Analysis of Reduced-Representation DNA Methylome and Transcriptome in Spontaneous Primary Age-related Cataract of Microtus fortis

Abstract Cataract is a major cause of visual impairment worldwide, and the underlying pathogenesis is not yet fully understood. In this study, the DNA methylation and transcription profiles of lens of primary age-related cataract (ARC) and healthy M. fortis were generated by reduced representation bisulfite sequencing (RRBS) and RNA sequencing (RNA-seq), to identify potential epigenetic biomarkers of ARC. Compared with the healthy M. fortis , 1903 significantly hypermethylated and 15297 hypomethylated differentially methylated regions (DMRs) were identified in the lens of cataract M. fortis. Pathway enrichment analyses reveal these DMR-associated genes were mainly enriched in nervous-related pathways, small guanosine triphosphatases (GTPase) binding, actin binding, wnt signaling pathway and calcium signaling pathway. And transcriptome analysis revealed 5792 DEGs in the cataract M. fortis compared with healthy M. fortis , including 3218 significantly upregulated and 2574 significantly downregulated genes. These DEGs were mainly enriched in ribosome-related pathways, JAK-STAT signaling pathway, and cytoskeleton in muscle cells. Furthermore, 147 upregulated genes with promoter hypomethylation and 51 downregulated genes with promoter hypermethylation in their promoter regions were obtained by integrated analysis of methylome and transcriptome. And these DEGs were mainly enriched in hypoxia-inducible factor-1 (HIF-1) signaling pathway, ferric iron binding, actin binding, small GTPase binding and JAK-STAT signaling pathway. Moreover, IGV results showed multiple genes including chemokine C-X-C motif Ligand 1 ( CXCL1) , granulocyte colony-stimulating factor ( CSF3) , transferrin ( TF) and RHOB genes exhibited markedly lower methylation levels in promoter regions, and transcription of these genes was upregulated in lens of cataract M. fortis . Crystallin gamma C ( CRYGC) , gap junction protein alpha 3 ( GJA3 ) genes exhibited markedly higher methylation levels in the cataract group, and the transcription of these genes in the cataract group was significantly lower than that in the control group. As a result, our findings indicated that aberrant DNA methylation is closely associated with the cataract formation and might provide a basis for future mechanistic studies of ARC.