TDP-43 binds to RNA G-quadruplex structure and regulates mRNA stability and translation

TDP-43 is a hallmark protein associated with neurodegenerative diseases. Recent studies revealed TDP-43 as an RNA G-quadruplex (rG4) binding protein, impacting mRNA transport and function. However, our understanding on the interaction between TDP-43 and RNA secondary structure remains poorly understood. Additionally, reports on specific rG4 targets regulated by TDP-43 are limited. Herein, we show that TDP-43 exhibits a preference for binding to the rG4 structure under K+ condition by a high-throughput RNA Bind-n-Seq method. Besides, we find that loss of TDP-43 contributes to a decrease in mRNA structure in the transcriptome by using the newly developed SHALiPE-seq technology. By analyzing the SHALiPE-seq data of TDP-43 binding sites, we further demonstrate that the reduction in structural complexity is likely due to the loss of TDP-43 binding to the RNA targets, especially in the 3'UTR. Importantly, our transcript-specific investigation reveals that TDP-43 binds to a novel rG4 structure in the 3'UTR of SLC1A5 mRNA, promoting the mRNA stability and translation. Our findings not only offer new insights into the role of TDP-43 in regulating RNA structure such as rG4, but also contribute to a better understanding of its broader functions and provide potential targets for therapeutic strategies in TDP43-related diseases. SHALiPE-seq of Ctrl HK293T and TDP-43 knockdown HEK293T cell line