Mapping of CELF1-RNA interactions reveals post-transcriptional control of lens development

Precise post-transcriptional regulation of gene expression is essential for vertebrate lens development. Disruption of the gene encoding the RNA-binding protein CELF1 leads to early-onset cataract in mice. Here, using iCLIP-seq in lenses, we mapped transcriptome-wide CELF1-binding sites, revealing interactions with the 3'UTRs of key transcripts involved in lens development and pathology like Gja8, Jag1, Maf, Pax6, or Prox1. Integrated analysis with transcriptomic data and luciferase reporter assays demonstrated that binding of CELF1 protein represses its target mRNAs by destabilizing transcripts and/or inhibiting their translation. Indeed, the cataract-linked genes Maf and Gja8 are upregulated in Celf1-cKO lenses. In Xenopus laevis, overexpression of maf resulted in abnormal lens structure and eye morphology, confirming the developmental relevance of CELF1-mediated repression. Our findings uncover a post-transcriptional network in which CELF1 controls lens morphogenesis by limiting the expression of critical genes at the mRNA level to achieve their proper dosage.