Isoform‐specific localization of DNMT3A regulates DNA methylation fidelity at bivalent CpG islands

Massimiliano Manzo,Christina Ambrosi,Tuncay Baubec,Joël Wirz,Rodrigo Villaseñor,Bernd Roschitzki

doi:10.15252/embj.201797038

Abstract

DNA methylation is a prevalent epigenetic modification involved in transcriptional regulation and essential for mammalian development. While the genome‐wide distribution of this mark has been studied to great detail, the mechanisms responsible for its correct deposition, as well as the cause for its aberrant localization in cancers, have not been fully elucidated. Here, we have compared the activity of individual DNMT3A isoforms in mouse embryonic stem and neuronal progenitor cells and report that these isoforms differ in their genomic binding and DNA methylation activity at regulatory sites. We identify that the longer isoform DNMT3A1 preferentially localizes to the methylated shores of bivalent CpG island promoters in a tissue‐specific manner. The isoform‐specific targeting of DNMT3A1 coincides with elevated hydroxymethylcytosine (5‐hmC) deposition, suggesting an involvement of this isoform in mediating turnover of DNA methylation at these sites. Through genetic deletion and rescue experiments, we demonstrate that this isoform‐specific recruitment plays a role in de novo DNA methylation at CpG island shores, with potential implications on H3K27me3‐mediated regulation of developmental genes.

Highlights

DNA methylation is a well-established epigenetic mark involved in gene regulation and genome stability
We have calculated statistically significant enriched regions for each individual DNMT protein, resulting in 3,970 regions exclusively enriched for DNMT3A1, 3,838 for DNMT3A2, 3,432 for DNMT3B, and sites that are shared between the de novo DNMT proteins (Fig EV1A and Appendix Fig S4A)
The de novo DNA methyltransferases DNMT3A and DNMT3B play an important role in mediating site-specific DNA methylation and are required to counteract active and passive removal of DNA methylation (Jackson et al, 2004; Goll & Bestor, 2005; Baubec et al, 2015; Ambrosi et al, 2017)

Summary

Introduction

DNA methylation is a well-established epigenetic mark involved in gene regulation and genome stability. Recent genome-wide initiatives explored the distribution of methylated CpGs in various cell types and tissues at single-base pair resolution (Lister et al, 2009; Stadler et al, 2011; Hon et al, 2013). These datasets were crucial in identifying the frequency and localization of methylated cytosines, and to monitor changes in methylation during cellular transitions, including differentiation in healthy individuals (Schultz et al, 2015) or cellular transformation (Akalin et al, 2012; Hovestadt et al, 2014). The discovery of 5-hydroxymethylcytosine (5-hmC) as an additional modification of mammalian genomes and the characterization of TET-mediated DNA methylation removal (Kriaucionis & Heintz, 2009; Tahiliani et al, 2009; Kohli & Zhang, 2013) provide compelling evidence that DNA methylation is highly dynamic and undergoes constant turnover at regulatory sites (Stroud et al, 2011; Feldmann et al, 2013; Kohli & Zhang, 2013)

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