RNA modification: mechanisms and therapeutic targets

Abstract

RNA modifications are dynamic and reversible chemical modifications on substrate RNA that are regulated by specific modifying enzymes. They play important roles in the regulation of many biological processes in various diseases, such as the development of cancer and other diseases. With the help of advanced sequencing technologies, the role of RNA modifications has caught increasing attention in human diseases in scientific research. In this review, we briefly summarized the basic mechanisms of several common RNA modifications, including m6A, m5C, m1A, m7G, Ψ, A-to-I editing and ac4C. Importantly, we discussed their potential functions in human diseases, including cancer, neurological disorders, cardiovascular diseases, metabolic diseases, genetic and developmental diseases, as well as immune disorders. Through the "writing-erasing-reading" mechanisms, RNA modifications regulate the stability, translation, and localization of pivotal disease-related mRNAs to manipulate disease development. Moreover, we also highlighted in this review all currently available RNA-modifier-targeting small molecular inhibitors or activators, most of which are designed against m6A-related enzymes, such as METTL3, FTO and ALKBH5. This review provides clues for potential clinical therapy as well as future study directions in the RNA modification field. More in-depth studies on RNA modifications, their roles in human diseases and further development of their inhibitors or activators are needed for a thorough understanding of epitranscriptomics as well as diagnosis, treatment, and prognosis of human diseases.

Keywords: Cancer; Cardiovascular diseases; Inhibitors; Metabolic diseases; Neurological disorders; RNA modification.

Fig. 1

Eukaryotic RNA modifications. a The chemical structures of ten RNA modifications marking on ribose are presented. b Various RNA modifications are enriched in different regions of mRNA. m7G, m1A, m5C are enriched in 5’ cap, 5’ UTR, 3’ UTR regions, respectively. The other modifications are all enriched in CDS region. c. The various “writers”, “readers” and “erasers” associated with RNA modifications are listed in the table

Fig. 2

The molecular mechanisms of seven common RNA modifications. a The m6A methyltransferase complex components including METTL3-METTL14, VIRMA, RBM15, WTAP mediate m6A installation, whereas ALKBH5 and FTO function as “erasers” to remove m⁶A modification. YTHDF1 ~ 3, YTHDC1 ~ 2 and IGF2BP1 ~ 3 are responsible for “reading” m6A on substrate and lead to various phenotypical conditions, such as translation, enhanced RNA stability, RNA decay, RNA splicing or nuclear transport. b NSUNs and DNMT2 act as the m5C “writers” in mRNAs, while TET family enzymes can erase m5C by catalyzing the oxidative hydroxylation of m5C to hm5C, ca5C and f5C. YTHDF2, ALYREF and YBX1 recognize m5C and regulate the fate of substrates. c TRMT family proteins deposit m1A on substrate RNAs. m1A can be “read” by YTHDF1 ~ 3 or “erased” by ALKBH1/3/7 or FTO. d The m7G methyltransferase complex discovered currently includes METTL1/WDR4, WBSCR22/TRMT112, RNMT/RAM, whereas “erasers” or “readers” of m7G have not yet been reported. PCIF1/METTL4 add the m6Am modification adjacent to m7G; FTO can also remove m7G modification. e Pseudouridylation is mediated by either snoRNA-dependent or RNA-independent mechanism. DKC1 in combination with three core proteins (NOP10, GAR1 and NHP2) form the RNP complex, which is guided by box H/ACA snoRNAs to catalyze pseudouridylation; the PUS enzymes RNA-independently modify uridine to form pseudouridine. f ADAR1/2 and ADAT2/3 catalyze adenosine-to-inosine editing on double-stranded RNAs. g NAT10 is currently discovered the only one ac4C “writer”; SIRT7 is considered as a candidate “eraser”; the identity of the ac4C “readers” are still undetermined

Fig. 3

The regulation of different RNA modifying enzymes in various tumors. a The m6A-associated RNA modifying enzymes involved in multiple tumors and their respective substrate RNAs. b The m5C-associated RNA modifying enzymes involved in multiple tumors and their respective substrate RNAs. c The roles of m1A-associated RNA modifying enzymes in tumors modulating various substrate RNAs. d The roles of m7G-associated methyltransferases regulating tRNAs and mRNAs in multiple tumors. e The roles of A-to-I editing modifiers in regulating substrate double-stranded RNAs in multiple tumors. f Regulation of substrate RNAs by ac4C modifiers, NAT10 and SIRT7, in various tumors

Fig. 4

Detailed mechanisms of anti-tumor drugs targeting RNA modifications. a 18097 inhibits FTO, thus increasing m6A modification on substrate mRNAs in breast cancer. b HUHS015 disturbs the function of ALKBH3, which serves as a prostate cancer antigen. c R-2HG prevents FTO removal of m6A modification from MYC/CEBPα in AML. d WBSCR22 knockdown enhances the sensitivity of colorectal cancer cells to oxaliplatin. e METTL1/NSUN2 knockdown sensitizes cervical cancer cells to 5-FU treatment. f NSUN3/DNMT2/CDK7/HnRNPK/CDK9/p-TEFb complex binds nascent nuclear RNA, forms a 5-AZA-sensitive chromatin structure in AML

Fig. 5

The domain structures of RNA modifying enzyme families. a METTL family members each contains a MTase domain that catalyzes the methylation. b ALKBH family members and FTO all contain Fe²⁺ binding and α-KG binding sites. c YTH-domain-containing family consists of YTHDC1/2 and YTHDF1/2/3. d IGF2BP family members each contains four KH domains and at least one RRM domain. e ADAR family binds dsRNA through RBD domains, whereas DM domains function as deaminase. f TRMT6 only possesses substrate binding sites, whereas TRMT61A/B contains substrate binding sites as well as SAM binding sites. TRMT10C functions as methyltransferase through its SAM-dependent MTase domain. The domain information of TRMT family proteins comes from the Uniprot database

Fig. 6

The chemical structures of inhibitors targeting RNA methylation. a Inhibitors against METTL3, b Inhibitors against FTO and c Inhibitors against ALKBH 3/5

Fig. 7

The chemical structures of inhibitors targeting RNA modifications. a Inhibitors against m1A/m6A. TRMT6/TRMT61A complex inhibitors target m1A, whereas YTHDF and IGF2BP1 inhibitors target m6A; b Inhibitors against m5C; c Inhibitors against ψ; d Inhibitors against A-to-I editing; e Inhibitors against ac4C