Extensive changes in DNA methylation are associated with expression of mutant huntingtin

Abstract

The earliest stages of Huntington disease are marked by changes in gene expression that are caused in an indirect and poorly understood manner by polyglutamine expansions in the huntingtin (HTT) protein. To explore the hypothesis that DNA methylation may be altered in cells expressing mutated HTT, we use reduced representation bisulfite sequencing (RRBS) to map sites of DNA methylation in cells carrying either wild-type or mutant HTT. We find that a large fraction of the genes that change in expression in the presence of mutant huntingtin demonstrate significant changes in DNA methylation. Regions with low CpG content, which have previously been shown to undergo methylation changes in response to neuronal activity, are disproportionately affected. On the basis of the sequence of regions that change in methylation, we identify AP-1 and SOX2 as transcriptional regulators associated with DNA methylation changes, and we confirm these hypotheses using genome-wide chromatin immunoprecipitation sequencing (ChIP-Seq). Our findings suggest new mechanisms for the effects of polyglutamine-expanded HTT. These results also raise important questions about the potential effects of changes in DNA methylation on neurogenesis and cognitive decline in patients with Huntington disease.epigenomics | transcription | mRNA-Seq H untington disease (HD) is a fatal, neurodegenerative disorder caused by an expanded CAG repeat in the huntingtin (HTT) gene, which encodes an abnormally long polyglutamine repeat in the HTT protein. In the early stages of the disease, patients are largely asymptomatic, although they may suffer from mild cognitive impairment and behavioral changes. With time, they develop severe motor dysfunction as well as more pronounced cognitive and psychiatric symptoms. Transcriptional dysregulation is a major component of the early stages of HD, before significant neuronal death. Changes in transcription have been detected in human postmortem tissue (1), mouse models (2-4), and cell culture models (5). Genes reproducibly shown to be differentially expressed across HD models are associated with processes including neurotransmission, neurotrophin receptor signaling, signal transduction, calcium ion transport, synaptic organization, chromatin remodeling, G-protein receptor-coupled signaling, and metabolism (6). The polyglutamine expanded form of HTT may have a direct role in causing these expression changes. A number of DNA-binding proteins have been shown to physically interact with either wild-type or mutant HTT. These include NRSF/REST, CBP, PGC1α, Sp1, BCL11b, p53, LXRα, polycombgroup proteins, SIN3A, and NCOR1 (6). Any effect of HTT on the subcellular localization, activity, or concentration of these proteins would be likely to directly change gene expression.Two lines of evidence suggest that alterations in HTT could also influence DNA methylation. First, histone marks are altered in HD (7-11) and SETD2, a SET domain regulator of H3K36me3, has been previously reported to interact with mutant HTT (12). Due to biochemical...

Plasticity of DNA methylation in a nerve injury model of pain

“…22 An increasing number of reports have further proposed that the methylome-transcriptome relationship cannot be represented by a simple model when considering large, high quality datasets. 10,21,23,36,37 In these studies, positive and negative correlations between methylation alterations and transcriptome changes were found only for a minority of CpGs. It was also suggested that the relationship depends on the CpG-content of the promoter region.…”

“…Based on prior observations by us and others suggesting that (1) HCP genes and LCP genes were regulated differently 13,20,21 and (2) the effects of promoter and gene body methylation diverged, 22,23 we analyzed these scenarios separately. We identified genes that were up-or down-regulated by nerve damage and harbored dDMCs in their promoter or gene body.…”

Epigenetic Mechanisms of Neurodegeneration in Huntington's Disease

“…1). Even though DNA methylation is the most studied epigenetic mechanism to date, epigenetic changes in terms of DNA methylation in HD are just beginning to be explored [44]. If DNA methylation is altered in HD it could affect many different aspects of gene expression because it is a highly conserved process.…”

“…Altered DNA methylation has recently been found in HD patients and HD transgenic mice [44][45][46]. Interestingly, Ng et al [44] showed that the promoter regions of the Ap-1, Sox2, Pax6, and Nes genes are highly methylated, and that expression levels of these genes are significantly reduced.…”

“…Interestingly, Ng et al [44] showed that the promoter regions of the Ap-1, Sox2, Pax6, and Nes genes are highly methylated, and that expression levels of these genes are significantly reduced. Because these genes are directly involved in neurogenesis, DNA methylation-dependent impairment of hippocampal neurogenesis may be casually and mechanistically linked to cognitive decline in HD (Fig.…”