Inherited photoreceptor degenerations (IPDs) are the most genetically heterogeneous of Mendelian diseases. Many IPDs exhibit substantial phenotypic variability, but the basis is usually unknown. Mutations in MERTK cause recessive IPD phenotypes associated with the RP38 locus. We have identified a murine genetic modifier of Mertk-associated photoreceptor degeneration, the C57BL/6 (B6) allele of which acts as a suppressor. Photoreceptors degenerate rapidly in Mertk-deficient animals homozygous for the 129P2/Ola (129) modifier allele, whereas animals heterozygous for B6 and 129 modifier alleles exhibit an unusual intermixing of degenerating and preserved retinal regions, with females more severely affected than males. Mertk-deficient mice homozygous for the B6 modifier allele display degeneration only in the far periphery, even at 8 months of age, and have improved retinal function compared to animals homozygous for the 129 allele. We genetically mapped the modifier to an approximately 2-megabase critical interval that includes Tyro3, a paralog of Mertk. Tyro3 expression in the outer retina varies with modifier genotype in a manner characteristic of a cis-acting expression quantitative trait locus (eQTL), with the B6 allele conferring an approximately three-fold higher expression level. Loss of Tyro3 function accelerates the pace of photoreceptor degeneration in Mertk knockout mice, and TYRO3 protein is more abundant in the retinal pigment epithelium (RPE) adjacent to preserved central retinal regions of Mertk knockout mice homozygous for the B6 modifier allele. Endogenous human TYRO3 protein co-localizes with nascent photoreceptor outer segment (POS) phagosomes in a primary RPE cell culture assay, and expression of murine Tyro3 in cultured cells stimulates phagocytic ingestion of POS. Our findings demonstrate that Tyro3 gene dosage modulates Mertk-associated retinal degeneration, provide strong evidence for a direct role for TYRO3 in RPE phagocytosis, and suggest that an eQTL can modify a recessive IPD.

The electroretinogram (ERG) is a sensitive and noninvasive method for testing retinal function. In this protocol, we describe a method for performing ERGs in mice. Contact lenses on the mouse cornea measure the electrical response to a light stimulus of photoreceptors and downstream retinal cells, and the collected data are analyzed to evaluate retinal function.

The retinal pigment epithelium (RPE) serves vital roles in ocular development and retinal homeostasis but has limited representation in large-scale functional genomics datasets. Understanding how common human genetic variants affect RPE gene expression could elucidate the sources of phenotypic variability in selected monogenic ocular diseases and pinpoint causal genes at genome-wide association study (GWAS) loci. We interrogated the genetics of gene expression of cultured human fetal RPE (fRPE) cells under two metabolic conditions and discovered hundreds of shared or condition-specific expression or splice quantitative trait loci (e/sQTLs). Co-localizations of fRPE e/sQTLs with age-related macular degeneration (AMD) and myopia GWAS data suggest new candidate genes, and mechanisms by which a common RDH5 allele contributes to both increased AMD risk and decreased myopia risk. Our study highlights the unique transcriptomic characteristics of fRPE and provides a resource to connect e/sQTLs in a critical ocular cell type to monogenic and complex eye disorders.

The eye is an intricate organ with limited representation in large-scale functional genomics datasets. The retinal pigment epithelium (RPE) serves vital roles in ocular development and retinal homeostasis. We interrogated the genetics of gene expression of cultured human fetal RPE (fRPE) cells under two metabolic conditions. Genes with disproportionately high fRPE expression are enriched for genes related to inherited ocular diseases. Variants near these fRPE-selective genes explain a larger fraction of risk for both age-related macular degeneration (AMD) and myopia than variants near genes enriched in 53 other human tissues.Increased mitochondrial oxidation of glutamine by fRPE promoted expression of lipid synthesis genes implicated in AMD. Expression and splice quantitative trait loci (e/sQTL) analysis revealed shared and metabolic condition-specific loci of each type and several eQTL not previously described in any tissue. Fine mapping of fRPE e/sQTL across AMD and myopia genome-wide association data suggests new candidate genes, and mechanisms by which the same common variant of RDH5 contributes to both increased AMD risk and decreased myopia risk. Our study highlights the unique transcriptomic characteristics of fRPE and provides a resource to connect e/sQTL in a critical ocular cell type to monogenic and complex eye disorders.3The importance of vision to humans and the accessibility of the eye to examination have motivated the characterization of more than one thousand genetic conditions involving ocular phenotypes 1 . Among these, numerous monogenic diseases exhibit significant inter-and intra-familial phenotypic variability 2-7 . Imbalance in allelic expression of a handful of causative genes has been documented 8 , but common genetic variants responsible for such effects remain to be discovered.Complementing our knowledge of numerous monogenic ocular disorders, recent genome-wide association studies (GWAS) 9 have identified hundreds of independent loci associated with polygenic ocular phenotypes such as age-related macular degeneration (AMD), the leading cause of blindness in elderly individuals in developed countries 10,11 , and myopia, the most common type of refractive error worldwide and an increasingly common cause of blindness 12-14 . Despite the rapid success of GWAS in mapping novel ocular disease susceptibility loci, the functional mechanisms underlying these associations are often obscure.Connecting changes in molecular functions such as gene expression and splicing with specific GWAS genomic variants has aided the elucidation of functional mechanisms. Non-coding variants account for a preponderance of the most significant GWAS loci 15,16 , and most expression quantitative trait loci (eQTL) map to non-coding variants 17 . Thousands of eQTL have been found in a variety of human tissues 18 , but ocular celltypes are underrepresented among eQTL maps across diverse tissues, and no systematic search for eQTL has so far been described for any cell type in the human eye.The retinal pigment epithelium ...

Neural progenitors transit through multiple competence states that restrict production of each neural cell type. In Drosophila neuroblasts, a timed genome reorganization relocates the cell fate gene, hunchback, to the nuclear periphery, terminating competence to produce early-born neurons. Distal antenna (Dan), a pipsqueak (Psq) superfamily protein, is transiently downregulated at mid-embryogenesis, which is required for this relocation. Here we find that Dan is a highly intrinsically disordered protein, and when its Psq DNA-binding domain is increasingly disrupted, Dan coalesces into steadily larger, interconnected hubs of rapid protein exchange. Consistent with these phase-separation properties, Dan has a predicted LARKS domain, a structural motif that forms reversible interactions associated with phase-separation. In the embryo, loss of either the Psq motif or the LARKS domain abrogates Dan's ability to maintain neuroblast early competence upon misexpression, suggesting that Dan requires both DNA-binding and phase-separation to regulate neuroblast competence. Finally, we found that Dan strongly interacts with proteins of the nuclear pore complex (NPC), and Elys, a core NPC scaffold protein known to regulate genome architecture, binds thehbintron and is required for competence termination. Together, the results support a model for how Dan's phase-separation properties can mediate dynamic restructuring by balancing genome-binding, self-association, and interaction among nuclear architecture regulators.