 according to gene annotation analysis and x QTL colocalization analysis.Gene expression analysis and transcript usage QTL(tu QTL)analysis identified the functional connection of rs4728142 to its target gene.And circularized chromosome conformation capture(4C)experiment suggested that the region of rs4728142 interaction with promoter of IRF5.We used some experimental validations to confirm these findings and reveal the molecular mechanism of rs4728142.Result and Conclusion:In general,the resource includes five key functions:(i)curates and compiles genome-wide QTLs summary statistics for 13 types of human molecular traits from 233 independent studies;(ii)maps QTL-relevant tissues/cell types to 78 unified terms according to standard anatomogram;(iii)uniformly normalizes variant and trait information,incorporated 171,524,441 significant associations(P-value ? 0.05),including 159,197,054 cis-QTLs and 12,327,378 trans-QTLs;(iv)introduces a rich web client enabling phenome-wise and tissue-wise visualization;(v)integrates the most comprehensive genomic features and functional predictions to annotate potential mechanisms of QTLs.QTLbase provides a one-stop shop of QTLs searching and comparison across multiple tissues and multiple layers of molecular complexity,and it will greatly help researchers interrogate the biological mechanism of causal variants and guide the direction of functional validation.QTLbase is freely available at http://mulinlab.org/qtlbase.We identified a pleiotropic SNP rs4728142 obtaining large regulatory potential from 440 pleiotropic SNPs associated with autoimmune disease by integrating the curated data in QTLbase,gene annotation information and x QTL colocalization analysis.QTLbase query result suggested rs4728142 that regulated IRF5 gene expression in different tissue/cell types.We used RNA-seq data from GTEx,Blueprint and Geuvadis to perform e QTL and tu QTL analysis in specific tissue/cell type.QTL analysis suggested rs4728142 can affect IRF5 expression and switch the short and long transcript usage under different alleles.Circular chromatin conformation capture experiments shown that ZBTB3 can mediate the binging effect of the loop structure between the rs4728142 and IRF5 promoter of different transcripts.RNA-seq experiments on normal and rs4728142-knockout cells showed that the differentially expressed genes can be enriched in autoimmune disease-related pathways.Finally,We demonstrated rs4728142 as tu QTL could affect the immune response by a hypothetically novel molecular mechanism.When the G allele of rs4728142 could weaken the binding of the transcript factor ZBTB3,so the enhancer located upstream of rs4728142 will regulate the expression of IRF5 long and short transcript without preference;when A allele is occurred,ZBTB3 can be recruited and a loop structure between rs4728142 and the promoter of IRF5 short transcript is formed,which could finally increase its expression.