# Reversible arginine methylation regulates mitochondrial IDH2 activity: coordinated control by CARM1 and KDM3A/4A

**Authors:** Yena Cho, Jessica Winarto, Dae-Geun Song, Dong Hee Na, Kyo Bin Kang, Su-Nam Kim, Yong Kee Kim

PMC · DOI: 10.1038/s41419-026-08444-3 · Cell Death & Disease · 2026-02-02

## TL;DR

The study reveals that reversible arginine methylation controls mitochondrial enzyme activity, specifically IDH2, through a balance between CARM1 and KDM3A/4A enzymes.

## Contribution

This work identifies reversible arginine methylation as a novel regulatory mechanism for mitochondrial enzyme function, specifically IDH2.

## Key findings

- CARM1 asymmetrically dimethylates IDH2 at R188, inhibiting its activity but increasing protein stability.
- KDM3A and KDM4A reverse this methylation, restoring IDH2 activity and promoting α-ketoglutarate production.
- Demethylated IDH2 enhances mitochondrial membrane potential and oxygen consumption despite reduced stability.

## Abstract

Mitochondria are essential for cellular homeostasis, supplying key metabolites and energy. While post-translational modifications regulate mitochondrial enzymes, their roles remain less explored compared to those in the nucleus and cytoplasm. Here, we demonstrate that reversible arginine methylation governs the activity of several mitochondrial enzymes, with a particular focus on isocitrate dehydrogenase 2 (IDH2). We identify coactivator-associated arginine methyltransferase 1 (CARM1) as a mitochondrial enzyme that asymmetrically dimethylates IDH2 at R188, leading to enzymatic inhibition while enhancing protein stability. This modification is dynamically reversed by the lysine demethylases KDM3A and KDM4A, which restore IDH2 activity. Notably, despite its reduced stability, demethylated IDH2 promotes α-ketoglutarate production, enhancing mitochondrial membrane potential and oxygen consumption. These findings highlight the critical role of reversible arginine methylation in fine-tuning mitochondrial enzyme function and maintaining mitochondrial homeostasis.

## Linked entities

- **Genes:** IDH2 (isocitrate dehydrogenase (NADP(+)) 2) [NCBI Gene 3418], CARM1 (coactivator associated arginine methyltransferase 1) [NCBI Gene 10498], KDM3A (lysine demethylase 3A) [NCBI Gene 55818], KDM4A (lysine demethylase 4A) [NCBI Gene 9682]

## Full-text entities

- **Genes:** KDM4A [NCBI Gene 100353935], IDH2 (isocitrate dehydrogenase (NADP(+)) 2) [NCBI Gene 3418] {aka D2HGA2, ICD-M, IDH, IDH-2, IDHM, IDP}, KDM6B (lysine demethylase 6B) [NCBI Gene 23135] {aka JMJD3, NEDCFSA, NEDSST}, KDM4E (lysine demethylase 4E) [NCBI Gene 390245] {aka JMJD2E, KDM4DL, KDM5E}, KDM3A (lysine demethylase 3A) [NCBI Gene 55818] {aka JHDM2A, JHMD2A, JMJD1, JMJD1A, TSGA}, Sdha (succinate dehydrogenase complex, subunit A, flavoprotein (Fp)) [NCBI Gene 66945] {aka 1500032O14Rik, 2310034D06Rik, 4921513A11, FP, SDH2, SDHF}, PRMT5 [NCBI Gene 100357415], ACO2 [NCBI Gene 100352714], KDM6B [NCBI Gene 100343083], CS (citrate synthase) [NCBI Gene 1431], KDM4A (lysine demethylase 4A) [NCBI Gene 9682] {aka JHDM3A, JMJD2, JMJD2A, TDRD14A}, KDM4C (lysine demethylase 4C) [NCBI Gene 23081] {aka GASC1, JHDM3C, JMJD2C, TDRD14C}, KDM3A [NCBI Gene 100358329], KDM5C [NCBI Gene 100341721], SDHA (succinate dehydrogenase complex flavoprotein subunit A) [NCBI Gene 6389] {aka CMD1GG, FP, MC2DN1, NDAXOA, PGL5, PPGL5}, KDM4C [NCBI Gene 100343440], SDHA [NCBI Gene 100328584], PRMT6 [NCBI Gene 100346377], PRMT7 [NCBI Gene 100349655], Carm1 (coactivator-associated arginine methyltransferase 1) [NCBI Gene 59035] {aka Prmt4, m9Bei}, JMJD6 [NCBI Gene 100356762], actin [NCBI Gene 100342017], VDAC1 [NCBI Gene 100008751], DNM1L (dynamin 1 like) [NCBI Gene 10059] {aka DLP1, DRP1, DVLP, DYMPLE, EMPF, EMPF1}, KDM5C (lysine demethylase 5C) [NCBI Gene 8242] {aka DXS1272E, JARID1C, MRX13, MRXJ, MRXS16, MRXSCJ}, CARM1 (coactivator associated arginine methyltransferase 1) [NCBI Gene 10498] {aka PRMT4}, FH (fumarate hydratase) [NCBI Gene 2271] {aka FMRD, HLRCC, HsFH, LRCC, MCL, MCUL1}, Histone H3 [NCBI Gene 103350067], CARM1 [NCBI Gene 100347951], IDH1 (isocitrate dehydrogenase (NADP(+)) 1) [NCBI Gene 3417] {aka HEL-216, HEL-S-26, IDCD, IDH, IDP, IDPC}, PRMT1 [NCBI Gene 100339538], ACO2 (aconitase 2) [NCBI Gene 50] {aka ACONM, HEL-S-284, ICRD, OCA8, OPA9}, DLST [NCBI Gene 100340017]
- **Diseases:** breast cancer (MESH:D001943), Metabolic Diseases (MESH:D008659), OCR (MESH:D000860), MMP (MESH:D015433), Cancer (MESH:D009369), mitochondrial dysfunction (MESH:D028361)
- **Chemicals:** water (MESH:D014867), NaCl (MESH:D012965), NADP (MESH:D009249), cycloheximide (MESH:D003513), FA (MESH:D005492), 2-hydroxyglutarate (MESH:C019417), disuccinimidyl suberate (MESH:C019358), TCA (MESH:D014233), CO2 (MESH:D002245), NAD+ (MESH:D009243), SDMA (MESH:C024917), CMXRos (MESH:C107472), ATP (MESH:D000255), oligomycin (MESH:D009840), rotenone (MESH:D012402), polyvinylidene fluoride (MESH:C024865), acids (MESH:D000143), lysine (MESH:D008239), oxygen (MESH:D010100), CCCP (MESH:D002258), streptomycin (MESH:D013307), ADMA (MESH:C018524), CaCl2 (MESH:D002122), Triton X-100 (MESH:D017830), mannitol (MESH:D008353), paraformaldehyde (MESH:C003043), Tween 20 (MESH:D011136), Ile (MESH:D007532), penicillin (MESH:D010406), Antimycin A (MESH:D000968), carbonyl cyanide 3-chlorophenylhydrazone (MESH:C070053), succinyl-CoA (MESH:C012046), Alpha Ketoglutarate (MESH:D007656), 2-DG (MESH:D003847), ascorbate (MESH:D001205), lactate (MESH:D019344), cysteines (MESH:D003545), acetonitrile (MESH:C032159), Met (MESH:D008715), CHX (-), GSK3326595 (MESH:C000631126), ACN (MESH:C084683), TBS-T (MESH:C027647), glutamine (MESH:D005973), sodium deoxycholate (MESH:D003840), Sepharose (MESH:D012685), 4',6-diamidino-2-phenylindole (MESH:C007293), methanol (MESH:D000432), glucose (MESH:D005947), ammonium ferrous sulfate hexahydrate (MESH:C038178), HCl (MESH:D006851), pyruvate (MESH:D019289), formic acid (MESH:C030544), glutaraldehyde (MESH:D005976), Val (MESH:D014633), SDS (MESH:D012967), MG132 (MESH:C072553), S-adenosyl-L-methionine (MESH:D012436), glutamate (MESH:D018698), MMA (MESH:D019323)
- **Species:** Oryctolagus cuniculus (domestic rabbit, species) [taxon 9986], Homo sapiens (human, species) [taxon 9606], Mus musculus (house mouse, species) [taxon 10090], Rattus norvegicus (brown rat, species) [taxon 10116]
- **Mutations:** R188, A300-929A, R188K
- **Cell lines:** HA- — Helicoverpa armigera (Cotton bollworm), Spontaneously immortalized cell line (CVCL_Z978), H9C2 — Rattus norvegicus (Rat), Spontaneously immortalized cell line (CVCL_0286), MEF — Mus musculus (Mouse), Finite cell line (CVCL_9115), MCF7 — Homo sapiens (Human), Invasive breast carcinoma of no special type, Cancer cell line (CVCL_0031), MCF7/ADR — Homo sapiens (Human), High grade ovarian serous adenocarcinoma, Cancer cell line (CVCL_1452), 10T1/2 — Mus musculus (Mouse), Spontaneously immortalized cell line (CVCL_0190), HEK293T — Homo sapiens (Human), Transformed cell line (CVCL_0063), mouse embryonic fibroblast — Mus musculus (Mouse), Transformed cell line (CVCL_4240), MDA-MB-231 — Homo sapiens (Human), Breast adenocarcinoma, Cancer cell line (CVCL_0062)

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## Figures

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## References

1 references — full list in the complete paper: https://tomesphere.com/paper/PMC12877120/full.md

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Source: https://tomesphere.com/paper/PMC12877120