Equivalent DNA methylation variation between monozygotic co-twins and unrelated individuals reveals universal epigenetic inter-individual dissimilarity

Abstract

Background Although the genomes of monozygotic twins are practically identical, their methylomes may evolve divergently throughout their lifetime as a consequence of factors such as the environment or aging. Particularly for young and healthy monozygotic twins, DNA methylation divergence, if any, may be restricted to stochastic processes occurring post-twinning during embryonic development and early life. However, to what extent such stochastic mechanisms can systematically provide a stable source of inter-individual epigenetic variation remains uncertain until now. Results We enriched for inter-individual stochastic variation by using an equivalence testing-based statistical approach on whole blood methylation microarray data from healthy adolescent monozygotic twins. As a result, we identified 333 CpGs displaying similarly large methylation variation between monozygotic co-twins and unrelated individuals. Although their methylation variation surpasses measurement error and is stable in a short timescale, susceptibility to aging is apparent in the long term. Additionally, 46% of these CpGs were replicated in adipose tissue. The identified sites are significantly enriched at the clustered protocadherin loci, known for stochastic methylation in developing neurons. We also confirmed an enrichment in monozygotic twin DNA methylation discordance at these loci in whole genome bisulfite sequencing data from blood and adipose tissue. Conclusions We have isolated a component of stochastic methylation variation, distinct from genetic influence, measurement error, and epigenetic drift. Biomarkers enriched in this component may serve in the future as the basis for universal epigenetic fingerprinting, relevant for instance in the discrimination of monozygotic twin individuals in forensic applications, currently impossible with standard DNA profiling.

Tissue- and ethnicity-independent hypervariable DNA methylation states show evidence of establishment in the early human embryo

“…We analysed CpGs identified as being ‘equivalently variable’ between MZ co-twins and between unrelated individuals (‘evCpGs (blood)’) by Planterose Jiménez et al. ( 53 ) using Illumina450K data in whole blood. 154 of these evCpGs replicated in adipose tissue from 97 MZ twin pairs (‘evCpGs (blood & adipose)’).…”

Tissue- and ethnicity-independent hypervariable DNA methylation states show evidence of establishment in the early human embryo

“…Hypervariable methylation states at the cPCDH gene locus may therefore be driven by early developmental and/or aging effects. Noting that evCpGs and MZ twinning CpGs (Table 2) have also been reported to colocalise with this locus 45,81 , hvCpGs annotated to cPCDH genes were ~8.5-fold enriched for MZ twinning CpGs (FET p-value = 1.04 x 10 -22 ) and ~3-fold enriched for evCpGs (FET p-value = 1.6 x 10 -3 ) relative to hvCpGs that were not.…”

“…We analysed CpGs identified as being 'equivalently variable' between MZ co-twins and between unrelated individuals ('evCpGs (blood)') by Planterose Jiménez et al 45 using Illumina450K data in whole blood. 154 of these evCpGs replicated in adipose tissue from 97 MZ twin pairs ('evCpGs (blood & adipose)').…”

“…To further probe the influence of genetic effects on hvCpG methylation we examined the overlap between hvCpGs and CpGs that show DNAm variation between monozygotic (MZ) co-twins that is equivalently variable (ev) to that between unrelated individuals, suggestive of genetically independent variable methylation establishment after MZ twin splitting 45 . In total, hvCpGs comprise 122 (42%) of the 317 evCpGs identified in blood (1.9-fold enrichment relative to distribution-matched controls) and 62% of those that were replicated as evCpGs in adipose tissue (2.8-fold enrichment relative to controls) (Supplementary Table 11), supporting the notion that hvCpGs are likely influenced but not determined by genetic variation in multiple tissues.…”

Long-term temporal stability of peripheral blood DNA methylation alterations in patients with inflammatory bowel disease

“…Previous literature has shown that the intra-individual variability of DNA methylation is most prominent during the early stages of life, which gradually diminishes and presents a more stable phenotype after 5 years of life 24, 25 . Nonetheless, the influence of ageing on genome-wide DNA methylation has been well-described in monozygotic twins 26, 27 and unrelated healthy populations 28, 29 , demonstrating a global decrease in methylation as individuals age, as well as site-specific increases in methylation in CpG-rich areas, both of which are thought to result from dynamic external and internal environmental changes 30–32 . As epigenetics and thus DNA methylation, is cell-type specific, observed differences found in heterogeneous populations such as PBL or tissue might reflect differences in the cellular composition 33–35 .…”