Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

An epigenetic mechanism for cavefish eye degeneration


Coding and non-coding mutations in DNA contribute significantly to phenotypic variability during evolution. However, less is known about the role of epigenetics in this process. Although previous studies have identified eye development genes associated with the loss-of-eyes phenotype in the Pachón blind cave morph of the Mexican tetra Astyanax mexicanus, no inactivating mutations have been found in any of these genes. Here, we show that excess DNA methylation-based epigenetic silencing promotes eye degeneration in blind cave A. mexicanus. By performing parallel analyses in A. mexicanus cave and surface morphs, and in the zebrafish Danio rerio, we have discovered that DNA methylation mediates eye-specific gene repression and globally regulates early eye development. The most significantly hypermethylated and downregulated genes in the cave morph are also linked to human eye disorders, suggesting that the function of these genes is conserved across vertebrates. Our results show that changes in DNA methylation-based gene repression can serve as an important molecular mechanism generating phenotypic diversity during development and evolution.

This is a preview of subscription content

Access options

Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Fig. 1: Eye phenotypes in A. mexicanus surface fish and cavefish, and D. rerio wild-type and dnmt3bb.1y258 mutants.
Fig. 2: Gene expression changes in cave versus surface fish morphs of A. mexicanus.
Fig. 3: Eye phenotype and associated gene expression changes in wild-type and DNA methylation-deficient D. rerio.
Fig. 4: Partial rescue of cavefish eyes by Aza-mediated inhibition of eye DNA methylation.


  1. Gross, J. B., Meyer, B. & Perkins, M. The rise of Astyanax cavefish. Dev. Dynam. 244, 1031–1038 (2015).

    Article  Google Scholar 

  2. Moran, D., Softley, R. & Warrant, E. J. The energetic cost of vision and the evolution of eyeless Mexican cavefish. Sci. Adv. 1, e1500363 (2015).

    Article  Google Scholar 

  3. Hinaux, H. et al. Lens defects in Astyanax mexicanus cavefish: evolution of crystallins and a role for alphaA-crystallin. Dev. Neurobiol. 75, 505–521 (2015).

    CAS  Article  Google Scholar 

  4. Casane, D. & Retaux, S. Evolutionary genetics of the cavefish Astyanax mexicanus. Adv. Genet. 95, 117–159 (2016).

    CAS  Article  Google Scholar 

  5. Ma, L., Parkhurst, A. & Jeffery, W. R. The role of a lens survival pathway including sox2 and alphaA-crystallin in the evolution of cavefish eye degeneration. EvoDevo 5, 28 (2014).

    Article  Google Scholar 

  6. McGaugh, S. E. et al. The cavefish genome reveals candidate genes for eye loss. Nat. Commun. 5, 5307 (2014).

    CAS  Article  Google Scholar 

  7. Hinaux, H. et al. De novo sequencing of Astyanax mexicanus surface fish and Pachón cavefish transcriptomes reveals enrichment of mutations in cavefish putative eye genes. PLoS ONE 8, e53553 (2013).

    CAS  Article  Google Scholar 

  8. Kim, E. B. et al. Genome sequencing reveals insights into physiology and longevity of the naked mole rat. Nature 479, 223–227 (2011).

    CAS  Article  Google Scholar 

  9. Zhu, H., Wang, G. & Qian, J. Transcription factors as readers and effectors of DNA methylation. Nat. Rev. Genet. 17, 551–565 (2016).

    CAS  Article  Google Scholar 

  10. Strickler, A. G., Yamamoto, Y. & Jeffery, W. R. The lens controls cell survival in the retina: evidence from the blind cavefish Astyanax. Dev. Biol. 311, 512–523 (2007).

    CAS  Article  Google Scholar 

  11. Csankovszki, G., Nagy, A. & Jaenisch, R. Synergism of Xist RNA, DNA methylation, and histone hypoacetylation in maintaining X chromosome inactivation. J. Cell Biol. 153, 773–784 (2001).

    CAS  Article  Google Scholar 

  12. Xu, F. et al. Molecular and enzymatic profiles of mammalian DNA methyltransferases: structures and targets for drugs. Curr. Med. Chem. 17, 4052–4071 (2010).

    CAS  Article  Google Scholar 

  13. Gore, A. V. et al. Epigenetic regulation of hematopoiesis by DNA methylation. eLife 5, e11813 (2016).

    Article  Google Scholar 

  14. Seritrakul, P. & Gross, J. M. Expression of the de novo DNA methyltransferases (dnmt3dnmt8) during zebrafish lens development. Dev. Dynam. 243, 350–356 (2014).

    CAS  Article  Google Scholar 

  15. Raymond, P. A., Barthel, L. K., Bernardos, R. L. & Perkowski, J. J. Molecular characterization of retinal stem cells and their niches in adult zebrafish. BMC Dev. Biol. 6, 36 (2006).

    Article  Google Scholar 

  16. Wan, Y. et al. The ciliary marginal zone of the zebrafish retina: clonal and time-lapse analysis of a continuously growing tissue. Development 143, 1099–1107 (2016).

    CAS  Article  Google Scholar 

  17. Stirzaker, C., Taberlay, P. C., Statham, A. L. & Clark, S. J. Mining cancer methylomes: prospects and challenges. Trends Genet. 30, 75–84 (2014).

    CAS  Article  Google Scholar 

  18. Ayyagari, R. et al. Bilateral macular atrophy in blue cone monochromacy (BCM) with loss of the locus control region (LCR) and part of the red pigment gene. Mol. Vis. 5, 13 (1999).

    CAS  PubMed  Google Scholar 

  19. Winderickx, J. et al. Defective colour vision associated with a missense mutation in the human green visual pigment gene. Nat. Genet. 1, 251–256 (1992).

    CAS  Article  Google Scholar 

  20. Arno, G. et al. Recessive retinopathy consequent on mutant G-protein β subunit 3 (GNB3). JAMA Ophthalmol. 134, 924–927 (2016).

    Article  Google Scholar 

  21. Vincent, A. et al. Biallelic mutations in GNB3 cause a unique form of autosomal-recessive congenital stationary night blindness. Am. J. Hum. Genet. 98, 1011–1019 (2016).

    CAS  Article  Google Scholar 

  22. Swaroop, A. et al. Leber congenital amaurosis caused by a homozygous mutation (R90W) in the homeodomain of the retinal transcription factor CRX: direct evidence for the involvement of CRX in the development of photoreceptor function. Hum. Mol. Genet. 8, 299–305 (1999).

    CAS  Article  Google Scholar 

  23. Swaroop, A., Kim, D. & Forrest, D. Transcriptional regulation of photoreceptor development and homeostasis in the mammalian retina. Nat. Rev. Neurosci. 11, 563–576 (2010).

    CAS  Article  Google Scholar 

  24. Li, C. et al. Overlapping requirements for Tet2 and Tet3 in normal development and hematopoietic stem cell emergence. Cell Rep. 12, 1133–1143 (2015).

    CAS  Article  Google Scholar 

  25. Ito, S. et al. Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature 466, 1129–1133 (2010).

    CAS  Article  Google Scholar 

  26. Ito, S. et al. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 333, 1300–1303 (2011).

    CAS  Article  Google Scholar 

  27. Jones, P. A. & Taylor, S. M. Cellular differentiation, cytidine analogs and DNA methylation. Cell 20, 85–93 (1980).

    CAS  Article  Google Scholar 

  28. Raj, K. & Mufti, G. J. Azacytidine (Vidaza®) in the treatment of myelodysplastic syndromes. Ther. Clin. Risk Manag. 2, 377–388 (2006).

    CAS  Article  Google Scholar 

  29. Martin, C. C., Laforest, L., Akimenko, M. A. & Ekker, M. A role for DNA methylation in gastrulation and somite patterning. Dev. Biol. 206, 189–205 (1999).

    CAS  Article  Google Scholar 

  30. Heyn, H. & Esteller, M. DNA methylation profiling in the clinic: applications and challenges. Nat. Rev. Genet. 13, 679–692 (2012).

    CAS  Article  Google Scholar 

  31. Suzuki, M. M. & Bird, A. DNA methylation landscapes: provocative insights from epigenomics. Nat. Rev. Genet. 9, 465–476 (2008).

    CAS  Article  Google Scholar 

  32. Kucharski, R., Maleszka, J., Foret, S. & Maleszka, R. Nutritional control of reproductive status in honeybees via DNA methylation. Science 319, 1827–1830 (2008).

    CAS  Article  Google Scholar 

  33. Kimmel, C. B., Ballard, W. W., Kimmel, S. R., Ullmann, B. & Schilling, T. F. Stages of embryonic development of the zebrafish. Dev. Dyn. 203, 253–310 (1995).

    CAS  Article  Google Scholar 

  34. Elipot, Y., Legendre, L., Pere, S., Sohm, F. & Retaux, S. Astyanax transgenesis and husbandry: how cavefish enters the laboratory. Zebrafish 11, 291–299 (2014).

    CAS  Article  Google Scholar 

  35. Bolger, A. M., Lohse, M., & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).

    CAS  Article  Google Scholar 

  36. Krueger, F., Andrews, S. R. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27, 1571–1572 (2011).

    CAS  Article  Google Scholar 

  37. Li, L. C. & Dahiya, R. MethPrimer: designing primers for methylation PCRs. Bioinformatics 18, 1427–1431 (2002).

    CAS  Article  Google Scholar 

  38. Kumaki, Y., Oda, M. & Okano, M. QUMA: quantification tool for methylation analysis. Nucleic Acids Res. 36, W170–W175 (2008).

    CAS  Article  Google Scholar 

Download references


We thank members of the Weinstein and Jeffery laboratories for support, help and suggestions. We thank staff at the NICHD's Molecular Genomics Laboratory for bisulfite and RNA-Seq assistance. We also thank members of the zebrafish and cavefish communities for sharing reagents and protocols. We thank K. Sampath for comments on the manuscript. We thank S. McGaugh for suggestions on cavefish sequence alignments and M. Goll for providing the zebrafish tet2,3 double mutant line. Work in the Weinstein and Jeffery laboratories is supported by the intramural programme of the NICHD and by R01EY024941, respectively.

Author information

Authors and Affiliations



A.V.G. and B.M.W. designed the study with input from K.A.T. and W.R.J. A.V.G. and K.A.T. performed the experiments with help from L.M., D.C. and A.E.D. J.I. analysed the sequencing data. D.C. and A.E.D. provided fish husbandry support. A.V.G. and B.M.W. wrote the manuscript with input from all authors.

Corresponding authors

Correspondence to Aniket V. Gore or Brant M. Weinstein.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplementary Figures

Supplementary Figures 1–7

Reporting Summary

Supplementary Data 1

Differentially up and down regulated genes from surface and cavefish eyes at 54 hpf by RNA seq analysis

Supplementary Data 2

Cavefish genes with significant promoter hypermethylation and reduced gene expression

Supplementary Data 3

Cavefish genes with substantial promoter hypermethylation and reduced gene expression and their linked human disease phenotypes

Supplementary Data 4

Primer sequences used in this study

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Gore, A.V., Tomins, K.A., Iben, J. et al. An epigenetic mechanism for cavefish eye degeneration. Nat Ecol Evol 2, 1155–1160 (2018).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

Further reading


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing