Genome-wide investigation of the dynamic changes of epigenome modifications after global DNA methylation editing

Abstract

Chromatin properties are regulated by complex networks of epigenome modifications. Currently, it is unclear how these modifications interact and if they control downstream effects such as gene expression. We employed promiscuous chromatin binding of a zinc finger fused catalytic domain of DNMT3A to introduce DNA methylation in HEK293 cells at many CpG islands (CGIs) and systematically investigated the dynamics of the introduced DNA methylation and the consequent changes of the epigenome network. We observed efficient methylation at thousands of CGIs, but it was unstable at about 90% of them, highlighting the power of genome-wide molecular processes that protect CGIs against DNA methylation. Partially stable methylation was observed at about 1000 CGIs, which showed enrichment in H3K27me3. Globally, the introduced DNA methylation strongly correlated with a decrease in gene expression indicating a direct effect. Similarly, global but transient reductions in H3K4me3 and H3K27ac were observed after DNA methylation but no changes were found for H3K9me3 and H3K36me3. Our data provide a global and time-resolved view on the network of epigenome modifications, their connections with DNA methylation and the responses triggered by artificial DNA methylation revealing a direct repressive effect of DNA methylation in CGIs on H3K4me3, histone acetylation, and gene expression.

Sequence determinants, function, and evolution of CpG islands

“…The inefficacy of 5mC to act as a dominant repressive mechanism is further supported by in vivo experiments in Xenopus embryos, which demonstrated that methylated CpG-rich promoter-reporter gene constructs are robustly expressed at late-blastula and gastrula stages [ 65 ]. Two different studies, which employed precise epigenome editing to target the catalytic domain of DNMT3A to CpG-rich genomic locations via a zinc finger effector, came to different conclusions related to the repressive potential of 5mC at CGIs [ 66 , 67 ]. While one study observed efficient 5mC-mediated gene repression [ 66 ], the other revealed varying effects including the compatibility of 5mC, H3K4me3 and RNA polymerase II at numerous genomic loci [ 67 ].…”

“…Two different studies, which employed precise epigenome editing to target the catalytic domain of DNMT3A to CpG-rich genomic locations via a zinc finger effector, came to different conclusions related to the repressive potential of 5mC at CGIs [ 66 , 67 ]. While one study observed efficient 5mC-mediated gene repression [ 66 ], the other revealed varying effects including the compatibility of 5mC, H3K4me3 and RNA polymerase II at numerous genomic loci [ 67 ]. Notably, these two studies were not carried out in the same cell line.…”

Functional Analysis of Non-Genetic Resistance to Platinum in Epithelial Ovarian Cancer Reveals a Role for the MBD3-NuRD Complex in Resistance Development

“…ChIP was performed as previously described [24]. In brief, 2.5 × 10 6 cells were harvested and washed with PBS supplemented with 500 nM Trichostatin A.…”

Current trends in toxicoepigenomics research, limitations and future perspective

“…The DNA methylation analysis investigations, for example, were conducted on human samples, whereas the miRNA research was primarily dominated by in vitro experiments. Based on current trends in toxicoepigenomics research, numerous gaps have been identified that must be filled to fully understand the molecular mechanisms behind toxicant-related epigenetic alterations [10,11]. The consistency of epigenetic modifications happening in the experimental platform and the type of designed study such as in vitro, in vivo, and human investigations, as well as the relevance of such epigenetic alterations in changing the risk of disease in the exposed populations.…”