DNA Methylation In The Psychiatric Disorders

Schizophrenia(SCZ),Bipolar Disorder(BDP)and Major Depression Disorder(MDD)are major psychiatric disorders.Psychiatric disorders are complex mental disorders with high heritability(80%),extensive genetic heterogeneity and environmental contributions.Non-Mendelian patterns such as discordant monozygotic twins and parent-of-origin effects also suggest epigenetic mechanisms,including DNA methylation,histone modification,non-coding RNAs and environmental factors in the etiology of psychiatric disorders.Though several candidate genes including COMT,DISC1,NRG1,BDNF and GABRB2 have been found in the recent years,the molecular mechanisms involved in the psychiatric disorder are not fully elucidated.DNA methylation is a key epigenetic mechanism in the developmental regulation of gene expression.DNA methylation alterations are known to contribute to interindividual phenotypic variation and have been related to the onset of major psychiatric disorders.For the GABAA receptor b2 subunit gene GABRB2,positive associations of SNPs and haplotypes located in the Alu-Yi6 region of the non-coding intron 8 and 9 sequences with schizophrenia have been identified in different human populations.Moreover,a genotype-dependent reduction in GABRB2 mRNA expression in schizophrenia results from aberrant imprinting,including allelic expression flipping and alterations in DNA methylation in patients,but the functional mechanisms for the relationships among SNPs,DNA methylation and RNA expression remain unidentified.To improve our understanding of the abnormalities and non-Mendelian inheritance characteristics of schizophrenia,the first part of this study examined DNA methylation(5mC)and hydroxymethylation(5hmC)in the schizophrenia-associated GABRB2 gene encoding the type A y-aminobutyric acid receptor P2 subunit.DNA from the peripheral white blood cells of 279 schizophrenic patients and 256 controls from the Chinese Han population were examined to reveal that significant increase promoter 5mC/5hmC levels in schizophrenia and significant association for SNP rs3811997(C/T)with schizophrenia susceptibility correlations.The promoter 5mC/5hmC levels with the genotypes of single nucleotide polymorphisms(SNPs)were observed with rs3811997(C/T).In schizophrenics,the heterozygous genotypes of rs72815526(C/A)were correlated with increased 5hmC levels whereas the heterozygous genotypes of rs3811997(C/T)were correlated with decreased 5mC levels.When the reporter containing a series of minor alleles of methylation-related SNP rs3811997(C/T),a 1.4-fold increase in promoter activity was observed in the minor T allele of rs3811997(C/T)relative to the major C allele(BPW).These results reveal alterations in GABRB2 genotype-dependent methylation and hydroxymethylation in schizophrenia and help elucidate the genetic-epigenetic interactions influencing schizophrenia.DNA methylation is assumed to be complementary on both alleles across the genome of a diploid cell.However,recent findings indicate allele-specific DNA methylation(ASM),characterized by subtle skewing of DNA methylation between two alleles,is a common feature across human genome including parental-origin-effect allele-specific DNA methylation of imprinted loci,parentally-derived X-chromosome inactivation of the female,and DNA methylation determined by DNA sequence in cis.ASM appears to be both quantitative and heterogenous varying across tissues and individuals,while cis-mediated ASM provides a functional implication for non-coding genetic variations obtained from genome-wide genetic association studies(GWAS)in complex diseases such as psychiatric disorders.To explore cis-mediated ASM involved in the phenotypic variation of psychiatric disorder,we performed a genome-wide methylated DNA immune precipitation sequencing(MeDIP-seq)and RNA-sequencing using whole blood derived DNA from 17 pairs of monozygotic twins including 8 twins discordant for psychiatric disorders,5 twins concordant for psychiatric disorders and 4 twins for healthy control.Disease-associated differentially methylation regions(DMRs)analysis showed that 2301 genes from Top5000 were annotated in the regions of gene promoter or gene body.Patients and healthy subjects could be clearly divided into two groups based on the Top5000 DMRs hierarchical cluster analysis.Top5000 DMRs were enriched in the mental illness associated transcription factor binding motif(TFBM),enhancer and transcriptional active regions of chromatin state.Top5000 DMRs were enriched in the schizophrenia associated different methylation regions and different expression genes in brain.More importantly,we screened 605 psychiatric-related ASM(PSY-ASM)sites including 530 genetic-independent and 86 genetic-dependent ASM sites,which displayed a significant difference in ASM pattern between patients and controls.Significant enrichment of PSY-ASM sites in TFBS,DNase I hypersensitive sites,enhancer region and SCZ-GWAS SNPs.Out of 605 PSY-ASM sites,318 were identified as regulatory SNPs(rSNPs)by rSNPBase database.117 out of 318 ASM sites were identified as privous reported brain eQTLs(expression quantitative trait loci)and regulated concordant target gene transcription in rSNPBase database.Out of 117 ASM sites,we identified 11 ASM sites showed transcription factor binding alterlation due to its allele variation,3 sites 1 showed miRNA binding alterlation due to its allele variation,9 sites located in the enhancer regions and 17 sites overlapped within the SCZ-GWAS locis.We found 63 genes overlapped within the gene list of psychiatric related DMRs and ASMs,and the binding region of CTCF and EBF1 were co-enriched in the gene list of DMRs and ASM loci.The correlation analysis of RNA expression and DNA methylation identified 8 eQTMs(methylation-expression associations)and 16 eQTASMs(ASM-expression associations)associated with psychiatric disorders.In conclusion,the present study examined the role of cis-mediated DNA methylations in GABRB2 gene and genome-wide ASM in the development of psychiatric disorders,and contributed to our understanding about interplay between genetic and epigenetic factors in mediating phenotypic variations associated with psychiatric disorder susceptibility.