The Crosstalk between RNA modification and RNA Binding Proteins (RBPs)

Chemical modifications of RNA establish an epitranscriptomic regulatory layer that shapes RNA fate and gene expression. Although more than 170 modifications have been identified, the mechanisms determining where they are deposited and how they generate functional outcomes remain incompletely understood. 5-methylcytosine (m⁵C), a modification found in DNA and first detected in RNA in 1958, remains challenging to study in mRNA, partly because of limitations in reliable single-nucleotide mapping. In contrast, N6-methyladenosine (m⁶A) is the most abundant and best-studied internal modification in eukaryotic mRNA.

Both modifications regulate RNA stability, localization, and translation and have been linked to development, stress and immune responses, DNA damage repair, and complex diseases such as cancer. Their effects depend not only on the chemical mark itself, but also on its local context and interactions with RNA-binding proteins (RBPs), which act as readers and regulators of these marks.

Here, we integrate single-nucleotide maps of m⁵C and m⁶A sites from multiple experimental systems and mapping technologies with analyses of RNA sequence, structure, and RBP binding, using motif-based predictions and eCLIP data. Preliminary analyses indicate that both modifications display local sequence signatures and selective RBP-binding patterns. Several proteins associated with modified regions are not canonical RNA-modification regulators, while others are known for one modification but not the other. This framework aims to uncover principles governing modification-site recognition and provide mechanistic insight into the interplay between RNA modifications, protein binding, and RNA fate, advancing our understanding of epitranscriptomic regulation in biology and disease.

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