Viewpoint Cite This: Biochemistry XXXX, XXX, XXX−XXX
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Acetylation Enhances mRNA Stability and Translation Xiaoyu Li,† Jinying Peng,† and Chengqi Yi*,†,‡ †
State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
‡
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whether ac4C impacts mRNA stability using BRIC sequencing (BRIC-seq). They found that the half-life of transcripts harboring ac4C, especially for those with CDS summits, is significantly longer than that of transcripts lacking ac4C. In addition, the half-life of transcripts harboring ac4C within the CDS region decreased significantly upon NAT10 depletion, compared to that of transcripts lacking ac4C. On the basis of the findings presented above, the authors concluded that ac4C acetylation, especially when occurring within CDS regions, promotes mRNA stability. As mRNA stability is related to translation, the authors then studied whether mRNA acetylation influences translation. By performing ribosome profiling in WT and NAT10−/− cell lines, they found that the translation efficiency of the acetylated transcript is higher in WT cell lines and also decreased significantly upon NAT10 depletion, compared to those of non-acetylated transcripts. This indicates that mRNA acetylation enhances translation. To further validate this, they also performed Western Blot for several acetylated and non-acetylated transcripts. The authors analyzed the codon bias of acetylated transcripts and found that acetylated transcripts enrich codons with cytidine in the wobble site, suggesting that ac4C influences decoding efficiency. Further in vivo and in vitro translation assays both showed that ac4C acetylation in the wobble site stimulates translation, suggesting that mRNA acetylation can influence tRNA discrimination to regulate translation. In addition, it is worth mentioning that Arango et al. also demonstrated that ac4C acetylation in mRNA can directly influence mRNA stability and translation, not as a side effect of acetylation in tRNA and rRNA, which emphasizes the differential roles of this modification in different RNA species. In summary, Arango et al. identified ac4C as a new mRNA modification in human cells, which regulates mRNA stability and translation. This study mainly focused on investigating the regulatory roles of ac4C in CDS, but whether and/or how ac4C in 5′UTR influences mRNA metabolism is still unknown. In addition, the precise positions of ac4C are still unresolved, which limits functional and mechanistic studies of ac4C. Therefore, development of the single-base resolution mapping technology is also necessary. The writer protein of ac4C has been identified, yet whether ac4C in mRNA is reversible remains to be determined. Moreover, the mechanisms of how mRNA acetylation regulates mRNA stability and translation are still unclear, and whether there are reader proteins participating in these processes remains to be investigated.
ore than 100 post-transcriptional modifications have been characterized in RNA to date.1 Most of these modifications are present in abundant noncoding RNAs (ncRNA) and play important roles in maintaining proper functions of these ncRNAs. However, progress of the prevalence and functional studies of these chemical modifications in mRNA has lagged, mainly due to the lack of sensitive detection and mapping methods.1 So far, only a few chemical modifications have been identified in eukaryotic internal mRNA, including N6-methyladenosine (m6A), N6,2′O-dimethyladenosine (m6Am), 5-methylcytidine (m5C), inosine (I), pseudouridine (Ψ), N1-methyladenosine (m1A), 5hydroxylmethylcytidine (hm5C), and 2′-O-methylation (Nm). Recently, more and more studies have revealed that these epitranscriptomic marks in mRNA are dynamically regulated and participate in various processes of RNA metabolism.2 N4-Acetylcytidine (ac4C) was originally identified in the first position of the Escherichia coli tRNAMet anticodon and found to promote decoding fidelity.3 Subsequently, ac4C was characterized in eukaryotic serine, leucine tRNAs, and 18S rRNA, which was catalyzed by N-acetyltransferase 10 (NAT10). In 2016, ac4C was detected in mRNA using liquid chromatography and tandem mass spectrometry (LC−MS/MS).4 However, the distribution of ac4C and its regulation of mRNA remain to be determined. Recently, a study by Arango et al. showed that ac4C does occur in mRNA, using dot blot, LC−MS/MS, and immuno-Northern blot assays, and found that the ac4C modification on mRNA was also catalyzed by NAT10 and ac4C on mRNA helps to promote its stability and enhance its translation efficiency.5 As NAT10 has been characterized as a poly(A)-interacting factor, the authors speculated that NAT10 may also act on mRNA. They generated NAT10 knockout cell lines using the CRISPR/Cas9 system and then compared the acetylation level of mRNA between WT and NAT10−/− cell lines. A dramatic reduction in the ac4C level of mRNA was observed in the NAT10−/− cells, supporting the possibility that NAT10 is also responsible for ac4C acetylation in mRNA. To map ac4C acetylation in a transcriptome-wide manner, the authors developed a method that combines ac4C-specific RNA immunoprecipitation with high-throughput sequencing (acRIP-seq). Using acRIP-seq, 4,250 ac4C peaks were identified and found to be enriched in 5′UTR and CDS regions. To investigate how ac4C regulates gene expression, the authors performed RNA-seq analysis in wild-type (WT) and NAT10−/− cell lines and found that compared to transcripts lacking ac4C, transcripts harboring ac4C demonstrate an overall tendency toward decreased levels of expression upon NAT10 depletion. Then the authors ruled out the possibility that ac4C acetylation influences transcription and further investigated © XXXX American Chemical Society
Received: January 22, 2019
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DOI: 10.1021/acs.biochem.9b00061 Biochemistry XXXX, XXX, XXX−XXX
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Biochemistry Furthermore, the physiological roles of mRNA acetylation in different biological processes are also worth exploring in the future. Nevertheless, this work identified ac4C as a new modification that increases the stability and translation in mRNA for the first time, expanding the repertoire of mRNA modifications.
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AUTHOR INFORMATION
Corresponding Author
*E-mail:
[email protected]. ORCID
Jinying Peng: 0000-0003-2679-856X Chengqi Yi: 0000-0003-2540-9729 Funding
This work was funded by the National Natural Science Foundation of China (Grants 21825701 and 91740112 to C.Y.) and joint laboratory of international scientific and technological cooperation funding to C.Y. by the Beijing municipal science and technology commission. Notes
The authors declare no competing financial interest.
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ACKNOWLEDGMENTS The authors apologize to all authors whose studies we could not cite in this review due to space limitations. REFERENCES
(1) Li, X., Xiong, X., and Yi, C. (2017) Epitranscriptome sequencing technologies: decoding RNA modifications. Nat. Methods 14, 23−31. (2) Roundtree, I. A., Evans, M. E., Pan, T., and He, C. (2017) Dynamic RNA Modifications in Gene Expression Regulation. Cell 169, 1187−1200. (3) Stern, L., and Schulman, L. H. (1978) The role of the minor base N4-acetylcytidine in the function of the Escherichia coli noninitiator methionine transfer RNA. J. Biol. Chem. 253, 6132−6139. (4) Dong, C., Niu, L., Song, W., Xiong, X., Zhang, X., Zhang, Z., Yang, Y., Yi, F., Zhan, J., Zhang, H., Yang, Z., Zhang, L. H., Zhai, S., Li, H., Ye, M., and Du, Q. (2016) tRNA modification profiles of the fast-proliferating cancer cells. Biochem. Biophys. Res. Commun. 476, 340−345. (5) Arango, D., Sturgill, D., Alhusaini, N., Dillman, A. A., Sweet, T. J., Hanson, G., Hosogane, M., Sinclair, W. R., Nanan, K. K., Mandler, M. D., Fox, S. D., Zengeya, T. T., Andresson, T., Meier, J. L., Coller, J., and Oberdoerffer, S. (2018) Acetylation of Cytidine in mRNA Promotes Translation Efficiency. Cell 175, 1872−1886.
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DOI: 10.1021/acs.biochem.9b00061 Biochemistry XXXX, XXX, XXX−XXX
