Single-cell sequencing analysis reveals the essential role of the m 6A reader YTHDF1 in retinal visual function by regulating TULP1 and DHX38 translation.

Abstract

N6-methyladenosine (m ⁶A) modification of mRNA is a critical post-transcriptional regulatory mechanism that modulates mRNA metabolism and neuronal function. The m ⁶A reader YTHDF1 has been shown to enhance the translational efficiency of m ⁶A-modified mRNAs in the brain and is essential for learning and memory. However, its role in the mature retina remains unclear. Herein, we report a novel role of Ythdf1 in the maintenance of retinal function using a genetic knockout model. Loss of Ythdf1 resulted in impaired scotopic electroretinogram (ERG) responses and progressive retinal degeneration. Detailed analyses of rod photoreceptors confirmed substantial degenerative changes in the absence of ciliary defects. Single-cell RNA sequencing revealed comprehensive molecular alterations across all retinal cell types in Ythdf1-deficient retinas. Integrative analysis of methylated RNA immunoprecipitation (MeRIP) sequencing and RIP sequencing identified Tulp1 and Dhx38, two inheritable retinal degeneration disease-associated gene homologs, as direct targets of YTHDF1 in the retina. Specifically, YTHDF1 recognized and bound m ⁶A-modified Tulp1 and Dhx38 mRNA at the coding sequence (CDS), enhancing their translational efficiency without altering mRNA levels. Collectively, these findings highlight the essential role of YTHDF1 in preserving visual function and reveal a novel regulatory mechanism of m ⁶A reader proteins in retinal degeneration, identifying potential therapeutic targets for severe retinopathies.