The conserved DNMT1-dependent methylation regions in human cells are vulnerable to neurotoxicant rotenone exposure

Abstract

Background: Allele-specific DNA methylation (ASM) describes genomic loci that maintain CpG methylation at only one inherited allele rather than having coordinated methylation across both alleles. The most prominent of these regions are germline ASMs (gASMs) that control the expression of imprinted genes in a parent of origin-dependent manner and are associated with disease. However, our recent report reveals numerous ASMs at non-imprinted genes. These non-germline ASMs are dependent on DNA methyltransferase 1 (DNMT1) and strikingly show the feature of random, switchable monoallelic methylation patterns in the mouse genome. The significance of these ASMs to human health has not been explored. Due to their shared allelicity with gASMs, herein, we propose that non-traditional ASMs are sensitive to exposures in association with human disease. Results:We first explore their conservancy in the human genome. Our data show that our putative non-germline ASMs were in conserved regions of the human genome and located adjacent to genes vital for neuronal development and maturation. We next tested the hypothesized vulnerability of these regions by exposing human embryonic kidney cell HEK293 with the neurotoxicant rotenone for 24 h. Indeed,14 genes adjacent to our identified regions were differentially expressed from RNA-sequencing. We analyzed the base-resolution methylation patterns of the predicted non-germline ASMs at two neurological genes, HCN2 and NEFM, with potential to increase the risk of neurodegeneration. Both regions were significantly hypomethylated in response to rotenone. Conclusions:Our data indicate that non-germline ASMs seem conserved between mouse and human genomes, overlap important regulatory factor binding motifs, and regulate the expression of genes vital to neuronal function. These results support the notion that ASMs are sensitive to environmental factors such as rotenone and may alter the risk of neurological disease later in life by disrupting neuronal development.

Epigenetic Vulnerability of Insulator CTCF Motifs at Parkinson’s Disease-Associated Genes in Response to Neurotoxicant Rotenone

“…The methylation status of these allele-specific methylated regions is critical to functional CTCF binding and can explain as much as 41% of its variability (Wang et al, 2012). We have previously identified allele-specific methylated regions in the human genome and verified their sensitivity to rotenone exposure (Martos et al, 2017;Freeman et al, 2020). Therefore, we hypothesized that CTCF binding sites at PD-associated genes would also be vulnerable to rotenone.…”

“…DNA methylation and histone acetylation are epigenetic modifications implicated in rotenone-induced neurotoxicity ( Huang et al, 2019 ). DNA hypomethylation has been reported in response to pesticide exposure ( Hou et al, 2012 ), and we discovered that rotenone reduces DNA methylation at DNMT1-dependent regions in the human genome ( Freeman et al, 2020 ). Histone acetylation patterns have been more extensively studied in rotenone-induced PD due to its high correlation with gene expression and enhancer activation ( Wang et al, 2008 ).…”

Rotenone, an environmental toxin, causes abnormal methylation of the mouse brain organoid's genome and ferroptosis

“…In general, DNA methylation blocks the transcription of genes and reduces their expression levels. Dana M Freeman et al found that non-germline allele-specific DNA methylation seem conserved between mouse and human genomes, which supported the notion that allele-specific DNA methylation are sensitive to environmental factors such as rotenone and may alter the risk of neurological disease later in life by disrupting neuronal development 33 . Gustavo Scola et al reported that rotenone decreased mitochondrial complex I activity and ATP production via increasing levels of 5-methylcytosine and hydroxymethylcytosine, suggesting a possible association between complex I dysfunction and DNA alterations 34 .…”

Folic Acid and Vitamin B12 Prevent Deleterious Effects of Rotenone on Object Novelty Recognition Memory and Kynu Expression in an Animal Model of Parkinson’s Disease

“…DNA methylation influences gene expression through different mechanisms. Those best described include interference with the recognition of DNA motifs by transcription factors (TFs) and the recruitment of specific methyl-CpG-binding proteins, which further recruit co-repressor protein complexes and mediate gene silencing on promoter regions [ 12 , 13 ]. Thus, the homeostasis of this process is fundamental for health [ 11 ].…”