Interrogating the Effect of 3'UTR RNA G-quadruplex Structure in MicroRNA Target Site Accessibility and Translational Regulation

Description

RNA G-quadruplex (rG4) structure have been proposed to play crucial roles in a number of fundamental biological processes that include the regulation of transcriptional, co-transcriptional, and post-transcriptional events. Emerging data suggest that rG4s are associated with human diseases and cancers, making rG4 an interesting structural motif and rG4 biology an appealing topic for intense study.The knowledge of rG4 structures – especially their formation in the transcriptome and their interplay with cis-regulatory elements – are important aspects for further exploring rG4 biology and its significance in both basic and applied biosciences.Our group have been at the leading-edge of investigating the rG4 structures and functions over the years. Recently, we have developed SHALiPE, DMSLiPE, and rG4-seq to detect rG4 in both transcript-specific and transcriptome-wide scale, in which the data offer unique insights into the prevalence and location of rG4s in the human transcriptome. Moreover, we have carried out functional assays to study the effect of rG4s at the untranslated regions (UTRs), and demonstrated that rG4s at UTRs can inhibit translation. In this project, we will improve these techniques to detect rG4 structures in both human and mouse transcriptomes, examine the rG4 conservation across mammalian species, assess the relationship between rG4 sites and microRNA (miRNA) target sites, and investigate the structural and functional role of rG4s in miRNA target site accessibility and translation. In collaboration with Prof. Ting Fung Chan, novel bioinformatics algorithm will be developed to analyse the rG4-seq data, which will enable robust scoring and evolutionary analysis of rG4s across transcriptomes, as well as establishing their association with miRNA target sites.One specific rG4 candidate of interest is located at the 3’UTR of APP, a gene that is linked to Alzheimer disease. Using optimized version of SHALiPE and DMSLiPE, the structure at the 3’UTR of APP RNA will be characterized to further study the crosstalk between rG4 and miRNA target site, and its effect on gene expression. In collaboration with Prof. Andrew Grimson, extensive functional assays will be performed to reveal the role of rG4 in miRNA-mediated translation regulation. Other interesting 3’UTR rG4 as identified above will also be studied.By combining our interdisciplinary expertise and unique experience in respective fields, we are confident that the proposed project will reveal new and important findings that will shed light into the mechanistic role of rG4 in post-transcriptional regulation, and advance our knowledge on rG4 biology and its significance in medicine.