Epigenetic and genetic variation at the IGF2/H19 imprinting control region on 11p15.5 is associated with cerebellum weight

Abstract

IGF2 is a paternally expressed imprinted gene with an important role in development and brain function. Allele-specific expression of IGF2 is regulated by DNA methylation at three differentially methylated regions (DMRs) spanning the IGF2/H19 domain on human 11p15.5. We have comprehensively assessed DNA methylation and genotype across the three DMRs and the H19 promoter using tissue from a unique collection of well-characterized and neuropathologically-dissected post-mortem human cerebellum samples (n = 106) and frontal cortex samples (n = 51). We show that DNA methylation, particularly in the vicinity of a key CTCF-binding site (CTCF3) in the imprinting control region (ICR) upstream of H19, is strongly correlated with cerebellum weight. DNA methylation at CTCF3 uniquely explains ~25% of the variance in cerebellum weight. In addition, we report that genetic variation in this ICR is strongly associated with cerebellum weight in a parental-origin specific manner, with maternally-inherited alleles associated with a 16% increase in cerebellum weight compared with paternally-inherited alleles. Given the link between structural brain abnormalities and neuropsychiatric disease, an understanding of the epigenetic and parent-of-origin specific genetic factors associated with brain morphology provides important clues about the etiology of disorders such as schizophrenia and autism.

Keywords: :

• DNA Methylation
• brain
• cerebellum
• epigenetic
• expression
• frontal cortex
• genetic
• genomic imprinting
• single nucleotide polymorphism

Disclosure of Potential Conflicts of Interest

No potential conflicts of interest were disclosed.

Ethical Statement

The HTA license number for the LBBND is 12,293. This work is covered by ethical approval from the local NHS ethical review board (REC reference 10/H0808/114).

Acknowledgments

Postmortem brain tissue was donated by the UK Medical Research Council (MRC) London Neurodegenerative Diseases Brain Bank and The Stanley Medical Research Institute (courtesy of Michael B. Knable, E. Fuller Torrey, Maree J. Webster and Robert H. Yolken). R.P. is funded by a Ph.D, studentship from the UK MRC. This work was supported by grants from the US National Institutes of Health (1R01AG036039) and funds from the London University Central Research Fund.

Figures and Tables

Figure 1 Schematic map of the human IGF2/H19 locus on chromosome 11p15.5, with paternal allele (♂) on the top and maternal allele (♀) on the bottom. DMRs are represented by circles: filled circles indicate a typically methylated allele and empty circles a typically unmethylated allele. In the current study, DNA methylation was assessed across amplicons spanning IGF2 DMR0, IGF2 DMR2, the 3rd and 6th CTCF binding sites of the IGF2/H19 ICR DMR (H19 CTCF3, H19 CTCF6), and the H19 promoter. SNPs genotyped are shown as gray triangles (from left to right rs3842773, rs3741211, rs3213221, rs3213223, rs680, rs3168310, rs10732516, rs2071094, rs2107425, rs2839701, rs217727).

Figure 2 Epigenetic variation at the IGF2/H19 ICR is associated with cerebellum weight in post-mortem brain samples. DNA methylation (metC) at H19 CTCF3 is significantly associated with cerebellum weight (r = −0.61, p = 1.55e-05).

Figure 3 Alleles of rs2107425 at H19 CTCF6 show a parental-origin-specific association with cerebellum weight. (A) No difference in cerebellum weight is observed between CC homozygotes and CT heterozygotes not stratified by parental origin (t = 0.184, p = 0.855). (B) CT heterozygotes stratified by the parental-origin of alleles are significantly different (t = −3.11, p = 0.005), with a paternally-inherited T allele being associated with a 16% lower cerebellum weight than a maternally inherited T allele. Bars represent mean ± SEM.

Table 1 Correlations between DNA methylation and total brain weight

Table 2 Correlations between DNA methylation and cerebellum weight