Genome-wide analysis of methylation in giant pandas with cataract by methylation-dependent restriction-site associated DNA sequencing (MethylRAD)

Abstract

The giant panda (Ailuropoda melanoleuca) is a native species to China. They are rare and endangered and are regarded as the ‘national treasure’ and ‘living fossil’ in China. For the time being, there are only about 2500 giant pandas in the world. Therefore, we still have to do much more efforts to protect the giant pandas. In captive wildlife, the cataract incidence of mammalian always increases with age. Currently, in China, the proportion of elderly giant pandas who suffering from cataract has reached 20%. The eye disorder thus has a strong influence on the physical health and life quality of the elderly giant pandas. To discover the genes associated with the pathogenesis of cataract in the elderly giant panda and achieve the goal of early assessment and diagnosis of cataract in giant pandas during aging, we performed whole genome methylation sequencing in 3 giant pandas with cataract and 3 healthy giant pandas using methylation-dependent restriction-site associated DNA sequencing (MethylRAD). In the present study, we obtained 3.62M reads, on average, for each sample, and identified 116 and 242 differentially methylated genes (DMGs) between the two groups under the context of CCGG and CCWGG on genome, respectively. Further KEGG and GO enrichment analyses determined a total of 110 DMGs that are involved in the biological functions associated with pathogenesis of cataract. Among them, 6 DMGs including EEA1, GARS, SLITRK4, GSTM3, CASP3, and EGLN3 have been linked with cataract in old age.

RNA-Seq analysis in giant pandas reveals the differential expression of multiple genes involved in cataract formation

“…Although genetic factors have been identified that promote age-related cataracts, the most important triggers are environmental, particularly oxidative stress and DNA damage [ 7 – 10 ]. We previously compared the DNA methylation status of giant pandas with and without cataracts in an attempt to identify epigenetic effects that might influence the expression of genes associated with cataract formation [ 17 ]. We identified multiple differentially methylated genes with potential roles in cataract-related pathways, including base excision repair, apoptosis and p53 signaling.…”

“…The genes most strongly associated with cataracts therefore include those related to oxidative stress responses, the production of antioxidant enzymes and metabolites, and various DNA repair pathways [ 11 – 13 ]. Previous studies identified changes in DNA methylation associated with cataract formation in several mammals [ 14 – 16 ] and we recently reported that 110 genes with functions relevant to cataract pathogenesis are differentially methylated in giant pandas, including six genes known to be associated with age-related cataracts in humans [ 17 ].…”

A novel missense mutation in the gene encoding major intrinsic protein (MIP) in a Giant panda with unilateral cataract formation

“…This phenomenon has been observed in companion animals: for example, cataract development in dogs is often associated with diabetes, obesity, prolonged use of corticosteroid, excessive exposure to sunlight, or previous eye injury/inflammation [ 52 , 53 ]. It is therefore unclear whether cataracts in captive pandas are age-related acquired or congenital lesions due to the absence of suitable genetic markers [ 54 ]. Here we used a functional candidate gene screening approach to test 11 known cataract-associated genes in giant panda specimens with and without cataracts.…”

A Novel Missense Mutation in the Gene Encoding Major Intrinsic Protein (MIP) in a Giant Panda with Cataracts

“…Although mutations affecting MIP have been shown to cause congenital cataracts in humans and mice, analogous mutations have not been reported in the giant panda (Ailuropoda melanoleuca). These animals tend to develop cataracts in captivity because they live much longer than their counterparts in the wild, but it is often unclear whether these are age-related or congenital lesions due to the absence of suitable disease markers (You et al 2019). Here we used a functional candidate gene screening approach to test for known cataract-associated genes in giant panda specimens with cataracts.…”