Dynamics and regulatory role of 5-methylcytosine modification in mRNA colocalized with RNA G-quadruplex structure in...

Post-transcriptional regulation is a pivotal event in controlling gene expression, modulated by various epitranscriptomic modifications and RNA secondary structures, including G-quadruplexes (G4s). Recent studies have shown the co-occurrence of various epitranscriptomic modifications with RNA G-quadruplexes (rG4s) and their potential role in regulatory pathways. However, to the best of our knowledge, no work has been carried out investigating the role of 5-methylcytosine (m⁵C) colocalization with rG4. Herein, we have demonstrated the dynamic changes in colocalization of m⁵C sites with potential quadruplexes forming sequence (PQS) capable of forming rG4 structure in mouse embryonic stem cell (mESC) and different mouse tissues. Our results indicate that variable sets of genes are modified and dynamically changing during the developmental processes. However, among these, a few genes, including oncogene Hdgf along with Med24 and Emc3 are commonly found and contains m⁵C nucleotide in almost all 10 mouse tissues (including mESC), implicating their potential role in post-transcriptional regulation. The Enrichr-based analysis shows the involvement of genes containing m⁵C colocalized PQS in key biological processes and diseases. Additionally, binding analysis of RNA binding proteins (RBP) with colocalized sites revealed that many of these colocalized sites are the binding targets of RBPs such as YY1, YTHDC2 and RBFOX2. Collectively, these analyses provide an insight into the interplay between the m⁵C modification and rG4 to fine-tune the post-transcriptional regulation during development. It also suggests the possible involvement of m⁵C colocalized sites with PQS in modulating the expression of oncogene Hdgf, as well as the oncogenic and therapeutic targets like Med24 and Emc3.