Table Info

Table 3.

Gene activation by lncRNAs through euchromatin regulation and histone marks

Gene	Interaction	Target	Histone mark	Reference
GClnc1	WDR5, KAT2A	SOD2 promoter	H3K4me3, H3K9ac	[84, 88]
GCAWKR	WDR5, KAT2A	PTP4A1	H3K4me3, H3K9ac	[85]
TM4SF19-AS1	WDR5	TM4SF19	H3K4me3	[84]
LincRNA-P21	hnRNPK	P21	H3K4me3, H3K9ac	[89]
Gm29348	-	-	H3K4me3, H3K9ac	[90]
TARID	GADD45A	TCF21	CpG	[105]
lncPRESS1	SIRT6	Embryogenesis	H3K56ac, H3K9ac	[106]
HOTTIP	WDR5	HOXA	H3K4me3	[107–109]
CCAT1-L, PVT1	CTCF, hnRNPK	MYC	Chromatin loop, NUP153 binding to cohesin	[110]
NRIP enhancer	Cohesin	ER dependent genes	Chromatin loop nuclear receptor interacting protein	[111, 112]
CHASERR	CHD2	CHD2 regulated promoters	Binding to nascent RNA	[44, 113]
HASTER	-	HNF1A	Promoter enhancer interaction	[114]
NEAT1_2	RBP14	Euchromatin binding	Paraspeckle condensates	[115]
THRIL	hnRNPs	TNF-α	Promoter/enhancer activation	[44, 101]
HOTAIR	LSD1	HBXIP-MYC dimer MYC target genes	Lysine demethylation	[44]
NeST	WDR5	IFN-gamma	H3K4me	[116]
Lnc13	hnRNPD	Suppress Inflammatory genes by chromatin access	Celiac disease	[12]

CCAT1-L: Colon cancer associated transcript 1-long; PVT1: plasmacytoma variant translocation 1; CHASERR: CHD2 adjacent suppressive regulatory RNA; MYC: viral myelocytomatosis homolog; LSD1: lysine-specific demethylase 1; NEAT1: nuclear enriched abundant transcript 1; GADD45A: growth arrest and DNA-damage-inducible alpha; CTCF: CCCTC-binding factor; CHD2: chromodomain-helicase DNA binding protein 2; -: blank cell

Declarations

Author contributions

PP: Writing—review and editing.

Conflicts of interest

The author declares that he has no conflicts of interest.

Ethical approval

Not applicable.

Consent to participate

Not applicable.

Consent to publication

Not applicable.

Availability of data and materials

Not applicable.

Funding

Not applicable.

Copyright

References

Farooqi AA, Fayyaz S, Poltronieri P, Calin G, Mallardo M. Epigenetic deregulation in cancer: Enzyme players and non-coding RNAs. Semin Cancer Biol. 2022;83:197–207. [DOI] [PubMed]

Mendes Soares LM, Valcárcel J. The expanding transcriptome: the genome as the ‘Book of Sand’. EMBO J. 2006;25:923–31. [DOI] [PubMed] [PMC]

Costa FF. Non-coding RNAs: new players in eukaryotic biology. Gene. 2005;357:83–94. [DOI] [PubMed]

Claverie JM. Fewer genes, more noncoding RNA. Science. 2005;309:1529–30. [DOI] [PubMed]

Mattick JS, Makunin IV. Non-coding RNA. Hum Mol Genet. 2006;15:R17–29. [DOI] [PubMed]

Pasquinelli AE, Hunter S, Bracht J. MicroRNAs: a developing story. Curr Opin Genet Dev. 2005;15:200–5. [DOI] [PubMed]

Cui H, Li H, Wu H, Du F, Xie X, Zeng S, et al. A novel 3’tRNA-derived fragment tRF-Val promotes proliferation and inhibits apoptosis by targeting EEF1A1 in gastric cancer. Cell Death Dis. 2022;13:471. [DOI] [PubMed] [PMC]

Mattick JS, Amaral PP, Carninci P, Carpenter S, Chang HY, Chen LL, et al. Long non-coding RNAs: definitions, functions, challenges and recommendations. Nat Rev Mol Cell Biol. 2023;24:430–47. [DOI] [PubMed] [PMC]

Ahmad A, Poltronieri P, Uddin S. Editorial: LncRNAs in Cancer Metastasis and Therapy Resistance. Front Oncol. 2021;11:813274. [DOI] [PubMed] [PMC]

10.

Moore LD, Le T, Fan G. DNA methylation and its basic function. Neuropsychopharmacology. 2013;38:23–38. [DOI] [PubMed] [PMC]

11.

Yang Z, Xu F, Teschendorff AE, Zhao Y, Yao L, Li J, et al. Insights into the role of long non-coding RNAs in DNA methylation mediated transcriptional regulation. Front Mol Biosci. 2022;9:1067406. [DOI] [PubMed] [PMC]

12.

Cusenza VY, Tameni A, Neri A, Frazzi R. The lncRNA epigenetics: The significance of m6A and m5C lncRNA modifications in cancer. Front Oncol. 2023;13:1063636. [DOI] [PubMed] [PMC]

13.

Ping XL, Sun BF, Wang L, Xiao W, Yang X, Wang WJ, et al. Mammalian WTAP is a regulatory subunit of the RNA N6-methyladenosine methyltransferase. Cell Res. 2014;24:177–89. [DOI] [PubMed] [PMC]

14.

Schubert M, Hackl H, Gassner FJ, Greil R, Geisberger R. Investigating epigenetic effects of activation-induced deaminase in chronic lymphocytic leukemia. PLoS One. 2018;13:e0208753. [DOI] [PubMed] [PMC]

15.

Jiao J, Jin Y, Zheng M, Zhang H, Yuan M, Lv Z, et al. AID and TET2 co-operation modulates FANCA expression by active demethylation in diffuse large B cell lymphoma. Clin Exp Immunol. 2019;195:190–201. [DOI] [PubMed] [PMC]

16.

Bannister AJ, Kouzarides T. Regulation of chromatin by histone modifications. Cell Res. 2011;21:381–95. [DOI] [PubMed] [PMC]

17.

Gardner KE, Allis CD, Strahl BD. Operating on chromatin, a colorful language where context matters. J Mol Biol. 2011;409:36–46. [DOI] [PubMed] [PMC]

18.

Jeltsch A, Broche J, Bashtrykov P. Molecular Processes Connecting DNA Methylation Patterns with DNA Methyltransferases and Histone Modifications in Mammalian Genomes. Genes (Basel). 2018;9:566. Erratum in: Genes (Basel). 2019;10:388. [DOI] [PubMed] [PMC]

19.

Bure IV, Nemtsova MV, Kuznetsova EB. Histone Modifications and Non-Coding RNAs: Mutual Epigenetic Regulation and Role in Pathogenesis. Int J Mol Sci. 2022;23:5801. [DOI] [PubMed] [PMC]

20.

Chen R, Zhao WQ, Fang C, Yang X, Ji M. Histone methyltransferase SETD2: a potential tumor suppressor in solid cancers. J Cancer. 2020;11:3349–56. [DOI] [PubMed] [PMC]

21.

Perez MF, Sarkies P. Histone methyltransferase activity affects metabolism in human cells independently of transcriptional regulation. PLoS Biol. 2023;21:e3002354. [DOI] [PubMed] [PMC]

22.

Wen H, Li Y, Xi Y, Jiang S, Stratton S, Peng D, et al. ZMYND11 links histone H3.3K36me3 to transcription elongation and tumour suppression. Nature. 2014;508:263–8. [DOI] [PubMed] [PMC]

23.

Sanulli S, Gross JD, Narlikar GJ. Biophysical Properties of HP1-Mediated Heterochromatin. Cold Spring Harb Symp Quant Biol. 2019;84:217–25. [DOI] [PubMed] [PMC]

24.

Lian C, Zhang C, Tian P, Tan Q, Wei Y, Zhang Q, et al. Epigenetic reader ZMYND11 noncanonical function restricts HNRNPA1-mediated stress granule formation and oncogenic activity. [Preprint]. 2023 [cited 2023 Nov 30]. Available from: https://doi.org/10.1101/2023.11.28.569112

25.

Chowdhury R, Yeoh KK, Tian YM, Hillringhaus L, Bagg EA, Rose NR, et al. The oncometabolite 2-hydroxyglutarate inhibits histone lysine demethylases. EMBO Rep. 2011;12:463–9. [DOI] [PubMed] [PMC]

26.

Bracken AP, Brien GL, Verrijzer CP. Dangerous liaisons: interplay between SWI/SNF, NuRD, and Polycomb in chromatin regulation and cancer. Genes Dev. 2019;33:936–59. [DOI] [PubMed] [PMC]

27.

Long Y, Hwang T, Gooding AR, Goodrich KJ, Rinn JL, Cech TR. RNA is essential for PRC2 chromatin occupancy and function in human pluripotent stem cells. Nat Genet. 2020;52:931–8. [DOI] [PubMed] [PMC]

28.

Long Y, Hwang T, Gooding AR, Goodrich KJ, Vallery TK, Rinn JL, et al. Evaluation of the RNA-dependence of PRC2 binding to chromatin in human pluripotent stem cells. [Preprint]. 2023 [cited 2024 May 2]. Available from: https://doi.org/10.1101/2023.08.17.553776

29.

Braga EA, Fridman MV, Burdennyy AM, Loginov VI, Dmitriev AA, Pronina IV, et al. Various LncRNA Mechanisms in Gene Regulation Involving miRNAs or RNA-Binding Proteins in Non-Small-Cell Lung Cancer: Main Signaling Pathways and Networks. Int J Mol Sci. 2023;24:13617. [DOI] [PubMed] [PMC]

30.

Yang X, Liu M, Li M, Zhang S, Hiju H, Sun J, et al. Epigenetic modulations of noncoding RNA: a novel dimension of Cancer biology. Mol Cancer. 2020;19:64. [DOI] [PubMed] [PMC]

31.

Willingham AT, Orth AP, Batalov S, Peters EC, Wen BG, Aza-Blanc P, et al. A strategy for probing the function of noncoding RNAs finds a repressor of NFAT. Science. 2005;309:1570–3. [DOI] [PubMed]

32.

Tiedge H. K-turn motifs in spatial RNA coding. RNA Biol. 2006;3:133–9. [DOI] [PubMed] [PMC]

33.

Nylund P, Garrido-Zabala B, Kalushkova A, Wiklund HJ. The complex nature of lncRNA-mediated chromatin dynamics in multiple myeloma. Front Oncol. 2023;13:1303677. [DOI] [PubMed] [PMC]

34.

Hu WL, Jin L, Xu A, Wang YF, Thorne RF, Zhang XD, et al. GUARDIN is a p53-responsive long non-coding RNA that is essential for genomic stability. Nat Cell Biol. 2018;20:492–502. [DOI] [PubMed]

35.

Hung T, Wang Y, Lin MF, Koegel AK, Kotake Y, Grant GD, et al. Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters. Nat Genet. 2011;43:621–9. [DOI] [PubMed] [PMC]

36.

Fernandes N, Buchan JR. RNAs as Regulators of Cellular Matchmaking. Front Mol Biosci. 2021;8:634146. [DOI] [PubMed] [PMC]

37.

Gong C, Popp MW, Maquat LE. Biochemical analysis of long non-coding RNA-containing ribonucleoprotein complexes. Methods. 2012;58:88–93. [DOI] [PubMed] [PMC]

38.

Alzrigat M, Párraga AA, Jernberg-Wiklund H. Epigenetics in multiple myeloma: From mechanisms to therapy. Semin Cancer Biol. 2018;51:101–15. [DOI] [PubMed]

39.

Shen Q, Zhang Q, Shi Y, Shi Q, Jiang Y, Gu Y, et al. Tet2 promotes pathogen infection-induced myelopoiesis through mRNA oxidation. Nature. 2018;554:123–7. [DOI] [PubMed]

40.

Cherney RE, Mills CA, Herring LE, Braceros AK, Calabrese JM. A monoclonal antibody raised against human EZH2 cross-reacts with the RNA-binding protein SAFB. Biol Open. 2023;12:bio059955. [DOI] [PubMed] [PMC]

41.

Mangoni D, Simi A, Lau P, Armaos A, Ansaloni F, Codino A, et al. LINE-1 regulates cortical development by acting as long non-coding RNAs. Nat Commun. 2023;14:4974. [DOI] [PubMed] [PMC]

42.

Uckelmann M, Davidovich C. Not just a writer: PRC2 as a chromatin reader. Biochem Soc Trans. 2021;49:1159–70. [DOI] [PubMed] [PMC]

43.

Xia M, Yao L, Zhang Q, Wang F, Mei H, Guo X, et al. Long noncoding RNA HOTAIR promotes metastasis of renal cell carcinoma by up-regulating histone H3K27 demethylase JMJD3. Oncotarget. 2017;8:19795–802. [DOI] [PubMed] [PMC]

44.

Yang Q, Chen Y, Guo R, Dai Y, Tang L, Zhao Y, Wu X, Li M, Du F, Shen J, Yi T, Xiao Z, Wen Q. Interaction of ncRNA and Epigenetic Modifications in Gastric Cancer: Focus on Histone Modification. Front Oncol. 2022;11:822745. [DOI] [PubMed] [PMC]

45.

Song Y, Wang R, Li LW, Liu X, Wang YF, Wang QX, et al. Long non-coding RNA HOTAIR mediates the switching of histone H3 lysine 27 acetylation to methylation to promote epithelial-to-mesenchymal transition in gastric cancer. Int J Oncol. 2019;54:77–86. [DOI] [PubMed] [PMC]

46.

Li H, An J, Wu M, Zheng Q, Gui X, Li T, et al. LncRNA HOTAIR promotes human liver cancer stem cell malignant growth through downregulation of SETD2. Oncotarget. 2015;6:27847–64. [DOI] [PubMed] [PMC]

47.

Davidovich C, Zheng L, Goodrich KJ, Cech TR. Promiscuous RNA binding by Polycomb repressive complex 2. Nat Struct Mol Biol. 2013;20:1250–7. [DOI] [PubMed] [PMC]

48.

Davidovich C, Cech TR. The recruitment of chromatin modifiers by long noncoding RNAs: lessons from PRC2. RNA. 2015;21:2007–22. [DOI] [PubMed] [PMC]

49.

Cifuentes-Rojas C, Hernandez AJ, Sarma K, Lee JT. Regulatory interactions between RNA and polycomb repressive complex 2. Mol Cell. 2014;55:171–85. [DOI] [PubMed] [PMC]

50.

Kretz M, Meister G. RNA binding of PRC2: promiscuous or well ordered? Mol Cell. 2014;55:157–8. [DOI] [PubMed]

51.

Wu L, Murat P, Matak-Vinkovic D, Murrell A, Balasubramanian S. Binding interactions between long noncoding RNA HOTAIR and PRC2 proteins. Biochemistry. 2013;52:9519–27. [DOI] [PubMed] [PMC]

52.

Wang G, Ye H, Wang X, Liu B. Polycomb repressive complex 2 controls cardiac cell fate decision via interacting with RNA: Promiscuously or well-ordered. Front Genet. 2022;13:1011228. [DOI] [PubMed] [PMC]

53.

Kanhere A, Viiri K, Araújo CC, Rasaiyaah J, Bouwman RD, Whyte WA, et al. Short RNAs are transcribed from repressed polycomb target genes and interact with polycomb repressive complex-2. Mol Cell. 2010;38:675–88. [DOI] [PubMed] [PMC]

54.

Betancur JG, Tomari Y. Cryptic RNA-binding by PRC2 components EZH2 and SUZ12. RNA Biol. 2015;12:959–65. [DOI] [PubMed] [PMC]

55.

Zimmerman SM, Lin PN, Souroullas GP. Non-canonical functions of EZH2 in cancer. Front Oncol. 2023;13:1233953. [DOI] [PubMed] [PMC]

56.

Portoso M, Ragazzini R, Brenčič Ž, Moiani A, Michaud A, Vassilev I, et al. PRC2 is dispensable for HOTAIR-mediated transcriptional repression. EMBO J. 2017;36:981–94. [DOI] [PubMed] [PMC]

57.

Majello B, Gorini F, Saccà CD, Amente S. Expanding the Role of the Histone Lysine-Specific Demethylase LSD1 in Cancer. Cancers (Basel). 2019;11:324. [DOI] [PubMed] [PMC]

58.

Han MH, Issagulova D, Park M. Interplay between epigenome and 3D chromatin structure. BMB Rep. 2023;56:633–44. [DOI] [PubMed] [PMC]

59.

Yoon JH, Abdelmohsen K, Kim J, Yang X, Martindale JL, Tominaga-Yamanaka K, et al. Scaffold function of long non-coding RNA HOTAIR in protein ubiquitination. Nat Commun. 2013;4:2939. [DOI] [PubMed] [PMC]

60.

Ye M, Xie L, Zhang J, Liu B, Liu X, He J, et al. Determination of long non-coding RNAs associated with EZH2 in neuroblastoma by RIP-seq, RNA-seq and ChIP-seq. Oncol Lett. 2020;20:1. [DOI] [PubMed] [PMC]

61.

Wang Y, Xie Y, Li L, He Y, Zheng D, Yu P, et al. EZH2 RIP-seq Identifies Tissue-specific Long Non-coding RNAs. Curr Gene Ther. 2018;18:275–85. [DOI] [PubMed] [PMC]

62.

Maciak P, Suder A, Wadas J, Aronimo F, Maiuri P, Bochenek M, et al. Dynamic changes in LINC00458/HBL1 lncRNA expression during hiPSC differentiation to cardiomyocytes. Sci Rep. 2024;14:109. [DOI] [PubMed] [PMC]

63.

Liu J, Liu S, Han L, Sheng Y, Zhang Y, Kim IM, et al. LncRNA HBL1 is required for genome-wide PRC2 occupancy and function in cardiogenesis from human pluripotent stem cells. Development. 2021;148:dev199628. [DOI] [PubMed] [PMC]

64.

Zhao S, Zhang X, Chen S, Zhang S. Long noncoding RNAs: fine-tuners hidden in the cancer signaling network. Cell Death Discov. 2021;7:283. [DOI] [PubMed] [PMC]

65.

Zhang F, Ruan X, Ma J, Liu X, Zheng J, Liu Y, et al. DGCR8/ZFAT-AS1 Promotes CDX2 Transcription in a PRC2 Complex-Dependent Manner to Facilitate the Malignant Biological Behavior of Glioma Cells. Mol Ther. 2020;28:613–30. [DOI] [PubMed] [PMC]

66.

Zang C, Nie FQ, Wang Q, Sun M, Li W, He J, et al. Long non-coding RNA LINC01133 represses KLF2, P21 and E-cadherin transcription through binding with EZH2, LSD1 in non small cell lung cancer. Oncotarget. 2016;7:11696–707. [DOI] [PubMed] [PMC]

67.

Li Y, Liu C, Fan H, Du Y, Zhang R, Zhan S, et al. Gli2-induced lncRNA Peg13 alleviates cerebral ischemia-reperfusion injury by suppressing Yy1 transcription in a PRC2 complex-dependent manner. Metab Brain Dis. 2023;38:1389–404. [DOI] [PubMed]

68.

Kong Y, Hsieh CH, Alonso LC. ANRIL: A lncRNA at the CDKN2A/B Locus With Roles in Cancer and Metabolic Disease. Front Endocrinol (Lausanne). 2018;9:405. [DOI] [PubMed] [PMC]

69.

Ding J, Xie M, Lian Y, Zhu Y, Peng P, Wang J, et al. Long noncoding RNA HOXA-AS2 represses P21 and KLF2 expression transcription by binding with EZH2, LSD1 in colorectal cancer. Oncogenesis. 2017;6:e288. [DOI] [PubMed] [PMC]

70.

Kozłowska J, Kolenda T, Poter P, Sobocińska J, Guglas K, Stasiak M, et al. Long Intergenic Non-Coding RNAs in HNSCC: From “Junk DNA” to Important Prognostic Factor. Cancers (Basel). 2021;13:2949. [DOI] [PubMed] [PMC]

71.

Ruan J, Zheng L, Hu N, Guan G, Chen J, Zhou X, et al. Long noncoding RNA SNHG6 promotes osteosarcoma cell proliferation through regulating p21 and KLF2. Arch Biochem Biophys. 2018;646:128–36. [DOI] [PubMed]

72.

Lian Y, Yan C, Ding J, Xia R, Ma Z, Hui B, et al. A novel lncRNA, LL22NC03-N64E9.1, represses KLF2 transcription through binding with EZH2 in colorectal cancer. Oncotarget. 2017;8:59435–45. [DOI] [PubMed] [PMC]

73.

Lian Y, Yang J, Lian Y, Xiao C, Hu X, Xu H. DUXAP8, a pseudogene derived lncRNA, promotes growth of pancreatic carcinoma cells by epigenetically silencing CDKN1A and KLF2. Cancer Commun (Lond). 2018;38:64. [DOI] [PubMed] [PMC]

74.

Luo J, Xiang H. LncRNA MYLK-AS1 acts as an oncogene by epigenetically silencing large tumor suppressor 2 (LATS2) in gastric cancer. Bioengineered. 2021;12:3101–12. [DOI] [PubMed] [PMC]

75.

Chen Z, Chen X, Chen P, Yu S, Nie F, Lu B, et al. Long non-coding RNA SNHG20 promotes non-small cell lung cancer cell proliferation and migration by epigenetically silencing of P21 expression. Cell Death Dis. 2017;8:e3092. [DOI] [PubMed] [PMC]

76.

Huang J, Zhou N, Watabe K, Lu Z, Wu F, Xu M, et al. Long non-coding RNA UCA1 promotes breast tumor growth by suppression of p27 (Kip1). Cell Death Dis. 2014;5:e1008. [DOI] [PubMed] [PMC]

77.

Huang MD, Chen WM, Qi FZ, Sun M, Xu TP, Ma P, et al. Long non-coding RNA TUG1 is up-regulated in hepatocellular carcinoma and promotes cell growth and apoptosis by epigenetically silencing of KLF2. Mol Cancer. 14:165. [DOI] [PubMed] [PMC]

78.

Bai Z, Wu Y, Bai S, Yan Y, Kang H, Ma W, et al. Long non-coding RNA SNGH7 Is activated by SP1 and exerts oncogenic properties by interacting with EZH2 in ovarian cancer. J Cell Mol Med. 2020;24:7479–89. [DOI] [PubMed] [PMC]

79.

Zhang G, Xu Y, Zou C, Tang Y, Lu J, Gong Z, et al. Long noncoding RNA ARHGAP27P1 inhibits gastric cancer cell proliferation and cell cycle progression through epigenetically regulating p15 and p16. Aging (Albany NY). 2019;11:9090–110. [DOI] [PubMed] [PMC]

80.

Zhang FF, Zhang L, Zhao L, Lu Y, Dong X, Liu YQ, et al. The circular RNA Rap1b promotes Hoxa5 transcription by recruiting Kat7 and leading to increased Fam3a expression, which inhibits neuronal apoptosis in acute ischemic stroke. Neural Regen Res. 2023;18:2237–45. [DOI] [PubMed] [PMC]

81.

Sarma K, Cifuentes-Rojas C, Ergun A, Del Rosario A, Jeon Y, White F, et al. ATRX directs binding of PRC2 to Xist RNA and Polycomb targets. Cell. 2014;159:869–83. Erratum in: Cell. 2014;159:1228. Erratum in: Cell. 2015;160:568–9. [DOI]

82.

Amin HM, Abukhairan R, Szabo B, Jacksi M, Varady G, Lozsa R, et al. KMT2D preferentially binds mRNAs of the genes it regulates, suggesting a role in RNA processing. Protein Sci. 2024;33:e4847. [DOI] [PubMed] [PMC]

83.

McHugh CA, Chen CK, Chow A, Surka CF, Tran C, McDonel P, et al. The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3. Nature. 2015;521:232–6. [DOI] [PubMed] [PMC]

84.

Wu X, Fu M, Ge C, Zhou H, Huang H, Zhong M, et al. m⁶A-Mediated Upregulation of lncRNA CHASERR Promotes the Progression of Glioma by Modulating the miR-6893-3p/TRIM14 Axis. Mol Neurobiol. 2024;[Epub ahead of print]. [DOI] [PubMed]

85.

Cable J, Heard E, Hirose T, Prasanth KV, Chen LL, Henninger JE, et al. Noncoding RNAs: biology and applications-a Keystone Symposia report. Ann N Y Acad Sci. 2021;1506:118–41. Erratum in: Ann N Y Acad Sci. 2022;1507:171. [DOI] [PubMed]

86.

Liu YW, Xia R, Lu K, Xie M, Yang F, Sun M, et al. LincRNAFEZF1-AS1 represses p21 expression to promote gastric cancer proliferation through LSD1-Mediated H3K4me2 demethylation. Mol Cancer. 2017;16:39. [DOI] [PubMed] [PMC]

87.

Wang F, Tang Z, Shao H, Guo J, Tan T, Dong Y, et al. Long noncoding RNA HOTTIP cooperates with CCCTC-binding factor to coordinate HOXA gene expression. Biochem Biophys Res Commun. 2018;500:852–9. [DOI] [PubMed]

88.

Sun TT, He J, Liang Q, Ren LL, Yan TT, Yu TC, et al. LncRNA GClnc1 Promotes Gastric Carcinogenesis and May Act as a Modular Scaffold of WDR5 and KAT2A Complexes to Specify the Histone Modification Pattern. Cancer Discov. 2016;6:784–801. [DOI] [PubMed]

89.

Dimitrova N, Zamudio JR, Jong RM, Soukup D, Resnick R, Sarma K, et al. LincRNA-p21 activates p21 in cis to promote Polycomb target gene expression and to enforce the G1/S checkpoint. Mol Cell. 2014;54:777–90. [DOI] [PubMed] [PMC]

90.

Ferrer J, Dimitrova N. Transcription regulation by long non-coding RNAs: mechanisms and disease relevance. Nat Rev Mol Cell Biol. 2024;25:396–415. [DOI] [PubMed] [PMC]

91.

Morlando M, Fatica A. Alteration of Epigenetic Regulation by Long Noncoding RNAs in Cancer. Int J Mol Sci. 2018;19:570. [DOI] [PubMed] [PMC]

92.

Di Ruscio A, Ebralidze AK, Benoukraf T, Amabile G, Goff LA, Terragni J, et al. DNMT1-interacting RNAs block gene-specific DNA methylation. Nature. 2013;503:371–6. [DOI] [PubMed] [PMC]

93.

Merry CR, Forrest ME, Sabers JN, Beard L, Gao XH, Hatzoglou M, et al. DNMT1-associated long non-coding RNAs regulate global gene expression and DNA methylation in colon cancer. Hum Mol Genet. 2015;24:6240–53. [DOI] [PubMed] [PMC]

94.

Somasundaram S, Forrest ME, Moinova H, Cohen A, Varadan V, LaFramboise T, et al. The DNMT1-associated lincRNA DACOR1 reprograms genome-wide DNA methylation in colon cancer. Clin Epigenetics. 2018;10:127. [DOI] [PubMed] [PMC]

95.

Wang Q, Mao X, Luo F, Wang J. LINC00511 promotes gastric cancer progression by regulating SOX4 and epigenetically repressing PTEN to activate PI3K/AKT pathway. J Cell Mol Med. 2021;25:9112–27. [DOI] [PubMed] [PMC]

96.

Song H, Chen L, Liu W, Xu X, Zhou Y, Zhu J, et al. Depleting long noncoding RNA HOTAIR attenuates chronic myelocytic leukemia progression by binding to DNA methyltransferase 1 and inhibiting PTEN gene promoter methylation. Cell Death Dis. 2021;12:440. [DOI] [PubMed] [PMC]

97.

Lu GH, Zhao HM, Liu ZY, Cao Q, Shao RD, Sun G. LncRNA SAMD12-AS1 Promotes the Progression of Gastric Cancer via DNMT1/p53 Axis. Arch Med Res. 2021;52:683–91. [DOI] [PubMed]

98.

Yu Y, Lu X, Yan Y, Wang Y, Meng J, Tian S, et al. The lncRNA KIF9-AS1 Accelerates Hepatocellular Carcinoma Growth by Recruiting DNMT1 to Promote RAI2 DNA Methylation. J Oncol. 2022;2022:3888798. [DOI] [PubMed] [PMC]

99.

Cheng D, Deng J, Zhang B, He X, Meng Z, Li G, et al. LncRNA HOTAIR epigenetically suppresses miR-122 expression in hepatocellular carcinoma via DNA methylation. EBioMedicine. 2018;36:159–70. [DOI] [PubMed] [PMC]

100.

Wang Q, Liu J, You Z, Yin Y, Liu L, Kang Y, et al. LncRNA TINCR favors tumorigenesis via STAT3-TINCR-EGFR-feedback loop by recruiting DNMT1 and acting as a competing endogenous RNA in human breast cancer. Cell Death Dis. 2021;12:83. [DOI] [PubMed] [PMC]

101.

Shaker OG, Hassan A, Mohammed AM, Mohammed SR. lincR-Ccr2-5’AS and THRIL as potential biomarkers of multiple sclerosis. Egypt J Med Hum Genet. 2021;22:32. [DOI]

102.

Latos PA, Pauler FM, Koerner MV, Şenergin HB, Hudson QJ, Stocsits RR, et al. Airn transcriptional overlap, but not its lncRNA products, induces imprinted Igf2r silencing. Science. 2012;338:1469–72. [DOI] [PubMed]

103.

Zhou J, Yang L, Zhong T, Mueller M, Men Y, Zhang N, et al. H19 lncRNA alters DNA methylation genome wide by regulating S-adenosylhomocysteine hydrolase. Nat Commun. 2015;6:10221. [DOI] [PubMed] [PMC]

104.

Shah M, Sarkar D. HCC-Related lncRNAs: Roles and Mechanisms. Int J Mol Sci. 2024;25:597. [DOI] [PubMed] [PMC]

105.

Arab K, Park YJ, Lindroth AM, Schäfer A, Oakes C, Weichenhan D, et al. Long noncoding RNA TARID directs demethylation and activation of the tumor suppressor TCF21 via GADD45A. Mol Cell. 2014;55:604–14. [DOI] [PubMed]

106.

Jain AK, Xi Y, McCarthy R, Allton K, Akdemir KC, Patel LR, et al. LncPRESS1 Is a p53-Regulated LncRNA that Safeguards Pluripotency by Disrupting SIRT6-Mediated De-acetylation of Histone H3K56. Mol Cell. 2016;64:967–81. [DOI] [PubMed] [PMC]

107.

Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y, et al. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature. 2011;472:120–4. [DOI] [PubMed] [PMC]

108.

Quagliata L, Matter MS, Piscuoglio S, Arabi L, Ruiz C, Procino A, et al. Long noncoding RNA HOTTIP/HOXA13 expression is associated with disease progression and predicts outcome in hepatocellular carcinoma patients. Hepatology. 2014;59:911–23. [DOI] [PubMed] [PMC]

109.

Statello L, Guo CJ, Chen LL, Huarte M. Gene regulation by long non-coding RNAs and its biological functions. Nat Rev Mol Cell Biol. 2021;22:96–118. Erratum in: Nat Rev Mol Cell Biol. 2021;22:159. [DOI] [PubMed] [PMC]

110.

Cai Z, Cao C, Ji L, Ye R, Wang D, Xia C, et al. RIC-seq for global in situ profiling of RNA-RNA spatial interactions. Nature. 2020;582:432–7. [DOI] [PubMed]

111.

Kadota S, Ou J, Shi Y, Lee JT, Sun J, Yildirim E. Nucleoporin 153 links nuclear pore complex to chromatin architecture by mediating CTCF and cohesin binding. Nat Commun. 2020;11:2606. [DOI] [PubMed] [PMC]

112.

Li W, Notani D, Ma Q, Tanasa B, Nunez E, Chen AY, et al. Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation. Nature. 2013;498:516–20. [DOI] [PubMed] [PMC]

113.

Rom A, Melamed L, Gil N, Goldrich MJ, Kadir R, Golan M, et al. Regulation of CHD2 expression by the Chaserr long noncoding RNA gene is essential for viability. Nat Commun. 2019;10:5092. [DOI] [PubMed] [PMC]

114.

Beucher A, Miguel-Escalada I, Balboa D, De Vas MG, Maestro MA, Garcia-Hurtado J, et al. The HASTER lncRNA promoter is a cis-acting transcriptional stabilizer of HNF1A. Nat Cell Biol. 2022;24:1528–40. [DOI] [PubMed] [PMC]

115.

Zhang H, Su X, Burley SK, Zheng XFS. mTOR regulates aerobic glycolysis through NEAT1 and nuclear paraspeckle-mediated mechanism in hepatocellular carcinoma. Theranostics. 2022;12:3518–33. [DOI] [PubMed] [PMC]

116.

Gomez JA, Wapinski OL, Yang YW, Bureau JF, Gopinath S, Monack DM, et al. The NeST long ncRNA controls microbial susceptibility and epigenetic activation of the interferon-γ locus. Cell. 2013;152:743–54. [DOI] [PubMed] [PMC]

117.

Yu XM, Li SJ, Yao ZT, Xu JJ, Zheng CC, Liu ZC, et al. N4-acetylcytidine modification of lncRNA CTC-490G23.2 promotes cancer metastasis through interacting with PTBP1 to increase CD44 alternative splicing. Oncogene. 2023;42:1101–16. [DOI] [PubMed]

118.

Zhang Y, Jing Y, Wang Y, Tang J, Zhu X, Jin WL, et al. NAT10 promotes gastric cancer metastasis via N4-acetylated COL5A1. Signal Transduct Target Ther. 2021;6:173. [DOI] [PubMed] [PMC]

119.

Safra M, Sas-Chen A, Nir R, Winkler R, Nachshon A, Bar-Yaacov D, et al. The m1A landscape on cytosolic and mitochondrial mRNA at single-base resolution. Nature. 2017;551:251–5. [DOI] [PubMed]

120.

Dou X, Huang L, Xiao Y, Liu C, Li Y, Zhang X, et al. METTL14 is a chromatin regulator independent of its RNA N6-methyladenosine methyltransferase activity. Protein Cell. 2023;14:683–97. [DOI] [PubMed] [PMC]

121.

Wang X, Lu Z, Gomez A, Hon GC, Yue Y, Han D, et al. N6-methyladenosine-dependent regulation of messenger RNA stability. Nature. 2014;505:117–20. [DOI] [PubMed] [PMC]

122.

Shen W, Zhu M, Wang Q, Zhou X, Wang J, Wang T, et al. DARS-AS1 recruits METTL3/METTL14 to bind and enhance DARS mRNA m⁶A modification and translation for cytoprotective autophagy in cervical cancer. RNA Biol. 2022;19:751–63. [DOI] [PubMed] [PMC]

123.

Liu H, Xu Y, Yao B, Sui T, Lai L, Li Z. A novel N6-methyladenosine (m6A)-dependent fate decision for the lncRNA THOR. Cell Death Dis. 2020;11:613. [DOI] [PubMed] [PMC]

124.

Ban Y, Tan P, Cai J, Li J, Hu M, Zhou Y, et al. LNCAROD is stabilized by m6A methylation and promotes cancer progression via forming a ternary complex with HSPA1A and YBX1 in head and neck squamous cell carcinoma. Mol Oncol. 2020;14:1282–96. [DOI] [PubMed] [PMC]

125.

Ni W, Yao S, Zhou Y, Liu Y, Huang P, Zhou A, et al. Long noncoding RNA GAS5 inhibits progression of colorectal cancer by interacting with and triggering YAP phosphorylation and degradation and is negatively regulated by the m⁶A reader YTHDF3. Mol Cancer. 2019;18:143. [DOI] [PubMed] [PMC]

126.

Wang J, Wang S, Shi K, Yang H, Wang R, et al. KDM5B/H3K4me3-mediated METTL14 regulates the function of LINC02747 through N6-methyladenosine modification in non-small cell lung cancer. [Preprint]. 2024 [cited 2024 Jan 19]. Available from: https://doi.org/10.21203/rs.3.rs-3873202/v1

127.

Su T, Liu J, Zhang N, Wang T, Han L, Wang S, et al. New insights on the interplays between m6A modifications and microRNA or lncRNA in gastrointestinal cancers. Front Cell Dev Biol. 2023;11:1157797. [DOI] [PubMed] [PMC]

128.

He Y, Yue H, Cheng Y, Ding Z, Xu Z, Lv C, et al. ALKBH5-mediated m⁶A demethylation of KCNK15-AS1 inhibits pancreatic cancer progression via regulating KCNK15 and PTEN/AKT signaling. Cell Death Dis. 2021;12:1121. [DOI] [PubMed] [PMC]

129.

Chen F, Li M, Wang L. LncRNA CASC11 Promotes Hepatocellular Carcinoma Progression via Upregulation of UBE2T in a m⁶A-Dependent Manner. Front Oncol. 2021;11:772671. [DOI] [PubMed] [PMC]

130.

Zhang J, Guo S, Piao HY, Wang Y, Wu Y, Meng XY, et al. ALKBH5 promotes invasion and metastasis of gastric cancer by decreasing methylation of the lncRNA NEAT1. J Physiol Biochem. 2019;75:379–89. [DOI] [PubMed] [PMC]

131.

Liu T, Wang H, Fu Z, Wang Z, Wang J, Gan X, et al. Methyltransferase-like 14 suppresses growth and metastasis of renal cell carcinoma by decreasing long noncoding RNA NEAT1. Cancer Sci. 2022;113:446–58. [DOI] [PubMed] [PMC]

132.

Li L, Chen J, Wang A, Yi K. ALKBH5 regulates ovarian cancer growth via demethylating long noncoding RNA PVT1 in ovarian cancer. J Cell Mol Med. 2024;28:e18066. [DOI] [PubMed] [PMC]

133.

Ross CJ, Rom A, Spinrad A, Gelbard-Solodkin D, Degani N, Ulitsky I. Uncovering deeply conserved motif combinations in rapidly evolving noncoding sequences. Genome Biol. 2021;22:29. [DOI] [PubMed] [PMC]

134.

Wei H, Huang L, Lu Q, Huang Z, Huang Y, Xu Z, et al. N⁶-Methyladenosine-Modified LEAWBIH Drives Hepatocellular Carcinoma Progression through Epigenetically Activating Wnt/β-Catenin Signaling. J Hepatocell Carcinoma. 2023;10:1991–2007. [DOI] [PubMed] [PMC]

135.

Bei M, Hao S, Lin K, Chen Q, Cai Y, Zhao X, et al. Splicing factor TRA2A contributes to esophageal cancer progression via a noncanonical role in lncRNA m6 A methylation. Cancer Sci. 2023;114:3216–29. [DOI] [PubMed] [PMC]

136.

Wang F, Hu Y, Wang H, Hu P, Xiong H, Zeng Z, et al. LncRNA FTO-IT1 promotes glycolysis and progression of hepatocellular carcinoma through modulating FTO-mediated N6-methyladenosine modification on GLUT1 and PKM2. J Exp Clin Cancer Res. 2023;42:267. [DOI] [PubMed] [PMC]

137.

Gong S, Wang S, Shao M. Mechanism of METTL14-mediated m⁶A modification in non-small cell lung cancer cell resistance to cisplatin. J Mol Med (Berl). 2022;100:1771–85. [DOI] [PubMed]

138.

Song B, Tang Y, Chen K, Wei Z, Rong R, Lu Z, et al. m7GHub: deciphering the location, regulation and pathogenesis of internal mRNA N7-methylguanosine (m⁷G) sites in human. Bioinformatics. 2020;36:3528–36. [DOI] [PubMed]

139.

Ma T, Zhou D, Hu B. The study of human mRNA m7G methylation writer molecule related lncRNA in gastric cancer. [Preprint]. 2024 [cited 2024 Jan 31]. Available from: https://doi.org/10.21203/rs.3.rs-3900295/v1

140.

Xie W, Sun Z, Fu Y. Bioinformatic analysis of N6-methyladenosine, 5-methylcytosine, and N1-methyladenosine co-regulation patterns and validation of NSUN6 as a protective protein in colon cancer. [Preprint]. 2024 [cited 2024 Jan 18]. Available from: https://doi.org/10.21203/rs.3.rs-3842256/v1

141.

Mazurov E, Sizykh A, Medvedeva YA. HiMoRNA: A Comprehensive Database of Human lncRNAs Involved in Genome-Wide Epigenetic Regulation. Noncoding RNA. 2022;8:18. [DOI] [PubMed] [PMC]

142.

Han J, Liu Q, Zhou Y, Li D, Wang R. Landscape of internal N7-methylguanosine of long non-coding RNA modifications in resistant acute myeloid leukemia. BMC Genomics. 2023;24:425. [DOI] [PubMed] [PMC]

143.

Butler K, Banday AR. APOBEC3-mediated mutagenesis in cancer: causes, clinical significance and therapeutic potential. J Hematol Oncol. 2023;16:31. [DOI] [PubMed] [PMC]

144.

Dodel M, Guiducci G, Dermit M, Krishnamurthy S, Alard EL, Capraro F, et al. TREX reveals proteins that bind to specific RNA regions in living cells. Nat Methods. 2024;21:423–34. [DOI] [PubMed] [PMC]

145.

An S, Huang W, Huang X, Cun Y, Cheng W, Sun X, et al. Integrative network analysis identifies cell-specific trans regulators of m⁶A. Nucleic Acids Res. 2020;48:1715–29. [DOI] [PubMed] [PMC]

146.

Zhang M, Peng S. The association and clinical relevance of phase-separating protein CAPRIN1 with noncoding RNA. Cell Stress Chaperones. 2023;28:125–32. [DOI] [PubMed] [PMC]

147.

Zeng C, Huang W, Li Y, Weng H. Roles of METTL3 in cancer: mechanisms and therapeutic targeting. J Hematol Oncol. 2020;13:117. [DOI] [PubMed] [PMC]

148.

Shaw A, Gullerova M. Home and Away: The Role of Non-Coding RNA in Intracellular and Intercellular DNA Damage Response. Genes (Basel). 2021;12:1475. [DOI] [PubMed] [PMC]

149.

Zhao K, Wang X, Xue X, Li L, Hu Y. A long noncoding RNA sensitizes genotoxic treatment by attenuating ATM activation and homologous recombination repair in cancers. PLoS Biol. 2020;18:e3000666. [DOI] [PubMed] [PMC]

150.

Sharma V, Khurana S, Kubben N, Abdelmohsen K, Oberdoerffer P, Gorospe M, et al. A BRCA1-interacting lncRNA regulates homologous recombination. EMBO Rep. 2015;16:1520–34. [DOI] [PubMed] [PMC]

151.

Hu Y, Lin J, Fang H, Fang J, Li C, Chen W, et al. Targeting the MALAT1/PARP1/LIG3 complex induces DNA damage and apoptosis in multiple myeloma. Leukemia. 2018;32:2250–62. [DOI] [PubMed] [PMC]

152.

Yadav A, Biswas T, Praveen A, Ganguly P, Bhattacharyya A, Verma A, et al. Targeting MALAT1 Augments Sensitivity to PARP Inhibition by Impairing Homologous Recombination in Prostate Cancer. Cancer Res Commun. 2023;3:2044–61. [DOI] [PubMed] [PMC]

153.

Zhao J, Xu J, Wu M, Wang W, Wang M, Yang L, et al. LncRNA H19 Regulates Breast Cancer DNA Damage Response and Sensitivity to PARP Inhibitors via Binding to ILF2. Int J Mol Sci. 2023;24:9157. [DOI] [PubMed] [PMC]

154.

Shi F, Wu L, Cui D, Sun M, Shen Y, Zhou Z, et al. LncFALEC recruits ART5/PARP1 and promotes castration-resistant prostate cancer through enhancing PARP1-meditated self PARylation. Cell Oncol (Dordr). 2023;46:761–76. [DOI] [PubMed]

155.

Fu D, Shi Y, Liu JB, Wu TM, Jia CY, Yang HQ, et al. Targeting Long Non-coding RNA to Therapeutically Regulate Gene Expression in Cancer. Mol Ther Nucleic Acids. 2020;21:712–24. [DOI] [PubMed] [PMC]

156.

Brownmiller T, Juric JA, Ivey AD, Harvey BM, Westemeier ES, Winters MT, et al. Y Chromosome LncRNA Are Involved in Radiation Response of Male Non-Small Cell Lung Cancer Cells. Cancer Res. 2020;80:4046–57. [DOI] [PubMed] [PMC]

157.

Long X, Wen F, Li J, Huang X. LncRNA FEZF1-AS1 accelerates multiple myeloma progression by regulating IGF2BP1/BZW2 signaling. Hematol Oncol. 2023;41:694–703. [DOI] [PubMed]

158.

Li J, Li Z, Bai X, Chen X, Wang M, Wu Y, et al. LncRNA UCA1 Promotes the Progression of AML by Upregulating the Expression of CXCR4 and CYP1B1 by Affecting the Stability of METTL14. J Oncol. 2022;2022:2756986. [DOI] [PubMed] [PMC]

159.

Liu H, Qin S, Liu C, Jiang L, Li C, Yang J, et al. m⁶A reader IGF2BP2-stabilized CASC9 accelerates glioblastoma aerobic glycolysis by enhancing HK2 mRNA stability. Cell Death Discov. 2021;7:292. [DOI] [PubMed] [PMC]

160.

Wang Y, Muylaert C, Wyns A, Vlummens P, De Veirman K, Vanderkerken K, et al. S-adenosylmethionine biosynthesis is a targetable metabolic vulnerability in multiple myeloma. Haematologica. 2024;109:256–71. [DOI] [PubMed] [PMC]

161.

Wang Y, Xie Q, Tan H, Liao M, Zhu S, Zheng LL, et al. Targeting cancer epigenetic pathways with small-molecule compounds: Therapeutic efficacy and combination therapies. Pharmacol Res. 2021;173:105702. [DOI] [PubMed]

162.

Qiu L, Jing Q, Li Y, Han J. RNA modification: mechanisms and therapeutic targets. Mol Biomed. 2023;4:25. [DOI] [PubMed] [PMC]

163.

Ofir-Rosenfeld Y, Rausch O, McMahon J, Vasiliauskaite L, Saunders C, Sapetschnig A, et al. STC-15, an oral small molecule inhibitor of the RNA methyltransferase METTL3, inhibits tumour growth through activation of anti-cancer immune responses and synergises with immune checkpoint blockade. J Immunother Cancer. 2022;10:A1427. [DOI]

164.

Albert L, Xu J, Wan R, Srinivasan V, Dou Y, Vázquez O. Controlled inhibition of methyltransferases using photoswitchable peptidomimetics: towards an epigenetic regulation of leukemia. Chem Sci. 2017;8:4612–8. [DOI] [PubMed] [PMC]

165.

Yankova E, Blackaby W, Albertella M, Rak J, De Braekeleer E, Tsagkogeorga G, et al. Small-molecule inhibition of METTL3 as a strategy against myeloid leukaemia. Nature. 2021;593:597–601. [DOI] [PubMed] [PMC]

166.

Huang Y, Su R, Sheng Y, Dong L, Dong Z, Xu H, et al. Small-Molecule Targeting of Oncogenic FTO Demethylase in Acute Myeloid Leukemia. Cancer Cell. 2019;35:677–91.e10. [DOI] [PubMed] [PMC]

167.

Su R, Dong L, Li Y, Gao M, Han L, Wunderlich M, et al. Targeting FTO Suppresses Cancer Stem Cell Maintenance and Immune Evasion. Cancer Cell. 2020;38:79–96.e11. [DOI] [PubMed] [PMC]

168.

Yang Q, Al-Hendy A. The Functional Role and Regulatory Mechanism of FTO m⁶A RNA Demethylase in Human Uterine Leiomyosarcoma. Int J Mol Sci. 2023;24:7957. [DOI] [PubMed] [PMC]

169.

Zuidhof HR, Calkhoven CF. Oncogenic and Tumor-Suppressive Functions of the RNA Demethylase FTO. Cancer Res. 2022;82:2201–12. [DOI] [PubMed]

170.

Bao Y, Zhai J, Chen H, Wong CC, Liang C, Ding Y, et al. Targeting m⁶A reader YTHDF1 augments antitumour immunity and boosts anti-PD-1 efficacy in colorectal cancer. Gut. 2023;72:1497–509. [DOI] [PubMed] [PMC]

171.

Chen B, Dragomir MP, Yang C, Li Q, Horst D, Calin GA. Targeting non-coding RNAs to overcome cancer therapy resistance. Signal Transduct Target Ther. 2022;7:121. [DOI] [PubMed] [PMC]

172.

You Y, Fu Y, Huang M, Shen D, Zhao B, Liu H, et al. Recent Advances of m6A Demethylases Inhibitors and Their Biological Functions in Human Diseases. Int J Mol Sci. 2022;23:5815. [DOI] [PubMed] [PMC]

173.

Kleinbielen T, Olasagasti F, Beristain E, Viguri-Díaz A, Guerra-Merino I, García-Orad A, et al. m⁶A levels and expression of its modification genes show significant differences in breast cancer molecular subtypes. Genes Dis. 2022;10:1751–4. [DOI] [PubMed] [PMC]

174.

Qing Y, Dong L, Gao L, Li C, Li Y, Han L, et al. R-2-hydroxyglutarate attenuates aerobic glycolysis in leukemia by targeting the FTO/m⁶A/PFKP/LDHB axis. Mol Cell. 2021;81:922–39.e9. [DOI] [PubMed] [PMC]

175.

Bove G, Amin S, Babaei M, Benedetti R, Nebbioso A, Altucci L, et al. Interplay between m⁶A epitranscriptome and epigenome in cancer: current knowledge and therapeutic perspectives. Int J Cancer. 2023;153:464–75. [DOI] [PubMed]

176.

Fiorentino F, Menna M, Rotili D, Valente S, Mai A. METTL3 from Target Validation to the First Small-Molecule Inhibitors: A Medicinal Chemistry Journey. J Med Chem. 2023;66:1654–77. [DOI] [PubMed] [PMC]

177.

Poole RM. Belinostat: first global approval. Drugs. 2014;74:1543–54. [DOI] [PubMed]

178.

Mann BS, Johnson JR, Cohen MH, Justice R, Pazdur R. FDA approval summary: vorinostat for treatment of advanced primary cutaneous T-cell lymphoma. Oncologist. 2007;12:1247–52. [DOI] [PubMed]

179.

VanderMolen KM, McCulloch W, Pearce CJ, Oberlies NH. Romidepsin (Istodax, NSC 630176, FR901228, FK228, depsipeptide): a natural product recently approved for cutaneous T-cell lymphoma. J Antibiot (Tokyo). 2011;64:525–31. [DOI] [PubMed] [PMC]

180.

Lu X, Ning Z, Li Z, Cao H, Wang X. Development of chidamide for peripheral T-cell lymphoma, the first orphan drug approved in China. Intractable Rare Dis Res. 2016;5:185–91. [DOI] [PubMed] [PMC]

181.

Garnock-Jones KP. Panobinostat: first global approval. Drugs. 2015;75:695–704. Erratum in: Drugs. 2015;75:929. [DOI] [PubMed]

182.

Ghasemi S. Cancer’s epigenetic drugs: where are they in the cancer medicines? Pharmacogenomics J. 2020;20:367–79. [DOI] [PubMed]

183.

Zhou Z, Li HQ, Liu F. DNA Methyltransferase Inhibitors and their Therapeutic Potential. Curr Top Med Chem. 2018;18:2448–57. [DOI] [PubMed]

184.

Kaminskas E, Farrell AT, Wang YC, Sridhara R, Pazdur R. FDA drug approval summary: azacitidine (5-azacytidine, Vidaza^TM) for injectable suspension. Oncologist. 2005;10:176–82. [DOI] [PubMed]

185.

Dhillon S. Decitabine/Cedazuridine: First Approval. Drugs. 2020;80:1373–8. Erratum in: Drugs. 2021;81:179. [DOI] [PubMed] [PMC]

186.

Kantarjian HM, Roboz GJ, Kropf PL, Yee KWL, O’Connell CL, Tibes R, et al. Guadecitabine (SGI-110) in treatment-naive patients with acute myeloid leukaemia: phase 2 results from a multicentre, randomised, phase 1/2 trial. Lancet Oncol. 2017;18:1317–26. [DOI] [PubMed] [PMC]

187.

Cheng Y, He C, Wang M, Ma X, Mo F, Yang S, et al. Targeting epigenetic regulators for cancer therapy: mechanisms and advances in clinical trials. Signal Transduct Target Ther. 2019;4:62. [DOI] [PubMed] [PMC]

188.

Jain AK, Barton MC. Bromodomain Histone Readers and Cancer. J Mol Biol. 2017;429:2003–10. [DOI] [PubMed]

189.

Albrecht BK, Gehling VS, Hewitt MC, Vaswani RG, Côté A, Leblanc Y, et al. Identification of a Benzoisoxazoloazepine Inhibitor (CPI-0610) of the Bromodomain and Extra-Terminal (BET) Family as a Candidate for Human Clinical Trials. J Med Chem. 2016;59:1330–9. [DOI] [PubMed]

190.

Bester AC, Lee JD, Chavez A, Lee YR, Nachmani D, Vora S, et al. An Integrated Genome-wide CRISPRa Approach to Functionalize lncRNAs in Drug Resistance. Cell. 2018;173:649–64.e20. [DOI] [PubMed] [PMC]

191.

Su K, Vázquez O. Enlightening epigenetics: optochemical tools illuminate the path. Trends Biochem Sci. 2024;49:290–304. [DOI] [PubMed]

192.

Yao RW, Wang Y, Chen LL. Cellular functions of long noncoding RNAs. Nat Cell Biol. 2019;21:542–51. [DOI] [PubMed]

193.

Fukunaga T, Iwakiri J, Ono Y, Hamada M. LncRRIsearch: A Web Server for lncRNA-RNA Interaction Prediction Integrated With Tissue-Specific Expression and Subcellular Localization Data. Front Genet. 2019;10:462. [DOI] [PubMed] [PMC]

194.

Guiducci G, Stojic L. Long Noncoding RNAs at the Crossroads of Cell Cycle and Genome Integrity. Trends Genet. 2021;37:528–46. [DOI] [PubMed]

195.

Hoy SM. Tazemetostat: First Approval. Drugs. 2020;80:513–21. [DOI] [PubMed]

196.

Yamagishi M, Hori M, Fujikawa D, Ohsugi T, Honma D, Adachi N, et al. Targeting Excessive EZH1 and EZH2 Activities for Abnormal Histone Methylation and Transcription Network in Malignant Lymphomas. Cell Rep. 2019;29:2321–37.e7. [DOI] [PubMed]

197.

Ren Y, Wang YF, Zhang J, Wang QX, Han L, Mei M, et al. Targeted design and identification of AC1NOD4Q to block activity of HOTAIR by abrogating the scaffold interaction with EZH2. Clin Epigenetics. 2019;11:29. [DOI] [PubMed] [PMC]

198.

Li Y, Ren Y, Wang Y, Tan Y, Wang Q, Cai J, et al. A Compound AC1Q3QWB Selectively Disrupts HOTAIR-Mediated Recruitment of PRC2 and Enhances Cancer Therapy of DZNep. Theranostics. 2019;9:4608–23. [DOI] [PubMed] [PMC]

199.

Wozniak M, Czyz M. lncRNAs-EZH2 interaction as promising therapeutic target in cutaneous melanoma. Front Mol Biosci. 2023;10:1170026. [DOI] [PubMed] [PMC]

200.

Yang L, Tang L, Min Q, Tian H, Li L, Zhao Y, et al. Emerging role of RNA modification and long noncoding RNA interaction in cancer. Cancer Gene Ther. 2024;31:816–30. [DOI] [PubMed] [PMC]

201.

He PC, Wei J, Dou X, Harada BT, Zhang Z, Ge R, et al. Exon architecture controls mRNA m6A suppression and gene expression. Science. 2023;379:677–82. [DOI] [PubMed] [PMC]

202.

Guan Q, Lin H, Miao L, Guo H, Chen Y, Zhuo Z, et al. Functions, mechanisms, and therapeutic implications of METTL14 in human cancer. J Hematol Oncol. 2022;15:13. [DOI] [PubMed] [PMC]

203.

Liu P, Li F, Lin J, Fukumoto T, Nacarelli T, Hao X, et al. m⁶A-independent genome-wide METTL3 and METTL14 redistribution drives the senescence-associated secretory phenotype. Nat Cell Biol. 2021;23:355–65. [DOI] [PubMed] [PMC]

204.

Gilbert LA, Horlbeck MA, Adamson B, Villalta JE, Chen Y, Whitehead EH, et al. Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation. Cell. 2014;159:647–61. [DOI] [PubMed] [PMC]

205.

Shamloo S, Kloetgen A, Petroulia S, Hockemeyer K, Sievers S, Tsirigos A, et al. Integrative CRISPR Activation and Small Molecule Inhibitor Screening for lncRNA Mediating BRAF Inhibitor Resistance in Melanoma. Biomedicines. 2023;11:2054. [DOI] [PubMed] [PMC]

206.

Han S, Yan Y, Ren Y, Hu Y, Wang Y, Chen L, et al. LncRNA SAMMSON Mediates Adaptive Resistance to RAF Inhibition in BRAF-Mutant Melanoma Cells. Cancer Res. 2021;81:2918–29. [DOI] [PubMed]

207.

Alabi S, Jaime-Figueroa S, Yao Z, Gao Y, Hines J, Samarasinghe KTG, et al. Mutant-selective degradation by BRAF-targeting PROTACs. Nat Commun. 2021;12:920. [DOI] [PubMed] [PMC]

208.

Zhang L, Xie X, Djokovic N, Nikolic K, Kosenkov D, Abendroth F, et al. Reversible Control of RNA Splicing by Photoswitchable Small Molecules. J Am Chem Soc. 2023;145:12783–92. [DOI] [PubMed]

209.

Hargrove AE. Small molecule-RNA targeting: starting with the fundamentals. Chem Commun (Camb). 2020;56:14744–56. [DOI] [PubMed] [PMC]

210.

Berdnikova DV. Photoswitches for controllable RNA binding: a future approach in the RNA-targeting therapy. Chem Commun (Camb). 2021;57:10819–26. [DOI] [PubMed]

211.

Pilsl S, Morgan C, Choukeife M, Möglich A, Mayer G. Optoribogenetic control of regulatory RNA molecules. Nat Commun. 2020;11:4825. [DOI] [PubMed] [PMC]

212.

Wang Q, Chen C, Xu X, Shu C, Cao C, Wang Z, et al. APAF1-Binding Long Noncoding RNA Promotes Tumor Growth and Multidrug Resistance in Gastric Cancer by Blocking Apoptosome Assembly. Adv Sci (Weinh). 2022;9:e2201889. [DOI] [PubMed] [PMC]

213.

Shaath H, Vishnubalaji R, Elango R, Khattak S, Alajez NM. Single-cell long noncoding RNA (lncRNA) transcriptome implicates MALAT1 in triple-negative breast cancer (TNBC) resistance to neoadjuvant chemotherapy. Cell Death Discov. 2021;7:23. [DOI] [PubMed] [PMC]

214.

Palcau AC, Brandi R, Mehterov NH, Botti C, Blandino G, Pulito C. Exploiting Long Non-Coding RNAs and Circular RNAs as Pharmacological Targets in Triple-Negative Breast Cancer Treatment. Cancers (Basel). 2023;15:4181. [DOI] [PubMed] [PMC]

215.

Arun G, Diermeier SD, Spector DL. Therapeutic Targeting of Long Non-Coding RNAs in Cancer. Trends Mol Med. 2018;24:257–77. [DOI] [PubMed] [PMC]

216.

Toden S, Zumwalt TJ, Goel A. Non-coding RNAs and potential therapeutic targeting in cancer. Biochim Biophys Acta Rev Cancer. 2021;1875:188491. [DOI] [PubMed] [PMC]

217.

Donlic A, Zafferani M, Padroni G, Puri M, Hargrove AE. Regulation of MALAT1 triple helix stability and in vitro degradation by diphenylfurans. Nucleic Acids Res. 2020;48:7653–64. [DOI] [PubMed] [PMC]

218.

Taiana E, Favasuli V, Ronchetti D, Todoerti K, Pelizzoni F, Manzoni M, et al. Long non-coding RNA NEAT1 targeting impairs the DNA repair machinery and triggers anti-tumor activity in multiple myeloma. Leukemia. 2020;34:234–44. [DOI] [PubMed]

219.

Shin VY, Chen J, Cheuk IW, Siu MT, Ho CW, Wang X, et al. Long non-coding RNA NEAT1 confers oncogenic role in triple-negative breast cancer through modulating chemoresistance and cancer stemness. Cell Death Dis. 2019;10:270. [DOI] [PubMed] [PMC]

220.

Chen B, Dragomir MP, Fabris L, Bayraktar R, Knutsen E, Liu X, et al. The Long Noncoding RNA CCAT2 Induces Chromosomal Instability Through BOP1-AURKB Signaling. Gastroenterology. 2020;159:2146–62.e33. [DOI] [PubMed] [PMC]

221.

Zhen S, Lu J, Chen W, Zhao L, Li X. Synergistic Antitumor Effect on Bladder Cancer by Rational Combination of Programmed Cell Death 1 Blockade and CRISPR-Cas9-Mediated Long Non-Coding RNA Urothelial Carcinoma Associated 1 Knockout. Hum Gene Ther. 2018;29:1352–63. [DOI] [PubMed]

222.

Vaidya AM, Sun Z, Ayat N, Schilb A, Liu X, Jiang H, et al. Systemic Delivery of Tumor-Targeting siRNA Nanoparticles against an Oncogenic LncRNA Facilitates Effective Triple-Negative Breast Cancer Therapy. Bioconjug Chem. 2019;30:907–19. [DOI] [PubMed] [PMC]

223.

Ehmann F, Kuhn A, Pasmooij AMG, Humphreys A, Van Hengel A, Dooley B, et al. Report of the European Medicines Agency Conference on RNA-Based Medicines. Nucleic Acid Ther. 2024;34:4–11. [DOI] [PubMed]

224.

Poller W, Sahoo S, Hajjar R, Landmesser U, Krichevsky AM. Exploration of the Noncoding Genome for Human—Specific Therapeutic Targets-Recent Insights at Molecular and Cellular Level. Cells. 2023;12:2660. [DOI] [PubMed] [PMC]

225.

Benhamou RI, Suresh BM, Tong Y, Cochrane WG, Cavett V, Vezina-Dawod S, et al. DNA-encoded library versus RNA-encoded library selection enables design of an oncogenic noncoding RNA inhibitor. Proc Natl Acad Sci U S A. 2022;119:e2114971119. [DOI] [PubMed] [PMC]

226.

Kovachka S, Panosetti M, Grimaldi B, Azoulay S, Di Giorgio A, Duca M. Small molecule approaches to targeting RNA. Nat Rev Chem. 2024;8:120–35. [DOI] [PubMed]

227.

Ricketts D, Sagaert B, De Koker S, Witman N. Next Steps for mRNA Vaccines and Therapeutics. Genet Eng & Biotechnol News. 2023;43:16–8. [DOI]

228.

Coan M, Haefliger S, Ounzain S, Johnson R. Targeting and engineering long non-coding RNAs for cancer therapy. Nat Rev Genet. 2024;[Epub ahead of print]. [DOI] [PubMed]