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

English version

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
prolekare.web.journal.doi_sk: https://doi.org/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 – Gene expression – Methylation – DNA-binding proteins – Gene regulation – Immune response – Cataracts – Giant pandas

Zdroje

1. Uno HJA. Age-related pathology and biosenescent markers in captive rhesus macaques. Age. 1997; 20:1–13. doi: 10.1007/s11357-997-0001-5 23604287

2. Asbell PA, Dualan I, Mindel JS, Brocks D, Ahmad M, Epstein SPJTL. Age-related cataract. The Lancet. 2005; 365:599–609.

3. Urfer SR, Greer K, Wolf NS. Age-related cataract in dogs: a biomarker for life span and its relation to body size. Age. 2011; 33:451–60. doi: 10.1007/s11357-010-9158-4 20607428

4. Truscott RJWJEER. Age-related nuclear cataract-oxidation is the key. Experimental Eye Research. 2005; 80:709–25. doi: 10.1016/j.exer.2004.12.007 15862178

5. Jin Y, Lin W, Huang S, Zhang C, Pu T, Ma W, et al. Dental Abnormalities in Eight Captive Giant Pandas (Ailuropoda melanoleuca) in China. Journal of Comparative Pathology. 2012; 146:357–64. doi: 10.1016/j.jcpa.2011.08.001 21906751

6. Jin Y, Chen S, Chao Y, Pu T, Xu H, Liu X, er al. Dental Abnormalities of Eight Wild Qinling Giant Pandas (Ailuropoda Melanoleuca Qinlingensis), Shaanxi Province, China. Journal of Wildlife Disease. 2015;51:849–59.

7. Hammond CJ, Duncan DD, Snieder H, De Lange M, West SK, Spector TD, et al. The heritability of age-related cortical cataract: The twin eye study. Investigative Ophthalmology & Visual Science. 2001; 42:601–5.

8. Ottonello S, Foroni C, Carta A, Petrucco S, Maraini GJO. Oxidative Stress and Age-Related Cataract. Ophthalmologica. 2000; 214:78–85. doi: 10.1159/000027474 10657746

9. Ho M, Peng Y, Chen S, Chiou SJJoCG, Geriatrics. Senile cataracts and oxidative stress. Journal of Clinical Gerontology and Geriatrics. 2010;1:17–21.

10. Tinaztepe OE, Ay M, Eser EJCER. Nuclear and Mitochondrial DNA of Age-Related Cataract Patients Are Susceptible to Oxidative Damage. Current Eye Research. 2017; 42:1–6. doi: 10.1080/02713683.2016.1175019

11. Billingsley G, Santhiya ST, Paterson AD, Ogata K, Wodak SJ, Hosseini SM, et al. CRYBA4, a Novel Human Cataract Gene, Is Also Involved in Microphthalmia. American Journal of Human Genetics. 2006; 79:702–9. doi: 10.1086/507712 16960806

12. Hasanova N, Kubo E, Kumamoto Y, Takamura Y, Akagi YJBJoO. Age-related cataracts and Prdx6: correlation between severity of lens opacity, age and the level of Prdx 6 expression. British Journal of Ophthalmology. 2009; 93:1081–4. doi: 10.1136/bjo.2008.152272 19429582

13. Zhang Y, Zhang L, Sun D, Li Z, Wang L, Liu PJMV. Genetic polymorphisms of superoxide dismutases, catalase, and glutathione peroxidase in age-related cataract. Molecular Vision. 2011; 17:2325–32. 21921984

14. Kim JK, Samaranayake M, Pradhan SJC, Sciences ML. Epigenetic mechanisms in mammals. Cellular and Molecular Life Sciences. 2009; 66:596–612. doi: 10.1007/s00018-008-8432-4 18985277

15. Xiao F, Kong Q, Perry B, He Y. Progress on the role of DNA methylation in aging and longevity. Briefings in Functional Genomics. 2016; 15:454–9. doi: 10.1093/bfgp/elw009 27032421

16. Liu X, Luo Y, Zhou P, Lu YJIO, Science V. DNA methylation mediated and oxidative stress related genes CRYAA and GJA3 in nuclear age-related cataract (ARC) and its mechanism. Investigative Ophthalmology & Visual Science. 2015; 56:5877.

17. Zhou P, Luo Y, Liu X, Fan L, Lu YJTFJ. Down-regulation and CpG island hypermethylation of CRYAA in age-related nuclear cataract. The FASEB Journal. 2012; 26:4897–902. doi: 10.1096/fj.12-213702 22889833

18. Wang Y, Li F, Zhang G, Kang L, Qin B, Guan HJCER. Altered DNA Methylation and Expression Profiles of 8-Oxoguanine DNA Glycosylase 1 in Lens Tissue from Age-related Cataract Patients. Current Eye Research. 2015; 40:815–21. doi: 10.3109/02713683.2014.957778 25310012

19. Wang S, Lv J, Zhang L, Dou J, Sun Y, Li X, et al. MethylRAD: a simple and scalable method for genome-wide DNA methylation profiling using methylation-dependent restriction enzymes. Open Biology. 2015; 5:150130. doi: 10.1098/rsob.150130 26581575

20. Li R, Yu C, Li Y, Lam TW, Yiu S, Kristiansen K, et al. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics. 2009; 25:1966–7. doi: 10.1093/bioinformatics/btp336 19497933

21. Shu X, Shu S, Cheng H, Tang S, Yang L, Li H, et al. Genome-Wide DNA Methylation Analysis During Palatal Fusion Reveals the Potential Mechanism of Enhancer Methylation Regulating Epithelial Mesenchyme Transformation. DNA and Cell Biology. 2018; 37:560–73. doi: 10.1089/dna.2018.4141 29608334

22. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010; 26:139–40. doi: 10.1093/bioinformatics/btp616 19910308

23. Cingolani P, Platts AE, Wang LL, Coon M, Nguyen T, Wang L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff. Fly. 2012; 6:80–92. doi: 10.4161/fly.19695 22728672

24. Quinlan AR, Hall IMJB. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010; 26:841–2. doi: 10.1093/bioinformatics/btq033 20110278

25. Kanehisa M, Goto SJNAR. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 1999; 28:27–30.

26. Ashburner M, Ball CA, Blake JA, Botstein D, Butler HL, Cherry JM, et al. Gene ontology: tool for the unification of biology. Nature Genetics. 2000; 25:25–9. doi: 10.1038/75556 10802651

27. Davis AP, King BL, Mockus S, Murphy CG, Saracenirichards CA, Rosenstein MT, et al. The Comparative Toxicogenomics Database: update 2011. Nucleic Acids Res. 2011; 39:1067–72.

28. Li BY, Han JA, Im JS, Morrone A, Johung K, Goodwin EC, et al. Senescence-associated β-galactosidase is lysosomal β-galactosidase. Aging Cell. 2006; 5:187–95. doi: 10.1111/j.1474-9726.2006.00199.x 16626397

29. Lawless C, Wang C, Jurk D, Merz A, Zglinicki T, Passos J. Quantitative assessment of markers for cell senesence. Experimental Gerontology. 2010; 45:772–8. doi: 10.1016/j.exger.2010.01.018 20117203

30. Charakidas A, Kalogeraki A, Tsilimbaris MK, Koukoulomatis P, Brouzas D, Delides GJEJoO. Lens epithelial apoptosis and cell proliferation In human age-related cortical cataract. European Journal of Ophthalmology. 2005; 15:213–20. doi: 10.1177/112067210501500206 15812762

31. Ji WJIO, Science V. αA-Crystallin Regulates p53-Mediated Signaling Pathway to Prevent Apoptosis of Lens Epithelial Cells and Cataractogenesis. Investigative Ophthalmology & Visual Science. 2012; 53:1043–1043.

32. Li B, Zhou J, Zhang G, Wang Y, Kang L, Wu J, et al. Relationship Between the Altered Expression and Epigenetics of GSTM3 and Age-Related Cataract. Investigative Ophthalmology & Visual Science. 2016; 57:4721–32.

33. Dor Y, Cedar HJTL. Principles of DNA methylation and their implications for biology and medicine. The Lancet. 2018; 392:777–786.

34. Doshna CW, Fortner JH, Pfohl JC, Aleo, Tengowski MW, Verdugo MEJIO, Science V. Investigation of the Role of Apoptosis in Drug-induced Cataract Formation. Investigative Ophthalmology & Visual Science. 2002; 43:2377.

35. Galichanin K, Svedlund J, Soderberg PGJEER. Kinetics of GADD45α, TP53 and CASP3 gene expression in the rat lens in vivo in response to exposure to double threshold dose of UV-B radiation. Experimental Eye Research. 2012; 97:19–23. doi: 10.1016/j.exer.2012.02.003 22559303

36. Mou K, Liu W, Han D, Li PJJoDS. HMGB1/RAGE axis promotes autophagy and protects keratinocytes from ultraviolet radiation-induced cell death. Journal of Dermatological Science. 2017; 85:162–9. doi: 10.1016/j.jdermsci.2016.12.011 28012822

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

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