Methylation pattern of polymorphically imprinted nc886 is not conserved across mammalia

Abstract

Background In humans, the nc886 locus is a polymorphically imprinted metastable epiallele. Periconceptional conditions have an effect on the methylation status of nc886, and further, this methylation status is associated with health outcomes in later life, in line with the Developmental Origins of Health and Disease (DOHaD) hypothesis. Animal models would offer opportunities to study the associations between periconceptional conditions, nc886 methylation status and metabolic phenotypes further. Thus, we set out to investigate the methylation pattern of the nc886 locus in non-human mammals. Data We obtained DNA methylation data from the data repository GEO for mammals, whose nc886 gene included all three major parts of nc886 and had sequency similarity of over 80% with the human nc886. Our final sample set consisted of DNA methylation data from humans, chimpanzees, bonobos, gorillas, orangutangs, baboons, macaques, vervets, marmosets and guinea pigs. Results In human data sets the methylation pattern of nc886 locus followed the expected bimodal distribution, indicative of polymorphic imprinting. In great apes, we identified a unimodal DNA methylation pattern with 50% methylation level in all individuals and in all subspecies. In Old World monkeys, the between individual variation was greater and methylation on average was close to 60%. In guinea pigs the region around the nc886 homologue was non-methylated. Results obtained from the sequence comparison of the CTCF binding sites flanking the nc886 gene support the results on the DNA methylation data. Conclusions Our results indicate that unlike in humans, nc886 is not a polymorphically imprinted metastable epiallele in non-human primates or in guinea pigs, thus implying that animal models are not applicable for nc886 research. The obtained data suggests that the nc886 region may be classically imprinted in great apes, and potentially also in Old World monkeys, but not in guinea pigs.

Non-coding 886 (nc886/vtRNA2-1), the epigenetic odd duck – implications for future studies

“…B) Schematic presentation of the nc886 gene, nc886 DMR and the CTCF-binding sites flanking the DMR. The telomeric CTCF-38 binding site has been suggested to interact with another binding site near the IL9 gene, bringing a suggested enhancer region close to the nc886 gene 1,27 . Made with BioRender.com.…”

“…The Dicer-dependent, but Dosha-independent production of the small RNAs derived from this region was later verified by Miñones-Moyano et al and Fort et al 9,16 . However, Fort et al demonstrated that the produced small RNAs associate with Argonaute, satisfying the attributes of miRNA, and further hypothesised that the suggested recent evolutionary origin of the nc886 gene would be the reason for the poor efficiency of Dicer to produce the mature miRNAs 9,27 . This work was again followed by the work of Lee et al describing the issues arising from the classification of nc886 as miRNA and further emphasising their previous view of nc886 being distinct from pre-miRNAs 10 .…”

Methylation status of VTRNA2-1/nc886 is stable across human populations, monozygotic twin pairs and in majority of somatic tissues

“…Currently, no animal models are available to study nc886 , as most species, including mice and rats, do not harbour the gene, and in species harbouring the nc886 gene, the locus is not polymorphically imprinted (26). Thus, we wanted to utilise available resources, the numerous existing DNA methylation datasets from humans, to gain insight on the methylation of nc886 , a unique polymorphically imprinted gene and a potential molecular mediator of DOHaD.…”

Methylation status of VTRNA2-1 / nc886 is stable across populations, monozygotic twin pairs and in majority of tissues

“…We found they present either intermediate methylation levels (methylation beta value 0.20-0.40; i.e., methylation level of 20-40%, in approximately 1-5% of the population) or methylation beta values >0.60 (methylation level of >60%), indicating that also the paternal allele has gained methylation in somatic tissues (in ∼0.1% of the population) [11]. The nc886 locus, flanked by two CTCF-binding sites, suggested to be important for its imprinting [14], codes for a 102nt long noncoding RNA, which might then be cleaved into miRNA-like short noncoding RNAs, although the nature of these RNAs is still widely debated [15,16].…”

“…In vitro methods are of limited feasibility, as both carcinogenesis [13] and pluripotency induction [11] have an effect on the methylation pattern at the nc886 locus. Currently, no animal models are available to study nc886 because most species, including mice and rats, do not harbor the gene, and in species harboring the nc886 gene, the locus is not polymorphically imprinted [14]. Thus, we wanted to use available resources -the numerous existing DNA methylation datasets from humans -to gain insight on the methylation of nc886, a unique polymorphically imprinted gene and a potential molecular mediator of DOHaD.…”