Methylation across the central dogma in health and diseases: new therapeutic strategies

Abstract

The proper transfer of genetic information from DNA to RNA to protein is essential for cell-fate control, development, and health. Methylation of DNA, RNAs, histones, and non-histone proteins is a reversible post-synthesis modification that finetunes gene expression and function in diverse physiological processes. Aberrant methylation caused by genetic mutations or environmental stimuli promotes various diseases and accelerates aging, necessitating the development of therapies to correct the disease-driver methylation imbalance. In this Review, we summarize the operating system of methylation across the central dogma, which includes writers, erasers, readers, and reader-independent outputs. We then discuss how dysregulation of the system contributes to neurological disorders, cancer, and aging. Current small-molecule compounds that target the modifiers show modest success in certain cancers. The methylome-wide action and lack of specificity lead to undesirable biological effects and cytotoxicity, limiting their therapeutic application, especially for diseases with a monogenic cause or different directions of methylation changes. Emerging tools capable of site-specific methylation manipulation hold great promise to solve this dilemma. With the refinement of delivery vehicles, these new tools are well positioned to advance the basic research and clinical translation of the methylation field.

Fig. 1

Biochemical processes of reversible DNA/RNA/protein methylation. a C⁵-cytosine methylation and demethylation in DNA and RNAs. Blue fonts and arrows represent components of the DNA methylation pathway, purple fonts and arrows represent components of the RNA methylation pathway, black fonts and arrows represent common components, and dashed arrows indicate potential steps. Methyl groups and carbon atoms are highlighted in gold. b N⁶-adenosine methylation and demethylation in DNA and RNAs. The rule of color usage is the same as that of in (a). c Protein lysine methylation and demethylation. d Protein arginine methylation and demethylation. Dashed arrows indicate potential steps

Fig. 2

Methylation of DNA/RNAs/proteins regulates the flow of genetic information. In the central dogma of molecular biology, genetic information is transmitted from DNA to RNA to protein. DNA and histone methylation has essential roles in regulating chromatin opening (involving activating histone methylation, e.g., H3K4me3, H3K36me3, and H3R2me2s) for gene transcription or compaction (involving DNA cytosine methylation and repressive histone methylation, e.g., H3K9me3, H3K27me3, and H3R8me2s) for gene silencing. The methylation of mRNAs (m⁶A and m⁵C) regulates the splicing, localization, translation, and stability of the mRNAs. Nonhistone protein methylation influences the activity, stability, and subcellular localization of translated proteins. Collectively, methylation of the different macromolecules constitutes a multilayer dynamic regulation of biological processes. A large array of readers that contain conserved methyl-group binding domains are involved in interpreting these post-synthesis chemical modifications

Fig. 3

Function of MeCP2 and FMR1 and their mutations in RTT and FXS respectively. a The majority of RTT-causing mutations are located in the methyl-CpG-binding domain (MBD) and transcriptional repression domain (TRD) of MeCP2. ID, intervening domain; NTD, N-terminal domain; CTD, C-terminal domain. b Molecular functions of MeCP2: MeCP2 recognizes mCpG and mCpA and recruits NCOR-SMRT co-repressor complex to compact chromatin and suppress transcription; MeCP2 binds the hydroxymethylated CA repeats and protects them from nucleosome invasion. Both functions are abolished upon RTT-causing mutations. c CGG trinucleotide repeat expansion (>200 repeats) in the 5′-untranslated region of the FMR1 gene causes DNA hypermethylation and histone methylation shift, which silences the FMR1 gene in FXS patients. d Multiple important domains of FMRP, including a tandem Agenet (Agn) domain that binds DNA and other proteins, a nuclear localization sequence (NLS), a nuclear export sequence (NES), and several RNA- binding domains (KH1, KH2, and RGG box). PRMT1 performs arginine methylation of RGG motifs within FMRP. e FMRP regulates the histone methylation states by modulating the translation of writers (MLL1 and SETD2), and binds a fraction of m⁶A-modified mRNAs (probably with a G-quadruplex structure) to modulate their nuclear export, stability, and translation, which is implicated in the regulation of neural differentiation, development, and function. f Methylation and phosphorylation of FMRP have opposing effects on the neuronal granule assembly and activity-dependent translation through modulating FMRP-mediated phase separation

Fig. 4

Mutational cancer driver methylation modifier genes and the role of methylation dysregulation across the central dogma in tumor initiation and progression. a Distribution of the prevalence of methylation modifiers with cancer driver mutations across 66 cancer types. All data are retrieved from IntOGen database. AML acute myeloid leukemia, SBCC skin basal cell carcinoma, MDPS myelodysplastic syndrome neoplasm, HC hepatic cancer, VV vulval cancer, SSCC skin squamous cell carcinoma, ESCA esophageal carcinoma, RCCC renal clear cell carcinoma, HNSC head and neck squamous cell carcinoma, ALL acute lymphoblastic leukemia, DLBCL diffuse large B cell lymphoma, LY lymphoma, AN anus cancer, MBL medulloblastoma, CM cutaneous melanoma of the skin, BLCA bladder cancer. b Methylation remodeling of DNA, RNA, histone, and nonhistone proteins contributes to tumor initiation and progression. Aging, genetic mutations, or environmental stimuli induce methylation remodeling of DNA/RNAs/proteins and causes oncogene activation and TSG silence. A gear set is used as a metaphor for the link between different methylation pathways and their roles in tumorigenesis. The common mechanisms that cause oncogene/TSG disturbance by methylation remodeling at DNA, RNA, and protein levels are recapitulated in the boxes

Fig. 5

Methylation remodeling of non-tumor cells in the tumor microenvironment (TME). The TME is populated by various cell types including immune cells (e.g., T lymphocytes, natural killer cells, macrophages, neutrophils, and dendritic cells), stromal cells (e.g., fibroblasts and mesenchymal stromal cells), and blood and lymphatic vessels. To support tumor development and immune evasion, tumor cells induce alterations of the methylome landscape and subsequent gene expression changes in these TME cells. Examples of methylation remodeling of chromatin, mRNAs, and nonhistone proteins (represented by cartoons in the figure) are summarized

Fig. 6

DNA methylation changes during aging and methylation clocks. Both global loss of and local gain of DNA methylation occur with age. age-associated differentially methylated positions (aDMPs) reflect an intrinsic age-related functional decline process occurring over chronological time in a population, while age-associated variably methylated positions (aVMPs) recapitulate the inter-individual heterogeneity in health status. A variety of DNA methylation clocks have been developed, generally using ElasticNet regression, to assess chronological age (chronological clocks) or biological age (biological clocks). A chronological clock can precisely predict calendar age irrespective of health conditions, while a biological clock can distinguish between people with different health conditions

Fig. 7

Histone, nonhistone protein, and RNA methylation changes with age. a Alterations in histone and nonhistone protein methylation and 3D genome structure with age. G9a/GLP-mediated methylation of Lamin B1 (LMNB1) promotes heterochromatin assembly at the nuclear periphery and formation of lamina-associated domains (LADs) in young cells, which ensures transcriptional silence; whereas defects in both histone methylation (H3K9me2/3) and nonhistone protein methylation are associated with chromatin detachment from the nuclear lamina and a shift to a euchromatin state. b Overall changes of m⁶A modification with age in different tissues including brain, peripheral blood mononuclear cells, ovary, and intestine, and crucial age-related targets. Changes in the expression of writers or erasers account for the methylation fluctuation. Although the m⁶A level and expression of modifiers do not differ significantly between young and old mouse hearts, they do show aging-related differences in response to acute cardiac ischemia/reperfusion injury, which may be associated with reduced tolerance to ischemic injury with age

Fig. 8

Principle of site-specific manipulating DNA, histone, and RNA methylation. a Three generations of programmable DNA-binding domain (DBD) platforms for site-specific chromatin methylation manipulation: zinc fingers (ZFs), transcription activator-like effectors (TALEs), and catalytically dead CRISPR-dCas system. b Fusion of dCas9 to DNA methyltransferases (e.g., DNMT3A) or demethylases (e.g., TET1) allows for targeted DNA methylation or demethylation, respectively. c Fusion of dCas9 to protein methylation machinery (e.g., KRAB) or demethylases (e.g., LSD1) enables artificial histone methylation or demethylation at defined loci, respectively. d Fusion of dCas13 to RNA methyltransferases (e.g., METTL3) or demethylases (e.g., FTO) allows for selective deposition or removal of m⁶A signals at specific transcripts, respectively

Fig. 9

Paradigm of site-specific manipulating chromatin methylation for precise cancer therapy. mRNAs encoding a methylation editor are delivered to liver cancer cells by lipid nanoparticles (LNPs), which suppresses oncogene expression by catalyzing DNA and/or histone methylation at the promoters of oncogenes (e.g., MYC) or at the CTCF-binding sites to abolish their interactions with potential enhancers