Citation: Jun Xiong, Ke-Ke Chen, Neng-Bin Xie, Wei Chen, Wen-Xuan Shao, Tong-Tong Ji, Si-Yu Yu, Yu-Qi Feng, Bi-Feng Yuan. Demethylase-assisted site-specific detection of N¹-methyladenosine in RNA[J]. Chinese Chemical Letters, ;2024, 35(5): 108953. doi: 10.1016/j.cclet.2023.108953 shu

Demethylase-assisted site-specific detection of N¹-methyladenosine in RNA

Jun Xiong ^{a, 1} ,
Ke-Ke Chen ^{a, 1} ,
Neng-Bin Xie ^{a, 1} ,
Wei Chen ^{b, 1} ,
Wen-Xuan Shao ^a ,
Tong-Tong Ji ^a ,
Si-Yu Yu ^a ,
Yu-Qi Feng ^a ,
Bi-Feng Yuan ^{a, *,}

a.
College of Chemistry and Molecular Sciences, Research Center of Public Health, Renmin Hospital of Wuhan University, School of Public Health, Wuhan University, Wuhan 430071, China
b.
Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China

bfyuan@whu.edu.cn

Received Date: 15 May 2023
Revised Date: 7 August 2023
Accepted Date: 21 August 2023
Available Online: 24 August 2023

Figures(4)

The dynamic RNA modifications have been viewed as new posttranscriptional regulator in modulating gene expression as well as in a broad range of physiological processes. N¹-methyladenosine (m¹A) is one of the most prevalent modifications existing in multiple types of RNAs. In-depth investigation of the functions of m¹A requires the site-specific assessment of m¹A stoichiometry in RNA. Herein, we established a demethylase-assisted method (DA-m¹A) for the site-specific detection and quantification of m¹A in RNA. N1-methyl group in m¹A could result in the stalling of reverse transcription at m¹A site, thus producing the truncated cDNA. E. coli AlkB is a demethylase that can demethylate m¹A to produce adenine in RNA, thus generating full-length cDNA from AlkB-treated RNA. Evaluation of the produced amounts of full-length cDNA by quantitative real-time PCR can achieve the site-specific detection and quantification of m¹A in RNA. With the DA-m¹A method, we examined and successfully confirmed the previously well-characterized m¹A sites in various types of RNAs with low false positive rate. In addition, we found that the level of m¹A was significantly decreased at the bromodomain containing 2 (BRD2) mRNA position 1674 and CST telomere replication complex component 1 (CTC1) mRNA position 5643 in human hepatocellular carcinoma tissues. The results suggest that these two m¹A sites in mRNA may be involved in liver tumorigenesis. Taken together, the DA-m¹A method is simple and enables the rapid, cost-effective, and site-specific detection and quantification of m¹A in RNA, which provides a valuable tool to decipher the functions of m¹A in human diseases.
- N¹-methyladenosine,
- RNA modification,
- AlkB demethylase,
- RNA epigenetics,
- Quantitative real-time PCR,
- Hepatocellular carcinoma
1. [1]
  D. Wiener, S. Schwartz, Nat. Rev. Genet. 22 (2021) 119–131.
2. [2]
  S. Moshitch-Moshkovitz, D. Dominissini, G. Rechavi, Cell 185 (2022) 764–776. doi: 10.1016/j.cell.2022.02.007
3. [3]
  Y. Zhao, X. Zuo, Q. Li, et al., Sci. China Chem. 64 (2021) 171–203. doi: 10.1007/s11426-020-9864-7
4. [4]
  P. Boccaletto, F. Stefaniak, A. Ray, et al., Nucleic Acids Res. 50 (2022) D231–D235. doi: 10.1093/nar/gkab1083
5. [5]
  M.Y. Chen, Z. Gui, K.K. Chen, et al., Chin. Chem. Lett. 33 (2022) 2086–2090. doi: 10.1016/j.cclet.2021.08.094
6. [6]
  X.J. You, S. Zhang, J.J. Chen, et al., Nucleic Acids Res. 50 (2022) 9858–9872. doi: 10.1093/nar/gkac770
7. [7]
  Y. Dai, C.B. Qi, Y. Feng, et al., Anal. Chem. 93 (2021) 6938–6946. doi: 10.1021/acs.analchem.0c04630
8. [8]
  M.Y. Cheng, X.J. You, J.H. Ding, et al., Chem. Sci. 12 (2021) 8149–8156. doi: 10.1039/D1SC01972D
9. [9]
  Y. Motorin, M. Helm, Wiley Interdiscip. Rev. RNA 13 (2022) e1691. doi: 10.1002/wrna.1691
10. [10]
  J.H. Ding, M.Y. Chen, N.B. Xie, et al., Biosens. Bioelectron. 219 (2023) 114821. doi: 10.1016/j.bios.2022.114821
11. [11]
  M.Y. Chen, C.B. Qi, X.M. Tang, et al., Chin. Chem. Lett. 33 (2022) 3772–3776. doi: 10.1016/j.cclet.2021.12.008
12. [12]
  T.R. Fischer, L. Meidner, M. Schwickert, et al., Nucleic Acids Res. 50 (2022) 4216–4245. doi: 10.1093/nar/gkac224
13. [13]
  F. Nie, P. Feng, X. Song, et al., Database 2020 (2020) baaa049. doi: 10.1093/database/baaa049
14. [14]
  H.L. Huang, H.Y. Weng, X.L. Deng, J.J. Chen, Annu. Rev. Cancer Biol. 4 (2020) 221–240. doi: 10.1146/annurev-cancerbio-030419-033357
15. [15]
  K. Chen, B.S. Zhao, C. He, Cell Chem. Biol. 23 (2016) 74–85. doi: 10.1016/j.chembiol.2015.11.007
16. [16]
  H. Shi, P. Chai, R. Jia, X. Fan, Mol. Cancer 19 (2020) 78. doi: 10.1186/s12943-020-01194-6
17. [17]
  M. Frye, B.T. Harada, M. Behm, C. He, Science 361 (2018) 1346–1349. doi: 10.1126/science.aau1646
18. [18]
  Y.Y. Chen, Z. Gui, D. Hu, et al., Chin. Chem. Lett. 34 (2023) 108522.
19. [19]
  J.J. Chen, X.J. You, L. Li, et al., Anal. Chem. 94 (2022) 8740–8747. doi: 10.1021/acs.analchem.2c01226
20. [20]
  S. Murakami, S.R. Jaffrey, Mol. Cell. 82 (2022) 2236–2251. doi: 10.1016/j.molcel.2022.05.029
21. [21]
  J. Li, H. Zhang, H. Wang, Comput. Struct. Biotechnol. J. 20 (2022) 6578–6585. doi: 10.1016/j.csbj.2022.11.045
22. [22]
  C. Zhang, G. Jia, Genom. Proteom. Bioinform. 16 (2018) 155–161. doi: 10.1016/j.gpb.2018.03.003
23. [23]
  X. Xiong, X. Li, C. Yi, Curr. Opin. Chem. Biol. 45 (2018) 179–186. doi: 10.1016/j.cbpa.2018.06.017
24. [24]
  S. Ozanick, A. Krecic, J. Andersland, J.T. Anderson, RNA 11 (2005) 1281–1290. doi: 10.1261/rna.5040605
25. [25]
  E. Vilardo, C. Nachbagauer, A. Buzet, et al., Nucleic Acids Res. 40 (2012) 11583–11593. doi: 10.1093/nar/gks910
26. [26]
  T. Chujo, T. Suzuki, RNA 18 (2012) 2269–2276. doi: 10.1261/rna.035600.112
27. [27]
  T. Waku, Y. Nakajima, W. Yokoyama, et al., J. Cell Sci. 129 (2016) 2382–2393.
28. [28]
  X. Li, X. Xiong, K. Wang, et al., Nat. Chem. Biol. 12 (2016) 311–316. doi: 10.1038/nchembio.2040
29. [29]
  D. Dominissini, S. Nachtergaele, S. Moshitch-Moshkovitz, et al., Nature 530 (2016) 441–446. doi: 10.1038/nature16998
30. [30]
  Y. Zhang, L. Lu, X. Li, Exp. Mol. Med. 54 (2022) 1601–1616. doi: 10.1038/s12276-022-00821-0
31. [31]
  H. Liu, Y. Wang, X. Zhou, RSC Chem. Biol. 3 (2022) 994–1007. doi: 10.1039/D2CB00087C
32. [32]
  A.S. Felix, A.L. Quillin, S. Mousavi, J.M. Heemstra, Acc. Chem. Res. 55 (2022) 2271–2279. doi: 10.1021/acs.accounts.2c00287
33. [33]
  D. Bartee, S. Thalalla Gamage, C.N. Link, J.L. Meier, Chem. Soc. Rev. 50 (2021) 9482–9502. doi: 10.1039/D1CS00214G
34. [34]
  J.D. Alfonzo, J.A. Brown, P.H. Byers, et al., Nat. Genet. 53 (2021) 1113–1116. doi: 10.1038/s41588-021-00903-1
35. [35]
  X.J. You, L. Li, T.T. Ji, et al., Chin. Chem. Lett. 34 (2023) 107181. doi: 10.1016/j.cclet.2022.01.074
36. [36]
  Q. Wang, J.H. Ding, J. Xiong, et al., Chin. Chem. Lett. 32 (2021) 3426–3430. doi: 10.1016/j.cclet.2021.05.020
37. [37]
  Q.F. Zhang, H.M. Xiao, J.T. Zhan, B.F. Yuan, Y.Q. Feng, Chin. Chem. Lett. 33 (2022) 4746–4749. doi: 10.1016/j.cclet.2022.01.004
38. [38]
  B. Chen, B.F. Yuan, Y.Q. Feng, Anal. Chem. 91 (2019) 743–756. doi: 10.1021/acs.analchem.8b04078
39. [39]
  X.M. Tang, T.T. Ye, X.J. You, et al., Chin. Chem. Lett. 34 (2023) 107531. doi: 10.1016/j.cclet.2022.05.045
40. [40]
  W.B. Tao, N.B. Xie, Q.Y. Cheng, Y.Q. Feng, B.F. Yuan, Chin. Chem. Lett. 34 (2023) 108243. doi: 10.1016/j.cclet.2023.108243
41. [41]
  S.C. Trewick, T.F. Henshaw, R.P. Hausinger, T. Lindahl, B. Sedgwick, Nature 419 (2002) 174–178. doi: 10.1038/nature00908
42. [42]
  P.O. Falnes, R.F. Johansen, E. Seeberg, Nature 419 (2002) 178–182. doi: 10.1038/nature01048
43. [43]
  M. Safra, A. Sas-Chen, R. Nir, et al., Nature 551 (2017) 251–255. doi: 10.1038/nature24456
44. [44]
  H. Zhou, S. Rauch, Q. Dai, et al., Nat. Methods 16 (2019) 1281–1288. doi: 10.1038/s41592-019-0550-4
45. [45]
  X. Li, X. Xiong, M. Zhang, et al., Mol. Cell. 68 (2017) 993–1005.e9. doi: 10.1016/j.molcel.2017.10.019
46. [46]
  J.H. Ding, C.J. Ma, M.Y. Chen, et al., Anal. Chem. 92 (2020) 2612–2619. doi: 10.1021/acs.analchem.9b04454
47. [47]
  I. Barbieri, T. Kouzarides, Nat. Rev. Cancer 20 (2020) 303–322. doi: 10.1038/s41568-020-0253-2
48. [48]
  J. Xiong, K.K. Chen, N.B. Xie, et al., Anal. Chem. 94 (2022) 15489–15498. doi: 10.1021/acs.analchem.2c03808
49. [49]
  N.B. Xie, M. Wang, T.T. Ji, et al., Chem. Sci. 13 (2022) 7046–7056. doi: 10.1039/D2SC01052F
50. [50]
  Y. Wang, J. Wang, X. Li, et al., Nat. Commun. 12 (2021) 6314. doi: 10.1038/s41467-021-26718-6
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通讯作者: 陈斌, bchen63@163.com

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沈阳化工大学材料科学与工程学院沈阳 110142

Demethylase-assisted site-specific detection of N1-methyladenosine in RNA

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通讯作者: 陈斌, bchen63@163.com

Demethylase-assisted site-specific detection of N¹-methyladenosine in RNA