DNA-guided photoactivatable probe-based chemical proteomics reveals the reader protein of mRNA methylation

Chemical modification on mRNA can recruit specific binding proteins (readers/partners) to determine post-transcriptional gene regulation. However, the identification of the reader is extremely limited owing to the rather weak and highly dynamic non-covalent interactions between mRNA modification and reader, and therefore the sensitive and robust approaches are desirable. Here, we report a DNA-guided photoactivatable-based chemical proteomic approach for profiling the readers of mRNA methylation. By use of N⁶-methyladenosine (m⁶A), we illustrated that this method can be successfully utilized for labelling and enriching the readers of mRNA modification, as well as for the discovery of new partners. Thus we applied this strategy to a new modification 2'-O-methyladenosine. As a result, DDX1 was identified and verified as a potential binding protein. Our study therefore provides a powerful chemical proteomics tool for identifying the binding factors of mRNA modification and reveals the underlying function of mRNA modification.