METTL16 maintains photoreceptor integrity via splicing fidelity, mRNA stability, and translational regulation

N6-methyladenosine (m⁶A) RNA modification is essential for retinal homeostasis. Pathogenic mutations in U6 snRNA have recently been identified in families with retinitis pigmentosa (RP), underscoring the importance of precise RNA processing in photoreceptor survival. METTL16 installs m⁶A at A43 of U6 snRNA, but its retinal role remains unknown.

To define the role of METTL16 in photoreceptor maintenance and determine how its deficiency contributes to retinal degeneration.

We generated rod-specificMettl16knockout (RKO) mice. Visual function was comprehensively evaluated by electroretinography, light-dark box test, and optomotor response. Retinal morphology was examined using immunohistochemical staining. Multi-omics profiling (RNA-seq, proteomics, MeRIP-seq) systematically identified differentially expressed genes and downstream targets. Translational efficiency was assessed through SUnSET assay and polysome profiling.

RKO mice exhibited progressive visual impairment, photoreceptor degeneration, and synaptic defects. Mechanistically, METTL16 deficiency disrupted multiple layers of RNA regulation. In the nucleus, loss of U6 snRNA A43 m⁶A modification impaired 5' splice-site selection, causing aberrant exon skipping in RP-associated genes, including Tulp1 and Pde6g, before overt degeneration. METTL16 deficiency also altered m⁶A-associated regulation of selected transcripts, including Tor1b and Nlgn2. In the cytoplasm, METTL16 associated with translation-related factors, and its loss was accompanied by reduced global translation efficiency and decreased levels of several phototransduction proteins.

These findings identify METTL16 as a regulator of photoreceptor integrity through U6 snRNA modification and m⁶A-associated transcript regulation, with additional evidence supporting a potential role in translational control. They provide a mechanistic link between RNA dysregulation and retinal degeneration.