Exploring the methyl-verse: Dynamic interplay of epigenome and m6A epitranscriptome

Abstract

The orchestration of dynamic epigenetic and epitranscriptomic modifications is pivotal for the fine-tuning of gene expression. However, these modifications are traditionally examined independently. Recent compelling studies have disclosed an interesting communication and interplay between m6A RNA methylation (m6A epitranscriptome) and epigenetic modifications, enabling the formation of feedback circuits and cooperative networks. Intriguingly, the interaction between m6A and DNA methylation machinery, coupled with the crosstalk between m6A RNA and histone modifications shape the transcriptional profile and translational efficiency. Moreover, m6A modifications interact also with non-coding RNAs, modulating their stability, abundance, and regulatory functions. In the light of these findings, m6A imprinting acts as a versatile checkpoint, linking epigenetic and epitranscriptomic layers toward a multilayer and time-dependent control of gene expression and cellular homeostasis. The scope of the present review is to decipher the m6A-coordinated circuits with DNA imprinting, chromatin architecture, and non-coding RNAs networks in normal physiology and carcinogenesis. Ultimately, we summarize the development of innovative CRISPR-dCas engineering platforms fused with m6A catalytic components (m6A writers or erasers) to achieve transcript-specific editing of m6A epitranscriptomes that can create new insights in modern RNA therapeutics.

Keywords: CRISPR-dCas; DNA methylation; RNA epigenetics; RNA modifications; epitranscriptome; histone modifications; m6A RNA methylation; m6A epitranscriptome editing tools; m6A modification; non-coding RNAs.

Graphical abstract

Figure 1

Representation of m6A epitranscriptome machinery, depicting catalytic modulators (m6A writers, erasers, and readers) and their downstream functions N⁶-methyladenosine (m6A) is introduced by a multicomponent complex, consisting of the main catalytic subunit, S-adenosylmethionine (SAM)-dependent methyltransferase METTL3, along with accessory subunits—most important, METTL14 methyltransferase—that stabilizes METTL3, and the scaffold components WTAP, VIRMA, and RBM15 (m6A writers). The reversible nature of m6A methylation is mediated by the FTO and ALKBH5 demethylases (m6A erasers), while the m6A downstream role is translated by m6A readers, primarily comprising YTH domain-containing proteins, IGF2BPs, and members of the HNRNP family. Specifically, YTHDF1/3 and YTHDC2 promote mRNA translation through interactions with initiation factors, YTHDC1 facilitates alternative splicing and transcriptional silencing, while YTHDF2 directs transcripts’ degradation by recruiting them to decay sites, such as P-bodies and stress granules. Additionally, IGF2BPs promote mRNA stability and storage, while HNRNPA2B1 supports primary miRNA processing and mRNA splicing. (Created with BioRender.com).

Figure 2

Crosstalk between m6A epitranscriptome and epigenetics (A) METTL3-mediated m6A imprinting of nascent transcripts leads to FXR1 (m6A reader)-dependent recruitment of TET1 demethylase in adjacent genomic regions, resulting in DNA demethylation, chromatin accessibility, and gene transcription. (B) METTL3-mediated m6A methylation co-transcriptionally promotes KDM3B localization in a YTHDC1-dependent manner, inducing H3K9me2 demethylation and gene expression. (C) METTL3-mediated m6A methylation of GAS5 lncRNA stimulates its YTHDF3-dependent decay, reducing GAS5-related YAP ubiquitination and degradation. Thereafter, YAP accumulation enhances YTHDF3 transcription, further contributing to GAS5 decay and tumor progression in colorectal carcinoma. (D) METTL3-mediated m6A imprinting of carRNAs triggers their YTHDC1-dependent degradation, while METTL3 knockout and downregulation of carRNAs m6A methylation recruited EP300 histone acetyltransferase and the YY1 transcription factor, leading to increased chromatin accessibility and gene expression. (Created with BioRender.com).

Figure 3

m6A epitranscriptome editing tools (A) CRISPR-dCasRx-METTL3 m6A imprinting on FOXM1 transcripts results in decreased mRNA levels and inhibition of cell proliferation in glioblastoma stem cells. (B) CRISPR-dCasRx-ALKBH5 demethylation of ITGA6 mRNA attenuates translation, inhibiting tumor growth and progression in bladder cancer. (C) CRISPR-dCas13-FTO demethylation of LINE1 RNA retrotransposons leads to increased chromatin accessibility and pluripotency in mouse embryos. (D) CRISPR-dCas13-ALKBH5 demethylation of SOX2 mRNA prevents decay and enhances stability, promoting differentiation of hESCs. (E) CRISPR-dCas13-METTL3 m6A methylation on HMBOX1 mRNA decreases its stability toward telomere dysfunction, genomic instability, and increased proliferation/migration of prostate cancer cells. (Created with BioRender.com).