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


Autoři: Yuyan You aff001;  Chao Bai aff001;  Xuefeng Liu aff001;  Maohua Xia aff002;  Ting Jia aff001;  Xiaoguang Li aff002;  Chenglin Zhang aff001;  Yucun Chen aff003;  Sufen Zhao aff001;  Liqin Wang aff004;  Wei Wang aff001;  Yanqiang Yin aff005;  Yunfang Xiu aff003;  Lili Niu aff004;  Jun Zhou aff005;  Tao Ma aff002;  Yang Du aff002;  Yanhui Liu aff002
Působiště autorů: Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China aff001;  Beijing Zoo, Beijing, China aff002;  Strait (Fuzhou) Giant Panda Research and Exchange Centers, Fuzhou, China aff003;  Chengdu Zoo, Chengdu, China aff004;  Chongqing Zoo, Chongqing, China aff005
Vyšlo v časopise: PLoS ONE 14(9)
Kategorie: Research Article
doi: 10.1371/journal.pone.0222292

Souhrn

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.

Klíčová slova:

DNA methylation – DNA-binding proteins – Gene expression – Gene regulation – Immune response – Methylation – Cataracts – Giant pandas


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