Mechanisms of DNA Methylation Regulatory Function and Crosstalk with Histone Lysine Methylation

Abstract

DNA methylation is a well-studied epigenetic modification that has key roles in regulating gene expression, maintaining genome integrity, and determining cell fate. Precisely how DNA methylation patterns are established and maintained in specific cell types at key developmental stages is still being elucidated. However, research over the last two decades has contributed to our understanding of DNA methylation regulation by other epigenetic processes. Specifically, lysine methylation on key residues of histone proteins has been shown to contribute to the allosteric regulation of DNA methyltransferase (DNMT) activities. In this review, we discuss the dynamic interplay between DNA methylation and histone lysine methylation as epigenetic regulators of genome function by synthesizing key recent studies in the field. With a focus on DNMT3 enzymes, we discuss mechanisms of DNA methylation and histone lysine methylation crosstalk in the regulation of gene expression and the maintenance of genome integrity. Further, we discuss how alterations to the balance of various sites of histone lysine methylation and DNA methylation contribute to human developmental disorders and cancers. Finally, we provide perspectives on the current direction of the field and highlight areas for continued research and development.

Keywords: DNA methylation; cancer; gene regulation; histone methylation; neurodevelopmental disorders.

Figure 1. DNA Methylation overview.

Schematic representation of DNA methylation establishment and maintenance. Enzymes denoted in black font refer to their well-studied, primary functions. Enzymes denoted in grey font refer to their more recently discovered, secondary functions. Created with Biorender.com

Figure 2:. DNMT domain map.

Annotated domain structure of mammalian DNMT proteins. Two isoforms are shown for DNMT3A that are produced by alternative promoter usage. Three isoforms are shown for DNMT3B that are produced by alternative splicing. Abbreviations used: DMAP – DNA methyltransferase associated protein 1 interacting domain. NLS – nuclear localization signal. RFTS – replication foci targeting sequence. BAH1/2 – bromo-adjacent homology domains 1 and 2. UDR – ubiquitin-dependent recruitment. ADD – ATRX-DNMT3-DNMT3L domain. MTase – methyltransferase. Created with Biorender.com

Figure 3:. DNA methylation and histone lysine methylation crosstalk.

(A) At actively transcribed genes, H3K4me3 deposition at promoters prevents DNA methylation deposition by DNMT3A/B. Intragenic deposition of H3K36me3 by SETD2 promotes intragenic DNA methylation deposition by DNMT3B. (B) Intragenic DNA methylation regulates alternative promoter usage. Loss of H3K4me3 allows DNMT3A/B to deposit DNA methylation near the canonical transcription start site while downstream loss of DNA methylation promotes usage of intragenic promoter sites. (C) Large domains of H3K36me2 in intergenic regions promote DNA methylation deposition by DNMT3A. (D) DNA methylation and H3K9me3 work cooperatively to maintain constitutive heterochromatin. Created with Biorender.com

Figure 4:. Imbalance of DNA methylation and histone lysine methylation drives molecular pathogenesis in human developmental disorders.

(A) Loss of H3K4 KMT function or loss of H3K27 lysine demethylase function leads to an imbalance of bivalent chromatin and site-specific alterations to DNA methylation. Loss of DNMT3A or DNMT3B methyltransferase and/or histone reader function also gives rise to DNA methylation defects. These molecular outcomes are characteristic of a group of distinct, but related developmental disorders that exhibit delayed growth and impaired mental development. (B) Levels of H3K27 and H3K36 methylation are antagonistic to one another. In wildtype cells these two PTMs are at equilibrium to ensure proper genome regulation. Loss of KMT function leads to an imbalance of methylation on H3K27 and H3K36 as well as alterations to DNA methylation. The dotted arrows represent the flux between levels of H3K27 and H3K36 methylation when their respective KMTs are mutated. Loss of DNMT3A function also leads to DNA methylation defects. Collectively, these molecular consequences give rise to a spectrum of developmental disorders referred to as overgrowth and intellectual disability syndromes. Syndrome names are color-coded according to their associated KMT or DNMT driver mutations. Created with Biorender.com

Figure 5:. Alterations to DNA methylation and histone lysine methylation in cancer formation.

Context-specific alterations to DNA methylation and imbalances of histone lysine methylation collectively contribute to carcinogenesis and leukemogenesis. Specifically, mutations that disrupt DNMT3A catalytic activity and/or histone lysine methylation reader function lead to DNA hypo- and hypermethylation, depending on the cancer type. Similarly, mutations which disrupt PRC2 catalytic activity or chromosomal rearrangements involving KMT2A lead to an imbalance of bivalent chromatin which may lead to pathogenic gene expression programs that promote a stem-like cellular state. Mutations across the SETD2 coding region prevent its function in key cellular processes such as DNA repair, ultimately leading to increased mutability and genomic instability. Additional mutations to PRC2 or NSD1/2 disrupt the balance between H3K27 and H3K36 methylation and promote oncogenic gene expression programs. Created with Biorender.com