From genes to function: new progress made in disease-related non-coding regions
It has been widely acknowledged that genetic factors play an important role in the development of psychiatric diseases. In addition, evidence from image genetics shows that genetic factors also exhibit in the behavioral/cognitive processes of normal phenomenon in psychology. Currently, a large number of studies on identifying susceptibility genes of psychiatric diseases and behavioral/cognitive processing have been published. However, the function of these susceptibility genes, particularly of non-protein-coding regions, is to be further investigated.
To solve this problem, our team developed a database of rSNPBase for curated regulatory SNPs. It provides curated rSNPs that analyses the regulatory features of all SNPs in the human genome with reference to experimentally supported regulatory elements. The achievement was published in the journal of Nucleic Acids Research.
In this study, genome-wide human SNPs and genes were filtered and mapped by experimentally validated regulatory elements, which are involved in four types of regulation: proximal transcriptional regulation, distal transcriptional regulation, RBP-mediated post-transcriptional regulation and miRNA-mediated post-transcriptional regulation. rSNPBase also analyses LD correlations between SNPs to annotate the regulatory feature to SNP-set rather than a single SNP. Furthermore, due to the importance of eQTL evidence for deciphering gene regulation and the spatio-temporal specificity of gene regulation, rSNPBase provides eQTL labels and spatiotemporal labels for the included SNPs.
rSNPBase provides functional annotations of rSNPs in a wide range of regulation types with up-to-date experimental evidences, which is freely available at http://rsnp.psych.ac.cn/. rSNPBase is targeted to assist researchers to have a deep understanding of the regulatory features of SNPs, and to support further genetic and molecular mechanism studies.
This work was supported by the the Chinese Academy of Sciences, State Administration of Foreign Experts Affairs, Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences and National Natural Science Foundation of China.
Guo, L., Du, Y., Chang, S., Zhang, K., & Wang, J. (2014). rSNPBase: a database for curated regulatory SNPs. Nucleic Acids Res, 42 (D1): D1033-D1039. doi: 10.1093/nar/gkt1167