Demethylation and derepression of genomic retroelements in the skeletal muscles of aged mice

Abstract

Changes in DNA methylation influence the aging process and contribute to aging phenotypes, but few studies have been conducted on DNA methylation changes in conjunction with skeletal muscle aging. We explored the DNA methylation changes in a variety of retroelement families throughout aging (at 2, 20, and 28 months of age) in murine skeletal muscles by methyl‐binding domain sequencing (MBD‐seq). The two following contrasting patterns were observed among the members of each repeat family in superaged mice: (a) hypermethylation in weakly methylated retroelement copies and (b) hypomethylation in copies with relatively stronger methylation levels, representing a pattern of “regression toward the mean” within a single retroelement family. Interestingly, these patterns depended on the sizes of the copies. While the majority of the elements showed a slight increase in methylation, the larger copies (>5 kb) displayed evident demethylation. All these changes were not observed in T cells. RNA sequencing revealed a global derepression of retroelements during the late phase of aging (between 20 and 28 months of age), which temporally coincided with retroelement demethylation. Following this methylation drift trend of “regression toward the mean,” aging tended to progressively lose the preexisting methylation differences and local patterns in the genomic regions that had been elaborately established during the early period of development.

Establishment of Quantitative PCR Assays for Active Long Interspersed Nuclear Element-1 Subfamilies in Mice and Applications to the Analysis of Aging-Associated Retrotransposition

“…Frontiers in Genetics | www.frontiersin.org 6 September 2020 | Volume 11 | Article 519206 widely used for LINE-1 copy number assay (Muotri et al, 2010;Bundo et al, 2014), other quantification approaches such as the Taqman-probes, the peptide nucleic acid-probes, and the droplet digital PCR technique (Newkirk et al, 2020) will improve the sensitivity and the specificity of LINE-1 copy number assay. Increased activity of LINE-1 in aging and senescent cells has been reported (De Cecco et al, 2013Liao and Kennedy, 2016;Giorgi et al, 2018;Min et al, 2019;Saleh et al, 2019;Simon et al, 2019). Our data showing an increased GfII copy number in the basal ganglia of aged Polg +/D257A mice seemed to be in accordance with these previous reports.…”

“…In senescent cells, an increased LINE-1 copy number is concomitant with increased expression of LINE-1, which is driven by increased expression of the activator FOXA1, decreased expression of the repressor RB1, and LINE-1 demethylation (De Cecco et al, 2019;Min et al, 2019). In addition, LINE-1 copy number in the cytosol is further increased by decreased TREX1 3' exonuclease (Thomas et al, 2017;De Cecco et al, 2019).…”

“…However, in addition to cancer (Rodic, 2018), accumulating evidence suggests that aging may be associated with increased LINE-1 activity (Saleh et al, 2019). The expression level and copy number of LINE-1 are increased with aging in liver and muscle tissue in mice (De Cecco et al, 2013;Min et al, 2019) and in senescent cells (De Cecco et al, 2019). An increase in LINE-1 copy number was also reported in the brains of adult rats compared to those of younger rats (Giorgi et al, 2018), and a similar increase was observed in mice with a deficiency in SIRT6, which is a regulator of longevity (Liao and Kennedy, 2016;Simon et al, 2019).…”

Dnmt1 binds and represses genomic retroelements via DNA methylation in mouse early embryos

“…Despite the transcriptional competency of the full-length LINE1 copies, their extremely small fraction among the whole LINE1 population in the genome seldom allows methylation changes to be perceived with a global methylation assay even though DNA methylation changes at these LINE1 5′-UTRs. We indeed observed, from a separate study with mouse skeletal muscle tissues, an age-associated, size-dependent change of DNA methylation among the retroelement copies, which was otherwise not unearthed from the whole copy-based analysis ( 33 ).…”

“…MBD-seq sensitivity and efficiency for each group were confirmed by estimating the relative amount of spike-in DNAs in elutes and flow-through. Illumina sequencing libraries were constructed using the captured DNA fragments as previously described ( 33 ), and sequencing data were generated by NextSeq 550 (Illumina).…”