Year: 2026
Type: preprint
Abstract: Genetic perturbation has been central to defining the functions of RNA modification binding proteins (readers), but knockout approaches remove the entire protein and cannot readily distinguish modification-dependent reader activity from other protein-associated functions. Small molecules provide an orthogonal strategy by directly perturbing the reader protein–RNA recognition event while preserving the reader protein. Here we report DF142, a cell-active pan-YTHDF chemical probe developed through an m6A-anchored design strategy. Structure-guided optimization yielded a high-affinity ligand that engages endogenous YTHDF proteins, blocks YTHDF–m6A RNA recognition, and displays a favorable selectivity profile. In mouse B cells, DF142 closely recapitulated the transcriptional effects of genetic Ythdf1/2 loss but induced minimal effects in Ythdf1/2-deficient cells at the applied dose range, distinguishing m6A-dependent from putative m6A-independent programs. In AML cells, application of DF142 revealed a leukemia-relevant RNA program associated with YTHDF–m6A interactions. Its activity in cancer cells and mouse models further demonstrates the utility of DF142 for interrogating YTHDF function in disease-relevant settings. Together, these findings establish DF142 as a chemical probe for dissecting m6A-dependent YTHDF biology.
Source: ChemRxiv
Language: English
Topic: RNA modifications and cancer
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7214067266