YTHDF proteins and m6A-RNA clients undergo autophagic turnover during contact inhibition.
The YTHDF protein family plays a critical role in cancer development by recognizing and regulating the stability of N6-methyladenosine (m6A)-modified RNA. Here, we reveal a novel autophagy-dependent mechanism controlling YTHDF protein levels. Upon contact inhibition, YTHDF proteins are rapidly degraded, coinciding with increased autophagy and decreased mTOR activity. Upon pharmacological mTOR-inhibition, YTHDF2 is downregulated via lysosomal degradation in high-density and low-density cultured cells. YTHDF2 selectively interacts with the autophagy modifier GABARAP L2 through LIR motifs in its unstructured N- and C-terminal regions. Autophagic YTHDF2 downregulation results in co-degradation of its bound m6A-modified RNA clients. While YTHDF depletion induces cell death in contact inhibition-deficient HCT116 cancer cells, contact-inhibited MRC5 and RPE1 cells remain unaffected. Our findings uncover a novel regulatory pathway that governs YTHDF protein stability and suggest the existence of an autophagy-mediated degradation pathway for m6Amodified RNA, with significant implications for cancer biology and cell fate determination.