Exaggerated CpH Methylation in the Autism-Affected Brain

Abstract

The etiology of autism, a complex neurodevelopmental disorder, remains largely unexplained. Here, we explore the role of CpG and CpH (H=A, C, or T) methylation within autism-affected cortical brain tissue. While no individual site of methylation was significantly associated with autism after multi-test correction, methylated CpH di-nucleotides were markedly enriched in autism-affected brains (~2-fold enrichment at p <0.05 cut-off, p=0.002). These results further implicate epigenetic alterations in pathobiological mechanisms that underlie autism. Main TextAutism is a heritable neurodevelopmental disorder affecting one in 68 individuals in the United States 1 . Recent genetic studies have identified a handful of genes that contribute to autism 2 and gene expression studies have begun to unravel how altered gene expression manifests within the autistic brain 3,4 ; however, the majority of risk remains unexplained. In addition to genetic causes, epigenetic mechanisms have been proposed to play an important role in the development of the disorder. Three lines of evidence initially supported this hypothesis. First, direct alterations in epigenetic pathways can dramatically alter early embryonic and neonatal neurodevelopment in the same critical periods as autism-associated changes in the brain 5 . Second, mutations in indirect epigenetic effectors can result in autism-spectrum and related disorders, such as Rett syndrome, Fragile X syndrome, and Angelman syndrome 6 . Finally, deficiencies in DNA methylation (DNAm), historically studied in CpG islands in gene promoters as an indicator of transcriptional repression, have previously been implicated in autism [7][8][9] .Initial studies of methylation in autism were limited by the number of sites investigated, a lack of dynamic range in microarrays, the number of samples available for study, and the use of DNA that was procured from cell lines and tissue other than the brain. To gain a more complete picture of altered DNAm in autism, we carried out Reduced Representation Bisulfite Sequencing (RRBS) in 71 post-mortem cortical brain samples (BA19) at single nucleotide resolution with a quantitative measurement of DNAm across CpG-dense regions of the genome 10 . RRBS, in addition to querying methylation at more sites than the previously-used Infinium HumanMethylation450 array (Illumina) 11,12 , enables measurement of methylation at cytosines outside of the classically studied CpG context. While CpH methylation (mCH, where H=A,C, or T) is rare in most tissues, it accumulates in DNA in human and mouse brain postnatally, . CC-BY-NC-ND 4.0 International license It is made available under a (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint . http://dx.doi.org/10.1101/069120 doi: bioRxiv preprint first posted online Aug. 11, 2016; ultimately reaching levels similar to that of CpG methylation (mCG) in brain DNA [13][14][15] . In contrast to mCG, which remains l...

Cord blood DNA methylome in newborns later diagnosed with autism spectrum disorder reflects early dysregulation of neurodevelopmental and X-linked genes

“…Gene lists were sourced from the reported hits of each paper [6,12,[21][22][23][24][25][26][27][28][29][30][37][38][39][40][87][88][89][90][91][92][93][94][95][96][97][98][99][100][101][102][103].…”

Peripheral blood DNA methylation and autism spectrum disorder

“…Several candidate gene-based studies have shown altered epigenetic states associated with autism [13][14][15][16][17][18]. Genome-scale screens have identified changes in DNA methylation (DNAm) at specific CpG sites [19,20] as well as global changes in non-CpG methylation levels [21] in postmortem cerebral tissue from individuals with ASD relative to controls. Studies of cerebral cortex tissue has revealed genomic spreading of histone H3 lysine 4 methylation and histone H3 lysine 27 acetylation marks, away from the promoter region, among a subset of individuals with ASD compared to controls [22,23].…”

DNA methylation signature as a biomarker of major neuropsychiatric disorders

“…The ratio of male/female of the disorder is 4.5 to 1 (192). The concordance of ASD among identical twins is high, suggesting complex inheritance and etiologic role of genetic factors (193,194). A combination of genetic, epigenetic and environmental factors plays important roles in ASD pathogenesis.…”