# Mechanisms at the Intersection of lncRNA and m6A Biology

**Authors:** Samuel J. Gonzalez, Edgardo Linares, Allison M. Porman Swain, Aaron M. Johnson

PMC · DOI: 10.3390/ncrna12010004 · Non-Coding RNA · 2026-01-31

## TL;DR

This review explores how the RNA modification m6A affects long noncoding RNAs and their roles in regulating biological processes.

## Contribution

The paper synthesizes current knowledge on the interplay between lncRNAs and m6A, highlighting new mechanistic insights.

## Key findings

- m6A modification influences lncRNA function through writers, erasers, and readers.
- Nuclear lncRNAs regulate chromatin and are modulated by m6A.
- Liquid–liquid phase separation is emerging as a key mechanism in lncRNA and m6A biology.

## Abstract

This review provides a thorough survey of long noncoding RNAs that bear the RNA modification N6-methyladenosine (m6A) and current work to understand the resulting mechanistic and biological consequences. We give an overview of lncRNA and m6A biology first, describing the writers, erasers, and readers of m6A and their targeting of lncRNAs. Next, we give an in-depth review of the field of nuclear lncRNAs that regulate chromatin and their regulation via m6A. We then describe the growing appreciation of liquid–liquid phase separation properties in lncRNA and m6A biology. Finally, we cover examples of cytoplasmic lncRNAs regulated by m6A. Overall, this review aims to emphasize how epitranscriptomics influences noncoding RNA mechanisms to provide additional layers of regulation, integrated into downstream biological processes.

## Full-text entities

- **Genes:** METTL3 (methyltransferase 3, N6-adenosine-methyltransferase complex catalytic subunit) [NCBI Gene 56339] {aka IME4, M6A, MT-A70, Spo8, hMETTL3}, KDM1A (lysine demethylase 1A) [NCBI Gene 23028] {aka AIMAH3, AOF2, BHC110, CPRF, KDM1, LSD1}, ZC3H13 (zinc finger CCCH-type containing 13) [NCBI Gene 23091] {aka KIAA0853, Xio}, SFPQ (splicing factor proline and glutamine rich) [NCBI Gene 6421] {aka POMP100, PPP1R140, PSF}, MACOM (macrophthalmia, colobomatous, with microcornea) [NCBI Gene 791229], NEAT1 (nuclear paraspeckle assembly transcript 1) [NCBI Gene 283131] {aka LINC00084, NCRNA00084, TP53LC15, TncRNA, VINC}, NANOG (Nanog homeobox) [NCBI Gene 79923], GPC4 (glypican 4) [NCBI Gene 2239] {aka K-glypican, KPTS}, RBM33 (RNA binding motif protein 33) [NCBI Gene 155435] {aka PRR8}, Rbm15b (RNA binding motif protein 15B) [NCBI Gene 109095] {aka 1810017N16Rik}, SETDB1 (SET domain bifurcated histone lysine methyltransferase 1) [NCBI Gene 9869] {aka ESET, H3-K9-HMTase4, KG1T, KMT1E, TDRD21}, RBM15 (RNA binding motif protein 15) [NCBI Gene 64783] {aka OTT, OTT1}, HSPA4 (heat shock protein family A (Hsp70) member 4) [NCBI Gene 3308] {aka APG-2, HEL-S-5a, HS24/P52, HSPH2, RY, hsp70}, METTL16 (methyltransferase 16, RNA N6-adenosine) [NCBI Gene 79066] {aka METT10D}, METTL14 (methyltransferase 14, N6-adenosine-methyltransferase non-catalytic subunit) [NCBI Gene 57721] {aka hMETTL14}, Wtap (WT1 associating protein) [NCBI Gene 60532] {aka 2810408K05Rik, 9430038B09Rik}, CCR4 (C-C motif chemokine receptor 4) [NCBI Gene 1233] {aka CC-CKR-4, CD194, CKR4, CMKBR4, ChemR13, HGCN:14099}, HNRNPA2B1 (heterogeneous nuclear ribonucleoprotein A2/B1) [NCBI Gene 3181] {aka HNRNPA2, HNRNPB1, HNRPA2, HNRPA2B1, HNRPB1, IBMPFD2}, CDKN3 (cyclin dependent kinase inhibitor 3) [NCBI Gene 1033] {aka CDI1, CIP2, KAP, KAP1}, YTHDC2 (YTH N6-methyladenosine RNA binding protein C2) [NCBI Gene 64848] {aka CAHL, hYTHDC2}, ATRX (ATRX chromatin remodeler) [NCBI Gene 546] {aka JMS, MRX52, RAD54, RAD54L, XH2, XNP}, SOX2 (SRY-box transcription factor 2) [NCBI Gene 6657] {aka ANOP3, MCOPS3}, YTHDC1 (YTH N6-methyladenosine RNA binding protein C1) [NCBI Gene 91746] {aka YT521, YT521-B}, PRC1 (protein regulator of cytokinesis 1) [NCBI Gene 9055] {aka ASE1, MAP65}, XPO1 (exportin 1) [NCBI Gene 7514] {aka CRM-1, CRM1, emb, exp1}, BRD4 (bromodomain containing 4) [NCBI Gene 23476] {aka CAP, CDLS6, FSHRG4, HUNK1, HUNKI, MCAP}, HOTAIR (HOX transcript antisense RNA) [NCBI Gene 100124700] {aka HOXAS, HOXC-AS4, HOXC11-AS1, NCRNA00072}, CBLL1 (Cbl proto-oncogene like 1) [NCBI Gene 79872] {aka HAKAI, RNF188}, YTHDF2 (YTH N6-methyladenosine RNA binding protein F2) [NCBI Gene 51441] {aka CAHL, DF2, HGRG8, NY-REN-2}, IGF2BP1 (insulin like growth factor 2 mRNA binding protein 1) [NCBI Gene 10642] {aka CRD-BP, CRDBP, IMP-1, IMP1, VICKZ1, ZBP1}, VIRMA (vir like m6A methyltransferase associated) [NCBI Gene 25962] {aka KIAA1429, MSTP054, fSAP121}, Cbx2 (chromobox 2) [NCBI Gene 12416] {aka M33, MOD2, pc}, SRSF9 (serine and arginine rich splicing factor 9) [NCBI Gene 8683] {aka SFRS9, SRp30c}, Ythdc1 (YTH domain containing 1) [NCBI Gene 231386] {aka A730098D12Rik, mKIAA1966}, LRPPRC (leucine rich pentatricopeptide repeat containing) [NCBI Gene 10128] {aka CLONE-23970, GP130, LRP130, LSFC, MC4DN5}, Spen (spen family transcription repressor) [NCBI Gene 56381] {aka Mint, mKIAA0929}, HNRNPC (heterogeneous nuclear ribonucleoprotein C) [NCBI Gene 3183] {aka HNRNP, HNRPC, MRD74, SNRPC}, HOXD@ (homeobox D cluster) [NCBI Gene 3230] {aka HOX4@}, Rbm15 (RNA binding motif protein 15) [NCBI Gene 229700] {aka C230088J01Rik, mKIAA1438}, Mettl3 (methyltransferase 3, N6-adenosine-methyltransferase complex catalytic subunit) [NCBI Gene 56335] {aka 2310024F18Rik, M6A, Spo8}, PTEN (phosphatase and tensin homolog) [NCBI Gene 5728] {aka 10q23del, BZS, CWS1, DEC, GLM2, MHAM}, ALKBH5 (alkB homolog 5, RNA demethylase) [NCBI Gene 54890] {aka ABH5, OFOXD, OFOXD1}, XIST (X inactive specific transcript) [NCBI Gene 7503] {aka DXS1089, DXS399E, LINC00001, NCRNA00001, SXI1, swd66}, ZFAS1 (ZNFX1 antisense RNA 1) [NCBI Gene 441951] {aka C20orf199, HSUP1, HSUP2, NCRNA00275, ZNFX1-AS1}, YTHDF1 (YTH N6-methyladenosine RNA binding protein F1) [NCBI Gene 54915] {aka C20orf21, DF1}, FTO (FTO alpha-ketoglutarate dependent dioxygenase) [NCBI Gene 79068] {aka ALKBH9, BMIQ14, GDFD, IFEX9}, NORAD (non-coding RNA activated by DNA damage) [NCBI Gene 647979] {aka LINC00657}, YTHDF3 (YTH N6-methyladenosine RNA binding protein F3) [NCBI Gene 253943] {aka DF3}, SQSTM1 (sequestosome 1) [NCBI Gene 8878] {aka A170, DMRV, EBIAP, FTDALS3, NADGP, OSIL}, GPX4 (glutathione peroxidase 4) [NCBI Gene 2879] {aka GPx-4, GSHPx-4, MCSP, PHGPx, SMDS, snGPx}, PABPC1 (poly(A) binding protein cytoplasmic 1) [NCBI Gene 26986] {aka PAB1, PABP, PABP1, PABPC2, PABPL1}, HOXC@ (homeobox C cluster) [NCBI Gene 3220] {aka HOX3@}, WTAP (WT1 associated protein) [NCBI Gene 9589] {aka Mum2}, IGF2BP3 (insulin like growth factor 2 mRNA binding protein 3) [NCBI Gene 10643] {aka CT98, IMP-3, IMP3, KOC, KOC1, VICKZ3}, MALAT1 (metastasis associated lung adenocarcinoma transcript 1) [NCBI Gene 378938] {aka HCN, LINC00047, NCRNA00047, NEAT2, PRO2853, miPEP-52}, NUCLEOLIN (nucleolin multifunctional protein) [NCBI Gene 4691] {aka C23, NCL, Nsr1}, TINCR (TINCR ubiquitin domain containing) [NCBI Gene 257000] {aka LINC00036, NCRNA00036, PLAC2, TUBL, onco-lncRNA-16}, ELAVL1 (ELAV like RNA binding protein 1) [NCBI Gene 1994] {aka ELAV1, HUR, Hua, MelG}, CXCL8 (C-X-C motif chemokine ligand 8) [NCBI Gene 3576] {aka GCP-1, GCP1, IL8, LECT, LUCT, LYNAP}, POU5F1 (POU class 5 homeobox 1) [NCBI Gene 5460] {aka OCT3, OCT4, OCT4Borf1, OTF-3, OTF3, OTF4}
- **Diseases:** cancer (MESH:D009369), pancreatic cancer (MESH:D010190), injury to (MESH:D014947), osteosarcoma (MESH:D012516), metastasis (MESH:D009362), LLPS (MESH:D000210), GBM (MESH:D005909), hypoxia (MESH:D000860), AML (MESH:D015470), triple (MESH:C536008), pulmonary fibrosis (MESH:D011658), gastric and colon cancer (MESH:D013274), degeneration of intervertebral discs (MESH:D055959), breast cancer (MESH:D001943)
- **Chemicals:** C (MESH:D002244), N6-hydroxymethyladenosine (MESH:C046517), N1-methyladenosine (MESH:C002230), inosines (MESH:D007288), BioRender (-), adenosine (MESH:D000241), doxycycline (MESH:D004318), N6-methyladenosine (MESH:C010223), adenine (MESH:D000225), poly-U (MESH:D011072), cytosine (MESH:D003596)
- **Species:** Homo sapiens (human, species) [taxon 9606], Mus musculus (house mouse, species) [taxon 10090]
- **Mutations:** A783 to uracil, guanine at the -1
- **Cell lines:** HEK293T — Homo sapiens (Human), Transformed cell line (CVCL_0063), ESCs — Mus musculus (Mouse), Embryonic stem cell (CVCL_9108), U2OS — Homo sapiens (Human), Osteosarcoma, Cancer cell line (CVCL_0042)

## Full text

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## Figures

4 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12922158/full.md

## References

156 references — full list in the complete paper: https://tomesphere.com/paper/PMC12922158/full.md

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Source: https://tomesphere.com/paper/PMC12922158