TABLE 2.
Representative lncRNAs that regulate DNA methylation of other genes in cancers and other disease.
| LncRNA name | Cofactor | Interaction mode | Target | Tissue/cancer | Function | References |
|---|---|---|---|---|---|---|
| DACOR1 | DNMT1 | Recruit | Genome wide | Colon cancer | TGF-β/BMP signaling | Merry et al. (2015); Somasundaram et al. (2018) |
| SAMD12-AS1 | DNMT1 | Recruit | p53 | Gastric cancer | P53 signaling pathway | Lu et al. (2021) |
| HOTAIR | DNMT1 | Recruit | PTEN | Chronic myelocytic leukemia | Song et al. (2021) | |
| HOTAIR | DNMT1 | Recruit | miR-122 | Hepatocellular carcinoma | Cyclin G1 repression | Cheng et al. (2018) |
| TINCR | DNMT1 | Recruit | miR-503-5p | Breast cancer | EGFR and JAK2–STAT3 signaling | Wang et al. (2021b) |
| ecCEBPA | DNMT1 | Sequester | CEBPA; genome wide | Di Ruscio et al. (2013); Ogunleye et al. (2021) | ||
| 91H | DNMT1 | Sequester | H19; IGF2 | Breast cancer | Vennin et al. (2017) | |
| HOTAIRM1 | DNMTs; G9a; EZH2 | Sequester | HOXA1 | Glioblastoma multiforme | Li et al. (2018) | |
| HOTAIRM1 | DNMT1 | Sequester | HOXA2 | Dental follicle stem cell | Osteogenesis | Chen et al. (2020b) |
| HOTAIR | DNMT3B | Recruit | HOXA5 | Acute myeloid leukemia | Apoptosis | Wang et al. (2019d) |
| MROS-1 | DNMT3A | Recruit | PRUNE2 | Su et al. (2021) | ||
| TTTY15 | DNMT3A | Sequester | TBX4 | Non-small cell lung cancer | Metastasis | Lai et al. (2019) |
| Dnmt3aos | DNMT3A | Expression | Genome wide | M(IL-4) macrophage | Macrophage polarization | Li et al. (2020a) |
| HOTAIR | DNMT1; DNMT3B | Expression | HOXA1 | Small cell lung cancer | Chemoresistance | Fang et al. (2016) |
| HOTAIR | DNMT3B | Expression | PTEN | Acute myeloid leukemia | Adriacin doxorubicin resistance | Zhou et al. (2021b) |
| H19 | miR-148a-3p—DNMT1 | ceRNA | MGMT; Genome wide | Laryngeal squamous cell carcinoma | Cell proliferation | Wu et al. (2016) |
| RP11-159K7.2 | miR-206—DNMT3B | ceRNA | miR-206 | Laryngeal squamous cell carcinoma | Wang et al. (2020) | |
| HOTAIR | miR-29b—DNMT3B | ceRNA | PTEN | Hepatocytes | Liver fibrosis | Yu et al. (2020a) |
| RMST | HuR—DNMT3B | RNA stability | Genome wide | Peng et al. (2020) | ||
| Linc-GALH | Ubiquitin—DNMT1 | Ubiquitination | Gankyrin | Hepatocellular carcinoma | AKT signaling | Xu et al. (2019c) |
| LUCAT1 | Ubiquitin—DNMT1 | Ubiquitination | Esophageal squamous cell carcinoma | Cell proliferation, apoptosis | Yoon et al. (2018) | |
| CCDC26 | DNMT1 | Subcellular location | Genome wide | Apoptosis | Jones et al. (2021) | |
| MAGI2-AS3 | TET1 | Recruit | MAGI2 | Breast cancer | Cell proliferation and migration | Xu et al. (2021b) |
| MAGI2-AS3 | TET2 | Recruit | LRIG1 | Acute myeloid leukaemia | Leukaemic stem cell self-renewal suppression | Chen et al. (2020a) |
| TARID | GADD45A—TET1 | Recruit | TCF21 | Arab et al. (2014); Arab et al. (2019) | ||
| HOTAIR | TET1 | Expression | SOX17; MAGI2 | Cervical cancer (Hela cell) | Wnt/β-catenin signaling | Salmeron-Barcenas et al. (2019) |
| H19 | let-7—TET1 | ceRNA | TGFBR2; TSP1 | Atherosclerotic coronary arteries | TGF-β signaling | Cao et al. (2020) |
| H19 | let-7—TET3 | ceRNA | HMGA2 | Uterine leiomyomas | Proliferation | Cao et al. (2019) |
| TETILA | TET2 | Ubiquitination; subcellular location; recruit | MMP-9 | Diabetic skin | Wound healing | Zhou et al. (2019a) |
| PYCARD-AS1 | G9a; DNMT1 | Recruit | PYCARD | Breast cancer | Miao et al. (2019) | |
| KCNQ1OT1 | HP1α | Recruit | Genome wide | Lung fibroblast | Heterochromatin reorganization | Zhang et al. (2022b) |
| LINC01133 | EZH2 | Recruit | DKK1 | Pancreatic cancer | Wnt signaling | Weng et al. (2019) |
| HOXB13-AS1 | EZH2; DNMT3B | Recruit | HOXB13 | Glioma | Xiong et al. (2018) | |
| Lnc-LALC | EZH2; DNMTs | Recruit | LZTS1 | Colorectal cancer | Liver metastasis | Zhang et al. (2021a) |
| LUCAT1 | EZH2; DNMTs | Recruit | CXXC4; SFRP2 | Gastric cancer | Wnt/β-catenin signaling | Byun et al. (2020) |
| SNHG22 | EZH2; DNMT1 | Recruit | miR-16-5p | Hepatocellular carcinoma | Cell proliferation | Zhang et al. (2021c) |
| GIHCG | EZH2; DNMT1 | Recruit | miR-200b/a/429 | Hepatocellular carcinoma | Cell proliferation and migration | Sui et al. (2016) |
| SChLAP1 | EZH2; DNMT3A; miR-340-5p—DNMT3A | Recruit; expression | miR-340-5p; miR-143-3p; miR-145-5p | Prostate cancer | Cell proliferation and migration | Huang and Tang, (2021) |
| HOXA11-AS | EZH2; LSD1; DNMT1; miR-1297—EZH2 | Recruit; ceRNA | PRSS8; KLF2 | Gastric cancer | Cell proliferation, migration and apoptosis | Sun et al. (2016) |
| LINC00470 | miR-101—EZH2; miR-101—EED | ceRNA | ELFN2 | Glioblastoma | Cell autophagy | Liu et al. (2018) |
| H19 | SAHH | Interaction | Nctc1; genome wide | Zhou et al. (2015) | ||
| H19 | SAHH | Interaction | HNF4α | Liver of metformin-exposed fetuses | Liver development and function | Deng et al. (2017) |
| H19 | SAHH | Interaction | Beclin1 | Breast cancer | Autophagy | Wang et al. (2019c) |
| H19 | SAHH | Interaction | LINE-1 | Lung | Fu et al. (2018) | |
| SNHG6 | miR-1297—MAT2A; MAT1A | ceRNA; subcellular location | Genome wide | Hepatocellular carcinoma | Guo et al. (2018) | |
| LINC00662 | MAT1A; SAHH | Interaction | Genome wide | Hepatocellular carcinoma | Guo et al. (2020) | |
| PARTICLE | G9a; SUZ12 | Recruit | MAT2A | Breast cancer cell line | Response to irradiation | O'Leary et al. (2015) |
| LINC00261 | DNMTs | Recruit | DYPD | Esophageal cancer | 5-fluorouracil resistance | Lin et al. (2019) |
| LINC01419 | DNMTs | Recruit | GSTP1 | Esophageal cancer | 5-fluorouracil resistance | Chen et al. (2019b) |
| LINC00673 | DNMTs | Recruit | KLF4 | Prostate cancer | Paclitaxel resistance | Jiang et al. (2020) |
| LINC00628 | DNMTs | Recruit | LAMA3 | Lung adenocarcinoma | Vincristine resistance | Xu et al. (2019b) |
| LINC00607 | DNMTs | Recruit | CASP9 | Thyroid cancer | Doxorubicin resistance | Li et al. (2021a) |
| 91H | DNMTs | Recruit | CDK4 | Osteosarcoma | Tumor migration and invasion | Cheng et al. (2021) |
| H19 | DNMT3B | Expression | Genome wide | Endometrial cancer; breast cancer | Cell proliferation | Zhong et al. (2017) |
| HOTAIR | EZH2; DNMTs | Interaction | ALDH1A1 | Ovarian cancer | Spheroid formation and colony-forming | Wang et al. (2021c) |
| HOTAIR | miR-126—DNMT1 | ceRNA | CDKN2A | Osteosarcoma | Cell viability and apoptosis | Li et al. (2017) |
| LINC00240 | miR-124-3p—DNMT3B | ceRNA | miR-124-3p | Gastric cancer | Cell proliferation, invasion and migration | Li et al. (2020c) |
| XIST | miR-149-5p—DNMT3A | ceRNA | miR-149-5p | Cartilage | Cell proliferation, apoptotic and ENC degradation | Liu et al. (2020d) |
| HOTTIP | miR-101—DNMT3B | ceRNA | HoxA13 | Cartilage | Cartilage development and destruction | Kim et al. (2013) |
| IRAIN | DNMT1; DNMT3A; DNMT3B | Recruit | VEGFA | Renal carcinoma | Cell proliferation, migration and apoptosis | Li et al. (2020b) |
| AS1DHRS4 | G9a; EZH2 | Recruit | DHRS4L1; DHRS4L2 | Li et al. (2012) | ||
| PRKCA-AS1 | DNMT1 | Recruit | PRKCA | Heart | p38/MAPK pathway | Xie et al. (2021) |
| LINC00518 | DNMT1; DNMT3A; DNMT3B | Recruit | CDX2 | Breast cancer | Cell proliferation, invasion, migration and EMT | Wang et al. (2019b) |
| RCPCD | DNMT1; DNMT2; DNMT3 | Recruit | HCN4 | Embryonic stem cells | Differentiation of ESCs into pacemakelike cells | Zhu et al. (2021) |
| LINC00313 | DNMT1; DNMT3B | Recruit | ALX4 | Thyroid cancer | AKT/mTOR signaling, cell proliferative, migratory, invasive abilities as well as EMT | Zhao and Hu, (2019) |
| LINC00152 | DNMTs | Recruit | BRCA1/PTEN | Breast cancer | Tumorigenesis and metastasis | Wu et al. (2018) |
| LINC00470 | DNMT3A | Recruit | PTEN | Endometrial cancer | Cell invasiveness, migration and angiogenesis, facilitate tumorigenesis and metastasis | Yi et al. (2021) |
| LINC00922 | DNMT1; DNMT3A; DNMT3B | Recruit | NKD2 | Breast cancer | Wnt signaling pathway | Wang et al. (2021d) |
| LINC01419 | DNMT1; DNMT3A; DNMT3B | Recruit | ZIC1 | Hepatocellular carcinoma | PI3K/Akt signaling pathway, tumor formation and metastasis | Hou et al. (2021) |
| MIR210HG | DNMT1 | Recruit | CACNA2D2 | Non-small cell lung cancer | Cell proliferation and migration | Kang et al. (2019) |
| SNHG1 | DNMT1 | Recruit | Bcl-2 | Sepsis | Cell inflammation and apoptotic | Zhang et al. (2022a) |
| ADAMTS9-AS2 | DNMT1; DNMT3A; DNMT3B | Recruit | CDH3 | Esophageal cancer | Cell proliferation, invasion and migration | Liu et al. (2020a) |
| ELFN1-AS1 | DNMT1; DNMT3A; DNMT3B | Recruit | ZBTB16 | Gastric cancer | PI3K/AKT signaling pathway | Zhuang et al. (2022) |
| IGF2-AS | DNMT1 | Recruit | IGF2 | Breast cancer | PI3K/AKT/mTOR signaling pathway | Zhang et al. (2021d) |
| NEAT1 | G9a; DNMT1; Snail | Recruit | CDH1 | Osteosarcoma | Metastasis in vitro and in vivo, EMT | Li and Cheng, (2018) |
| PCAT-14 | DNMT1; DNMT3A; DNMT3B | Recruit | miR-372 | Hepatocellular carcinoma | Cell proliferation, invasion, cell cycle arrest | Wang et al. (2017) |
| HAGLR | DNMT1 | Recruit | E2F1 | Lung adenocarcinoma | Cell growth | Guo et al. (2019) |
| XIST | DNMT1; DNMT3A; DNMT3B | Recruit | TIMP-3 | Cartilage | Collagen degradation | Chen et al. (2019a) |
| RAMP2-AS1 | DNMT1; DNMT3B | Recruit | CXCL11 | Breast cancer | Tumor growth | Li et al. (2022a) |
| TNRC6C-AS1 | DNMT1; DNMT3A; DNMT3B | Recruit | STK4 | Thyroid cancer | Hippo signaling pathway | Yang et al. (2019a) |
| yylncT | DNMT3B | Recruit | Embryo | Embryonic cell fate transition | Frank et al. (2019) | |
| SNHG1 | DNMT1 | Expression | PTBP1 | Bone marrow | Adipogenic differentiation and contributed to osteoporosis | Yu et al. (2022a) |
| FAS-AS1 | DNMT3B | Expression | SIRT1; FAS | Leukemia | Yuan et al. (2020) | |
| Linc-POU3F3 | EZH2; DNMT1; DNMT3A; DNMT3B | Recruit | POU3F3 | Esophageal squamous cell carcinoma | Cell proliferation and ability to form colonies | Li et al. (2014) |
| PVT1 | EZH2; DNMT1 | Recruit | miR-18b-5p; HIF1A | Gallbladder cancer | Cell proliferation | Jin et al. (2020) |
| ROIT | DNMT3A | Ubiquitination | Nkx6.1 | Pancreas islet | Glucose homeostasis and insulin transcription | Zhang et al. (2020a) |
| Platr10 | TET1 | Recruit | Oct4 | Modulating chromatin architecture | Du et al. (2021b) | |
| WT1-AS | TET2; TET3; DNMTs | Recruit | WT1 | Leukemia | McCarty and Loeb, (2015) | |
| NEAT1 | DNMTs | Recruit | miR-129-5p; WNT4 | Breast cancer | WNT signaling | Lo et al. (2016) |
| Evf2 | MECP2 | Recruit | DLX1/2 | Forebrain | Berghoff et al. (2013) | |
| NKILA | NF-κB; DNMT3A | Recruit | KLF4 | Vascular endothelium | Endothelium inflammation | Zhu et al. (2019) |
| HOTAIR | DNMT1; DNMT3B; EZH2 | Expression | HOXA1 | Small cell lung cancer | Multidrug resistance | Fang et al. (2018) |
| ANRIL | EZH2 | Recruit | ERRFI1 | Cholangiocarcinoma | Cell proliferation and migration | Yu et al. (2020b) |
| LINC00858 | DNMTs | Recruit | WNK2 | Colon cancer | Cell apoptosis, autophagy and senescence | Wu et al. (2020) |
| UCA1 | EZH2 | Recruit | p21 | Breast cancer | PI3K/AKT signaling pathway | Li et al. (2019) |
| H19 | EZH2 | Recruit | BIK | Breast cancer | Paclitaxel (PTX) resistance | Si et al. (2016) |
| AC092723.1 | TET1 | Recruit | IRF8 | Zhou et al. (2022) | ||
| HOTAIR | EZH2 | Recruit | E-cadherin | Oral squamous cell carcinoma | Cell invasion, migration and apoptosis | Wu et al. (2015) |
| LINC00887 | DNMT1 | Recruit | CA9 | Tongue squamous carcinoma | Suppress oncogenic CA9 | Shen et al. (2021b) |
| LINC00472 | DNMTs | Recruit | MCM6 | Breast cancer | Inhibite tumor growth and metastasis | Shao et al. (2021) |
| LINC01270 | DNMTs | Recruit | GSTP1 | Esophageal cancer | Cell proliferation, migration, invasion and drug resistance | Li et al. (2021b) |
| HOTAIR | DNMTs | Recruit | MTHFR | Esophageal cancer | Cell apoptosis and proliferation | Zhang et al. (2020b) |
| BZRAP1-AS1 | DNMT3B | Recruit | THBS1 | Hepatocellular carcinoma | Angiogenesis and tumor growth | Wang et al. (2019e) |
| PVT1 | DNMT1 | Recruit | BNIP3 | Gastric cancer | Cell proliferation | Xin et al. (2021) |
| SNHG3 | EZH2 | Recruit | MED18 | Gastric cancer | Cell migration and invasion | Xuan and Wang, (2019) |
| HOTAIR | DNMT1; EZH2 | Recruit | miR-454-3p | Gastric cancer | Cell apoptosis and autophagy | Bao et al. (2017) |
| LINC00630 | DNMT3B; EZH2 | Recruit | BEX1 | Colorectal cancer | Cell apoptosis and radio-resistance | Liu et al. (2020b) |
| Lnc34a | DNMT3A; PHB2 | Recruit | miR-34a | Colorectal cancer | Cell proliferation | Wang et al. (2016) |
| SATB2-AS1 | TETs; GADD45A | Recruit | SATB2 | Colorectal cancer | Cell metastasis and immune response | Xu et al. (2019a) |
| Dali | DNMT1 | Recruit | Pou3f3; genome wide | Central nervous system | Cell differentiation | Chalei et al. (2014) |
| Dum | DNMT1; DNMT3A; DNMT3B | Recruit | Dppa2 | Skeletal myoblast cell | Myogenesis | Wang et al. (2015) |
| lincRNA-p21 | HNRNPK – DNMT1; SETDB1 | Recruit | Nanog | Pluripotent stem cell | Cell differentiation | Bao et al. (2015) |
| Kcnq1ot1 | DNMT1; EZH2; G9a | Recruit | Kcnq1 | Placenta | Gene imprinting | Mohammad et al. (2010) |
| THAP9-AS1 | DNMTs | Recruit | SOCS3 | Osteosarcoma | JAK2/STAT3 signaling | Yang et al. (2021b) |
| H19 | PRC2 | Recruit | genome wide | Neuroendocrine prostate cancer | Metastatic | Singh et al. (2021) |
| KCNQ1OT1 | DNMT1 | Recruit | PTEN | Triple negative breast cancer | Cell proliferation, invasion, and migration | Shen et al. (2021a) |
| KCNQ1OT1 | DNMT1; DNMT3A; DNMT3B | Recruit | EIF2B5 | Ovarian cancer | Metastasis | He et al. (2022) |
| KAT7 | DNMTs | Recruit | miR-10a | Non-small cell lung cancer | Gao et al. (2021) | |
| SNHG3 | miR-448—DNMT1 | ceRNA | SEPT9 | Gastric cancer | Cell growth, metastasis | Li et al. (2022d) |
| KIF9-AS1 | DNMT1 | Recruit | RAI2 | Hepatocellular carcinoma | Cell proliferation, migration, apoptosis | Yu et al. (2022b) |
| PVT1 | EZH2; DNMT1 | Recruit | ZBP1 | Liver cell | Response to nonylphenol | Qiannan et al. (2022) |
| ZFAS1 | DNMT3B | Recruit | Notch1 | Myocardial ischemia-reperfusion injury | Apoptosis | Li et al. (2022b) |
| UCA1 | EZH2; DNMT1 | Recruit | APAF1 | Myocardial ischemia-reperfusion injury | Jin et al. (2022) | |
| LINC01270 | DNMT1; DNMT3A; DNMT3B | Recruit | LAMA2 | Breast cancer | MAPK signaling pathway | Li et al. (2022c) |
| UCA1 | DNMT1; DNMT3A; DNMT3B | Recruit | METTL14 | Breast cancer | Cell proliferation, invasion, metastasis | Zhao et al. (2022a) |