• This article reviews the ENCyclopedia Of DNA Elements (ENCODE) project and its implications for eye disease research.

    Approximately 10 years after the Human Genome Project unraveled the sequence of our DNA, the ENCODE Project sought to interpret it. Data from this recently completed project have shed new light on the proportion of biologically active human DNA, assigning a biochemical role to much of the sequence previously considered to be “junk.” Many of these newly catalogued functional elements represent epigenetic mechanisms involved in regulating gene expression.

    The authors write that despite many inroads being made into understanding the genetic mechanisms of many ocular diseases, we are only beginning to uncover similarly important epigenetic factors. A limited number of epigenetic factors have now been implicated in the pathogenesis of AMD and cataract, although other diseases, such as glaucoma and diabetic retinopathy, have to date been poorly studied on the epigenetic front.

    However, a major shortfall in the application of ENCODE data for ocular research is in the relative paucity of eye tissue used for analysis. Given the high cost associated with analysis, ENCODE investigators have studied only widely used cell lines. Therefore, no in-depth expression or histone analysis was performed on ocular-specific cell lines. Nonetheless, ENCODE data can provide general insight into global gene regulation and could still be used to explore loci of interest.

    They conclude that novel insights from the ENCODE project will eventually assist in the development of new therapeutic strategies for common blinding disorders.