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

Dana M Freeman,Zhibin Wang,Dan Lou,Yanqiang Li,Suzanne N Martos

doi:10.1186/s13072-020-00338-8

Dana M Freeman, Zhibin Wang + Show 3 more

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https://doi.org/10.1186/s13072-020-00338-8

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Abstract

BackgroundAllele-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.ResultsWe 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.ConclusionsOur 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.

Highlights

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
We focused on 207 overlapped regions (i.e., ‘no-rescued DMRs (NORED) + MethylMosaic’ regions) to initiate our investigation
We have shown that non-germline ASMs are dependent on DNA methyltransferase 1 (DNMT1) in mice

Summary

Introduction

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. 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. Investigations demonstrate that two types of genomic regions, imprinted germline ASMs and intracisternal A-particle (IAP)-like retrotransposons, seem vulnerable to environmental factors These two regions are proposed to be pivotal for understanding human disease in response to exposure and popularly pursued in animal and epidemiological studies [32, 51]. The latter is exemplified in mice by the bisphenol A-hypomethylated IAP at the agouti gene for variations of coat color and obesity, as well as by altered methylation of IAPs at AxinFu for tail kinkiness [17, 61, 83]

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