# The methyltransferase-like proteins as core regulators of nucleic acid modifications and post-translation modification of proteins in disease pathogenesis and therapeutic implications

**Authors:** Shenyuqi Wu, Duancheng Guo, Xichun Hu, Mengdi Yang

PMC · DOI: 10.1186/s40364-025-00858-z · Biomarker Research · 2025-11-05

## TL;DR

This review explores how METTL proteins regulate gene expression through methylation and their role in diseases, offering insights for precision therapies.

## Contribution

The paper systematically explores METTL proteins' regulatory mechanisms and their clinical translation potential, organized by signaling pathways.

## Key findings

- METTL proteins dynamically regulate gene expression through nucleic acid and protein methylation.
- Dysregulation of METTL proteins is linked to tumorigenesis, neurodegeneration, and immune dysfunction.
- Emerging METTL inhibitors show promise for precision therapies targeting methylation modifications.

## Abstract

The methyltransferase-like (METTL) family members are the central ‘writers’ of epitranscriptome modifications, catalyzing N6-methyladenosine (m6A), N7-methylguanosine (m7G), 3-methylcytosine (m3C) and other chemical markers that modify DNA, RNA, and proteins (both histones and non-histone proteins) to dynamically regulate gene expression. The METTL family is distinguished by structural diversity, substrate specificity and multifaceted roles in epigenetic regulation. Dysregulation of METTL proteins has been demonstrated to disrupt RNA stability, translational efficiency and signaling pathways, which has been associated with tumorigenesis, neurodegeneration and immune dysfunction. At present, there are still limitations in the knowledge of the cooperative networks among METTL members and with other major signaling pathways. The objective of the present study is to elucidate the regulatory mechanisms mediated by METTL across different levels, laying the groundwork for subsequent development of precision therapies targeting phenotypic enzyme modifications. This review comprehensively delineates the structural characteristics and molecular functions of METTLs, their cooperative interactions, and their pathophysiological regulatory networks organized by signaling pathways rather than disease categories. We evaluate their diagnostic potential as biomarkers and their therapeutic implications, with particular focus on emerging METTL inhibitors that have entered clinical trials. By systematically exploring the mechanisms behind their context-dependent functions and analyzing their potential for clinical translation, we provide a foundation for precision therapies targeting these core regulators of nucleic acid and protein methylation.

## Linked entities

- **Chemicals:** N6-methyladenosine (PubChem CID 102175), N7-methylguanosine (PubChem CID 135445750), 3-methylcytosine (PubChem CID 140523)
- **Diseases:** immune dysfunction (MONDO:0005046)

## Full-text entities

- **Genes:** CDKN1B (cyclin dependent kinase inhibitor 1B) [NCBI Gene 1027] {aka CDKN4, KIP1, MEN1B, MEN4, P27KIP1}, YTHDF1 (YTH N6-methyladenosine RNA binding protein F1) [NCBI Gene 54915] {aka C20orf21, DF1}, TMT1A (thiol methyltransferase 1A) [NCBI Gene 25840] {aka AAM-B, AAMB, METTL7A}, VCP (valosin containing protein) [NCBI Gene 7415] {aka CDC48, FTDALS6, TERA, p97}, CD44 (CD44 molecule (IN blood group)) [NCBI Gene 960] {aka CDW44, CSPG8, ECM-III, ECMR-III, H-CAM, HCELL}, Mettl16 (methyltransferase 16, N6-methyladenosine) [NCBI Gene 67493] {aka 2610100D03Rik, 2810013M15Rik, A830095F14Rik, Mett10d}, Yap1 (yes-associated protein 1) [NCBI Gene 22601] {aka Yap, Yap65, Yki, Yorkie}, MTOR (mechanistic target of rapamycin kinase) [NCBI Gene 2475] {aka FRAP, FRAP1, FRAP2, RAFT1, RAPT1, SKS}, METTL2B (methyltransferase 2B, tRNA N3-cytidine) [NCBI Gene 55798] {aka METL, METTL2, PSENIP1}, METTL9 (methyltransferase 9, His-X-His N1(pi)-histidine) [NCBI Gene 51108] {aka CGI-81, DREV, DREV1, PAP1, hMETTL9}, NFKB1 (nuclear factor kappa B subunit 1) [NCBI Gene 4790] {aka CVID12, EBP-1, KBF1, NF-kB, NF-kB1, NF-kappa-B1}, ETFBKMT (electron transfer flavoprotein subunit beta lysine methyltransferase) [NCBI Gene 254013] {aka C12orf72, ETFB-KMT, METTL20}, METTL1 (methyltransferase 1, tRNA methylguanosine) [NCBI Gene 4234] {aka C12orf1, TRM8, TRMT8, YDL201w}, MIR126 (microRNA 126) [NCBI Gene 406913] {aka MIRN126, miRNA126, mir-126}, S100A9 (S100 calcium binding protein A9) [NCBI Gene 6280] {aka 60B8AG, CAGB, CFAG, CGLB, L1AG, LIAG}, CS (citrate synthase) [NCBI Gene 1431], CD8A (CD8 subunit alpha) [NCBI Gene 925] {aka CD8, CD8alpha, IMD116, Leu2, p32}, METTL21C (methyltransferase 21C, AARS1 lysine) [NCBI Gene 196541] {aka C13orf39}, PAK2 (p21 (RAC1) activated kinase 2) [NCBI Gene 5062] {aka KNO2, PAK65, PAKgamma}, MT1E (metallothionein 1E) [NCBI Gene 4493] {aka MT-1E, MT-IE, MT1, MTD}, Mettl23 (methyltransferase like 23) [NCBI Gene 74319] {aka 1110005A03Rik, 1500035B17Rik, 4933424L15Rik}, DALRD3 (DALR anticodon binding domain containing 3) [NCBI Gene 55152] {aka DEE86, EIEE86}, CDK4 (cyclin dependent kinase 4) [NCBI Gene 1019] {aka CMM3, MCPH31, PSK-J3}, MAP2K7 (mitogen-activated protein kinase kinase 7) [NCBI Gene 5609] {aka JNKK2, MAPKK7, MEK, MEK 7, MKK7, PRKMK7}, CCND2 (cyclin D2) [NCBI Gene 894] {aka KIAK0002, MPPH3}, BMPR1B (bone morphogenetic protein receptor type 1B) [NCBI Gene 658] {aka ALK-6, ALK6, AMD3, AMDD, BDA1D, BDA2}, YTHDF2 (YTH N6-methyladenosine RNA binding protein F2) [NCBI Gene 51441] {aka CAHL, DF2, HGRG8, NY-REN-2}, SNAI2 (snail family transcriptional repressor 2) [NCBI Gene 6591] {aka SLUG, SLUGH, SLUGH1, SNAIL2, WS2D}, EEF1AKMT3 (EEF1A lysine methyltransferase 3) [NCBI Gene 25895] {aka FAM119B, METTL21B}, HSPA4 (heat shock protein family A (Hsp70) member 4) [NCBI Gene 3308] {aka APG-2, HEL-S-5a, HS24/P52, HSPH2, RY, hsp70}, Ccl2 (C-C motif chemokine ligand 2) [NCBI Gene 20296] {aka HC11, JE, MCAF, MCP-1, MCP1, SMC-CF}, Prkce (protein kinase C, epsilon) [NCBI Gene 18754] {aka 5830406C15Rik, PKC[e], PKCepsilon, Pkce}, MIR380 (microRNA 380) [NCBI Gene 494329] {aka MIR380-3p, MIRN380, hsa-mir-380, mir-380}, NCBP1 (nuclear cap binding protein subunit 1) [NCBI Gene 4686] {aka CBP80, NCBP, Sto1}, ATF5 (activating transcription factor 5) [NCBI Gene 22809] {aka ATFX, HMFN0395}, Marcks (myristoylated alanine rich protein kinase C substrate) [NCBI Gene 17118] {aka Macs, PKCSL}, METTL13 (methyltransferase 13, eEF1A N-terminus and K55) [NCBI Gene 51603] {aka 5630401D24Rik, CGI-01, DFNB26, DFNB26M, DFNM1, EEF1AKNMT}, CCNL2 (cyclin L2) [NCBI Gene 81669] {aka ANIA-6B, CCNM, CCNS, HCLA-ISO, HLA-ISO, PCEE}, AGR2 (anterior gradient 2, protein disulphide isomerase family member) [NCBI Gene 10551] {aka AG-2, AG2, GOB-4, HAG-2, HEL-S-116, HPC8}, PMEPA1 (prostate transmembrane protein, androgen induced 1) [NCBI Gene 56937] {aka STAG1, TMEPAI}, G6PD (glucose-6-phosphate dehydrogenase) [NCBI Gene 2539] {aka CNSHA1, G6PD1}, CDC25B (cell division cycle 25B) [NCBI Gene 994] {aka MPIP2}, VCPKMT (valosin containing protein lysine methyltransferase) [NCBI Gene 79609] {aka C14orf138, METTL21D, VCP-KMT}, NORAD (non-coding RNA activated by DNA damage) [NCBI Gene 647979] {aka LINC00657}, Sptbn2 (spectrin beta, non-erythrocytic 2) [NCBI Gene 20743] {aka Spnb3}, Myc (Myc proto-oncogene, bHLH transcription factor) [NCBI Gene 17869] {aka Myc2, Niard, Nird, bHLHe39}, TEAD2 (TEA domain transcription factor 2) [NCBI Gene 8463] {aka ETF, TEAD-2, TEF-4, TEF4}, METTL6 (methyltransferase 6, tRNA N3-cytidine) [NCBI Gene 131965] {aka hMETTL6}, METTL16 (methyltransferase 16, RNA N6-adenosine) [NCBI Gene 79066] {aka METT10D}, EGR1 (early growth response 1) [NCBI Gene 1958] {aka AT225, G0S30, KROX-24, NGFI-A, TIS8, ZIF-268}, CDK1 (cyclin dependent kinase 1) [NCBI Gene 983] {aka CDC2, CDC28A, P34CDC2}, EIF4E (eukaryotic translation initiation factor 4E) [NCBI Gene 1977] {aka AUTS19, CBP, EIF4E1, EIF4EL1, EIF4F, eIF-4E}, TMT1B (thiol methyltransferase 1B) [NCBI Gene 196410] {aka ALDI, METTL7B}, EGFR (epidermal growth factor receptor) [NCBI Gene 1956] {aka ERBB, ERBB1, ERRP, HER1, NISBD2, NNCIS}, CBLL1 (Cbl proto-oncogene like 1) [NCBI Gene 79872] {aka HAKAI, RNF188}, EEF2 (eukaryotic translation elongation factor 2) [NCBI Gene 1938] {aka EEF-2, EF-2, EF2, SCA26}, Jak2 (Janus kinase 2) [NCBI Gene 16452] {aka Fd17}, ACSL3 (acyl-CoA synthetase long chain family member 3) [NCBI Gene 2181] {aka ACS3, FACL3, LACS 3, LACS3, PRO2194}, IGF2BP1 (insulin like growth factor 2 mRNA binding protein 1) [NCBI Gene 10642] {aka CRD-BP, CRDBP, IMP-1, IMP1, VICKZ1, ZBP1}, Mettl17 (methyltransferase like 17) [NCBI Gene 52535] {aka 2310032K15Rik, D14Ertd209e, Mett11d1}
- **Diseases:** hypoxia (MESH:D000860), immune dysfunction (MESH:D007154), R (MESH:C580424), liver and metabolic diseases (MESH:D008107), HF (MESH:D006333), cisplatin resistance (OMIM:613290), cognitive impairment (MESH:D003072), cardiovascular diseases (MESH:D002318), AML (MESH:D015470), myeloid leukemia (MESH:D007951), AD (MESH:D000544), AS (MESH:D050197), metastasis (MESH:D009362), hypoxic pulmonary hypertension (MESH:D006976), ICC (MESH:D018281), ischaemic (MESH:D018917), insulin deficiency (MESH:D007333), NAFLD (MESH:D065626), atrial fibrillation (MESH:D001281), hematological tumors (MESH:D019337), memory deficits (MESH:D008569), type 1 diabetes (MESH:D003922), DM (MESH:D003920), hypertrophic (MESH:D002312), inflammation (MESH:D007249), autism (MESH:D001321), metabolic diseases (MESH:D008659), Arrhythmia (MESH:D001145), CM (MESH:D009202), fracture (MESH:D050723), Ischaemic heart disease (MESH:D006331), Breast invasive carcinoma (MESH:D001943), tumorigenesis (MESH:D063646), LUAD (MESH:D000077192), Ovarian serous cystadenocarcinoma (MESH:D010049), uveal melanoma (MESH:C536494), intellectual disability (MESH:D008607), ischemia-reperfusion injury (MESH:D015427), acute lymphoblastic leukemia (MESH:D054198), MI (MESH:D009203), cardiomyocyte hypertrophy (MESH:D006984), NPC (MESH:D000077274), brittleness (MESH:D010013), vascular diseases (MESH:D014652), aortic dissection (MESH:D000784), CRC (MESH:D015179), arteriovenous malformation (MESH:D001165), NSCLC (MESH:D002289), neurodegeneration (MESH:D019636), hepatobiliary malignancies (MESH:D004066), infarct (MESH:D007238), beta-cell failure (MESH:D051437), HNSCC (MESH:D000077195), hyperglycemia (MESH:D006943), pancreatic cancer (MESH:D010190), OA (MESH:D010003), endometriosis (MESH:D004715), mitochondrial dysfunction (MESH:D028361), Cardiac hypertrophy (MESH:D006332), GBM (MESH:D005910)
- **Chemicals:** Lenvatinib (MESH:C531958), 1-methylhistidine (MESH:C028120), 5-methylcytosine (MESH:D044503), N6-methyladenosine (MESH:C010223), lysine (MESH:D008239), oxygen (MESH:D010100), Cisplatin (MESH:D002945), Arg (MESH:D001120), ROS (MESH:D017382), quercetin (MESH:D011794), testosterone (MESH:D013739), docetaxel (MESH:D000077143), pentose phosphate (MESH:D010428), gemcitabine (MESH:D000093542), PD407824 (MESH:C544549), 5-FU (MESH:D005472), His (MESH:D006639), Taselisib (MESH:C582924), eltrombopag (MESH:C520809), sinefungin (MESH:C006235), bisphosphonate (MESH:D004164), anlotinib (MESH:C000625192), dithiothreitol (MESH:D004229), glucose (MESH:D005947), platinum (MESH:D010984), lipid (MESH:D008055), glutathione (MESH:D005978), imidazole (MESH:C029899), aminopyrimidine (MESH:C012180), AdoMet (MESH:D012436), fatty acid (MESH:D005227), tanespimycin (MESH:C112765), nitrogen (MESH:D009584), Trifluridine (MESH:D014271), oxaliplatin (MESH:D000077150), FFA (MESH:D005230), Adriamycin (MESH:D004317), entacapone (MESH:C071192), Fe (MESH:D007501), mephedrone (MESH:C548233), (S) (MESH:D013455), N7-methylguanosine (MESH:C016578), zinc (MESH:D015032), crizotinib (MESH:D000077547), apatinib (MESH:C553458), CIDBA (-), methionine (MESH:D008715), N4-methylcytosine (MESH:C039052), 3-methylcytosine (MESH:C036386), cysteine (MESH:D003545), 3-methylhistidine (MESH:C028118), thiol (MESH:D013438)
- **Species:** Mus musculus (house mouse, species) [taxon 10090], Homo sapiens (human, species) [taxon 9606], Staphylococcus aureus (species) [taxon 1280]

## Full text

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## Figures

9 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12590641/full.md

## References

5 references — full list in the complete paper: https://tomesphere.com/paper/PMC12590641/full.md

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Source: https://tomesphere.com/paper/PMC12590641