Many cave-dwelling animals adapt to their environment through the degeneration of eyesight or even complete eye loss. A new study reports that epigenetic repression of gene expression during development can underlie this trait regression.

Credit: Paulo Oliveira/Alamy

While the eyeless morphs of Astyanax mexicanus (Mexican tetra) from the Pachón caves are morphologically indistinguishable from their surface-dwelling counterparts during initial stages of eye development, eye tissue degeneration initiates around 2 days after fertilization, leading to complete loss of eyes in adult cavefish. Genome analyses have failed to attribute this phenotypic variability to inactivating null mutations in genes essential for eye development, raising the possibility that eye gene expression is altered indirectly through cis-regulatory mutations that affect DNA methylation.

increasing DNA methylation levels led to reduced eye gene expression

Expression of the DNA methyltransferase-encoding gene dnmt3bb.1 was increased 1.5-fold in cavefish compared with surface fish as determined by reverse transcription quantitative PCR (RT-qPCR) and confirmed by RNA sequencing (RNA-seq). RNA-seq also showed reduced expression of a large number of eye development genes in cavefish compared with surface-living relatives. Zebrafish mutants lacking dnmt3bb.1 exhibited larger eye size and increased expression of several eye-relevant genes, including crx, gnb3a and opn1lw1 compared to wild-type control animals, suggesting that hypermethylation mediated by Dnmt3bb.1 could underlie the repression of eye gene expression in cavefish.

RNA-seq and whole-genome bisulfite sequencing of genomic DNA identified 128 genes with markedly increased promoter methylation and decreased expression in cavefish versus surface fish embryonic eyes. Of these, 39 genes had been shown to be expressed in human eyes, with 19 genes having been linked previously to human eye disorders.

Looking at previously described zebrafish tet double mutants, which harbour genome-wide DNA hypermethylation, the authors found that increasing DNA methylation levels led to reduced eye gene expression and smaller eye size. This phenotype could be partially rescued by administration of 5-azacytidine, a well-known DNA methylation inhibitor, confirming the role of DNA methylation in teleost eye development.