Mapping and Targeting of RNA G-quadruplex Structures in the Human Non-coding Transcriptome

Description

RNA G-quadruplex (rG4) structures have been shown to have a myriad of functional and regulatory roles in fundamental biological processes. Latest findings have revealed formation of rG4s in the non-coding RNAs and their effect on gene regulation and RNA metabolism, highlighting the importance of studying rG4s in the non-coding transcriptome and designing molecular tools to target them.The knowledge of rG4 structures – especially their prevalence and location in the non-coding transcriptome, as well as their structural features– are two key aspects for further exploring rG4 biology and developing new strategy for targeting and gene manipulation purposes.Our group have a long-standing track record of studying the rG4 structures and functions. Recently, we have revealed the formation of rG4s in precursor and mature microRNAs, and demonstrated their roles in microRNA biogenesis and post-transcriptional regulation. Moreover, we have developed rG4-seq and applied it on polyA-enriched RNA to identify thousands of rG4s in the human transcriptome, of which some of them were from long non-coding RNAs such as NEAT1 and human telomerase RNA (hTR). In this project, we will refine the rG4-seq to map the rG4s in the human non-coding transcriptome, develop L-RNA aptamers that can selectively interact with rG4s, and investigate the potential of using L-RNA aptamers to interfere with rG4-protein interactions as well as gene activity.In collaboration with Prof. Ting Fung Chan, we will adapt the rG4-seeker that we recently developed to analyse the new rG4-seq data from the non-coding transcriptome, which will allow detail examination of rG4 structural motifs in non-coding RNAs.One specific rG4 candidate of interest is located at the 5’ end of hTR, an RNA that is linked to telomere maintenance and cancers. Using a combination of biophysical and biochemical assays, the structural features of the hTR rG4 and its interaction with the L-RNA aptamer will be characterized.In collaboration with Prof. Julian Tanner, we will optimize the L-RNA aptamer selection method, isolate aptamers that can bind to the rG4 in hTR, and test their effect on interfering rG4-protein binding and gene activity. Other interesting rG4s in non-coding RNAs as identified above will also be studied.By coupling our crossdisciplinary expertise and unique experience, we will reveal repertoire of rG4s in the non-coding transcriptome, uncover novel strategy to target rG4s, as well as important findings that will provide valuable insights into the role of rG4 in noncoding RNA, further advancing our knowledge on rG4 biology.