Comparative profiles of DNA methylation and differential gene expression in osteocytic areas from aged and young mice

Abstract

Altered DNA methylation upon ageing may result in many age‐related diseases such as osteoporosis. However, the changes in DNA methylation that occur in cortical bones, the major osteocytic areas, remain unknown. In our study, we extracted total DNA and RNA from the cortical bones of 6‐month‐old and 24‐month‐old mice and systematically analysed the differentially methylated regions (DMRs), differentially methylated promoters (DMPs) and differentially expressed genes (DEGs) between the mouse groups. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the DMR‐related genes revealed that they were mainly associated with metabolic signalling pathways, including glycolysis, fatty acid and amino acid metabolism. Other genes with DMRs were related to signalling pathways that regulate the growth and development of cells, including the PI3K‐AKT, Ras and Rap1 signalling pathways. The gene expression profiles indicated that the DEGs were mainly involved in metabolic pathways and the PI3K‐AKT signalling pathway, and the profiles were verified through real‐time quantitative PCR (RT‐qPCR). Due to the pivotal roles of the affected genes in maintaining bone homeostasis, we suspect that these changes may be key factors in age‐related bone loss, either together or individually. Our study may provide a novel perspective for understanding the osteocyte and its relationship with osteoporosis during ageing.Significance of the studyOur study identified age‐related changes in gene expressions in osteocytic areas through whole‐genome bisulfite sequencing (WGBS) and RNA‐seq, providing new theoretical foundations for the targeted treatment of senile osteoporosis.

Analysis of DNA Methylation Profiles in Mandibular Condyle of Chicks With Crossed Beaks Using Whole-Genome Bisulfite Sequencing

“…However, there were differences among three mC contexts which might be related to differences in the sequences of different genetic elements ( Fang et al, 2017 ). Approximately 4.3% of cytosine sites were methylated, which is lower than the cortical bones in mice from 6.06 to 6.48% ( Wei et al, 2020 ). The highest proportion of CG methylation in this study was similar to that found in other species ( Wei et al, 2020 ) and tissues ( Li C. W. et al, 2015 ; Li J. X. et al, 2015 ; Zhang et al, 2018 ; Tan et al, 2020 ).…”

“…Approximately 4.3% of cytosine sites were methylated, which is lower than the cortical bones in mice from 6.06 to 6.48% ( Wei et al, 2020 ). The highest proportion of CG methylation in this study was similar to that found in other species ( Wei et al, 2020 ) and tissues ( Li C. W. et al, 2015 ; Li J. X. et al, 2015 ; Zhang et al, 2018 ; Tan et al, 2020 ). Among the gene functional regions, TSSs presented the lowest methylation levels, which was consistent with the results in chickens’ liver ( Tan et al, 2020 ) and blood ( Zhang et al, 2018 ), but inconsistent in cortical bones of mice ( Wei et al, 2020 ).…”

Prioritization of Genes Relevant to Bone Fragility Through the Unbiased Integration of Aging Mouse Bone Transcriptomics and Human GWAS Analyses

“…Here, we analyzed cortical bone gene expression across four time points, the longest of which is older than prior analyses. (56,57) Relative to pairwise analysis of two time points, the continuous analysis of all four time points increased statistical power in identifying differentially expressed genes and revealed nine distinct temporal patterns of gene expression. Reassuringly, the results of pathway analysis using the pairwise and continuous approaches were largely similar and also correspond to prior analysis of gene expression in 19-week-versus 19-month-old mouse cortical bone, (56) with an age-dependent decrease in Wnt signaling and increase in immunomodulatory cytokine signaling.…”

Benchmarking DNA methylation analysis of 14 alignment algorithms for whole genome bisulfite sequencing in mammals

“…More recently, WGBS is at the forefront of epigenetic analysis and popularly utilized to investigate the genome-wide DNA methylation dynamics of mammalian developments [15] , [16] as well as the epigenetic marks of diseases [17] . But the bisulfite treatment converts unmethylated cytosine as thymine, reduces the complexity of reads, and thus causes a mapping challenge to aligners in WGBS [18] .…”