Many years before the beginning of the Common Era, the ancient Greek philosopher and scientist Aristotle first exclaimed that the “the whole is more than the sum of its parts”. Now, collaborative research led by Wei Li and Margaret A. Goodell (Baylor College of Medicine, Texas, USA) that sought to describe the interplay of epigenetic modifiers in stem cells has proven this statement true! Their synergistic study hoped to decipher how cooperation between the de novo DNA methyltransferase DNMT3A and Ten-eleven translocation methylcytosine dioxygenase TET1 regulates DNA methylation at regulatory regions such as promoters, CpG islands (CGIs), and large under-methylated regions known as canyons/valleys.
So, stop, collaborate and listen…..and we will provide you with all the details of this fantastic joint effort!
- Initial whole genome bisulfite sequencing (WGBS) experiments highlighted the overarching importance of DNMT3A rather than DNMT3B in maintaining global DNA methylation in mESCs
- While mESCs express high levels of the DNMT3A2 isoform, they also express a longer DNMT3A1 isoform that displays unique binding properties
- Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) demonstrated that DNMT3A1 and TET1 display reciprocal binding patterns in mESCs with little overlap
- DNMT3A1 binds exclusively to distal promoters and canyon edges (sites of high DNA methylation)
- TET1 binds to proximal promoters and throughout canyons (sites of low DNA methylation)
- Using the Foxo1 (transcription factor) locus as an example, DNMT3A1 accumulates at canyon edges and doesn’t accumulate at the TSS, while TET1 binds the entire canyon length and the TSS
- The differential binding capacity of these two enzymes may be due to differing levels of CpG density within the different DNA regions
- While TET1 CRISPR/Cas9-facilitated knockout increases DNMT3A1 binding at previously TET1-associated genes, DNMT3A knockout does not significantly affect TET1 binding
- These findings indicate that TET1 serves as an “anchor protein” to establish boundaries for DNMT3A binding to limit the spread of DNA methylation
- Furthermore, analysis of enzyme-knockouts suggests that DNMT3A/TET1 dynamically regulate gene expression in mouse ESCs
- Gene regulatory regions bound by DNMT3A1 and TET1 display high levels of the H3K4me3 and H3K27me3 histone modifications, suggesting that DNMT3A1 and TET1 regulate the expression of bivalent genes
- The authors propose that DNMT3A and TET1 aid the deposition of H3K27me3 by the Polycomb Repressive Complex 2 (PRC2) to inhibit gene expression from bivalent promoters
- Gene expression changes occurring in the DNMT3A/TET1 knockout mESCs correlate with histone modification alterations; the gain of H3K4me3 generally correlates with increased gene expression while the gain of H3K27me3 correlates with decreased gene expression
While the authors highlight how synergism between DNMT3A1 and TET1 helps to regulate both the epigenome and gene expression, they also note that their findings emphasize how the interplay between DNA methylation and histone modifications regulates gene expression, rather than one epigenetic mechanism predominating.
Let’s hope that another 2000 or more years don’t pass until we learn more on how epigenetic teamwork makes the stem cell dream work! For all the details on this collaborative study, see Genome Biology, July 2018!