Catalytic activity of nuclear METTL3 promotes functional m6A modifications that drive retinal development [eCLIP]

METTL3 catalyzes N6-methyladenosine (m6A) on mRNA, regulating RNA metabolism, but its role in early retinal development remains virtually unstudied. Using stem cell-derived 3D retinal organoids to model retinal progenitor cell (RPC) differentiation, we found that loss of METTL3 nuclear m6A enzymatic activity impairs formation of the Rx+ retinal anlage in vitro. Through dCas13b-FTO m6A engineering, we demonstrate that m6A modifications at the Six3 3'UTR control its stability. While Mettl3 loss altered histone modifications, direct METTL3 chromatin targets were not transcriptionally functional. Integration of transcriptome-wide m6A and protein-RNA mapping with a degron-based strategy revealed immediate effects of METTL3 degradation in RPCs, uncovering a regulatory interaction between METTL3 and its RNA target Ythdf1. We demonstrate uncoupling of chromatin accessibility from changes in retinal transcription and m6A modifications. In vivo studies of Mettl3-deficient RPCs showed altered cell cycle and impaired retinal ganglion cell generation. Our findings establish METTL3-dependent m6A modifications as an essential post-transcriptional layer that drives retinal development. METTL3 eCLIP assay of day 6 retinal organoids of WT Rx:GFP and Mettl3 KO line. METTL3 antibody (Abcam, Ab195352) was used for this eCLIP assay.