Viewpoint Cite This: Biochemistry XXXX, XXX, XXX−XXX
pubs.acs.org/biochemistry
Coupling Transcription and Translation via the Epitranscriptomic m6A Mark Kun Wang† and Chengqi Yi*,†,‡,§ †
State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China Academy for Advanced Interdisciplinary Studies, 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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camptothecin (CPT) can reduce the transcription rate of RNA polymerase II (RNAPII). Compared with untreated cells, CPT-treated cells exhibited a notable reduction in mRNA and a more significant reduction in protein, and the positive determinant of TE requires cap-dependent translation initiation. Moreover, CPT-induced TE reduction was observed in approximately 700 genes. On the basis of all of these findings, the authors concluded that transcription rate is an important determinant of TE. Figuring out the underlying mechanism(s) linking transcription and translation represents a major challenge. Considering that the effect of transcription on translation refers to multiple genes, the authors hypothesized that m6A, a prevalent mRNA mark in higher eukaryotes, can bridge transcription and translation. m6A is reversible and dynamic;3 it is catalyzed by the METTL3 and METTL14 methyltransferase complex and can be removed by the demethylases FTO and ALKBH5 in mammals. m6A has been shown to modulate mRNA metabolism via different reader proteins. Via m6A immunoprecipitation of induced and noninduced TRex-Rluc mRNA, the authors showed enrichment of noninduced mRNA compared with induced mRNA and demonstrated that this difference in enrichment did not result from mRNA levels. Next, the authors transcribed Rluc in vitro under normal conditions and conditions with a reduced transcription rate and then investigated the m6A content of the resulting transcripts. They found that transcripts contain a higher content of m6A modification when transcription was reduced. Additionally, the TE of these transcripts was reduced. Furthermore, cells treated with CPT and cells expressing the RNAPII mutant displayed the consistent phenotype that attenuated transcription was associated with reduced mRNA levels and enhanced methylation. These results demonstrated that m6A deposition is negatively associated with the dynamics of RNAPII. To investigate whether m6A occurs cotranscriptionally, the authors performed RNAPII immunoprecipitation in normal and CPT-treated cells. Indeed, METTL3 could be immunoprecipitated in CPT-treated cells but not in normal cells. Finally, the authors showed that m6A negatively regulates TE. When knocking-down METTL14, the mRNA levels and TE of Rluc increased significantly. The authors transcribed Rluc
he central dogma of molecular biology states that DNA makes RNA and RNA makes protein. Genetic information flows from DNA to RNA and then to protein via two main processes, transcription and translation. Both of these processes are tightly regulated by various mechanisms. Given that transcription and translation occur with different timings and at different cellular locations, these two processes are mainly regarded as relatively independent. However, recent studies have revealed a potential association between transcription rate and translation efficiency (TE).1 An elegant study by Slobodin et al.2 established a general link between transcription and translation of mRNAs, which is mediated, at least partly, by the cotranscriptional m6A in mRNA. The authors developed an approach named barcoded polysomal profiling (BPP) to examine the effect of different human promoters on the translation of Renilla luciferase (Rluc), a reporter gene. The authors cloned hundreds of promoters to drive the expression of Rluc and different barcodes, using Firefly luciferase (Fluc) as a control. Using polysomal profiling, the authors examined Rluc mRNA in different fractions whose segregation reflects the translation efficiency of Rluc. They found that 12 promoters gave rise to a shift of Rluc mRNA to heavier polysomal fractions. Moreover, 8 of these promoters have a TATA-box or a TATA-box-like sequence. To test the hypothesis that the TATA element could induce translation, the authors introduced an artificial TATA element to several natural TATA-less promoters to examine changes in TE. Indeed, this additional TATA element increased TE and protein production without changing the 5′ UTR of transcripts. The authors further confirmed this positive effect in an endogenous gene by destroying the endogenous TATA-box. What factors directly contribute to TE? The authors then separated their BPP data into a group with a lower TE and a group with a higher TE, respectively. They found a positive correlation between TE and mRNA levels, which was independent of the TATA element. By performing the BPP experiment with another inducible reporter gene (TRex-Rluc), the authors substantiated this observation. To further investigate whether the correlation between TE and mRNA levels is global, the authors analyzed genome-wide sequencing data and observed a weak but statistically significant correlation between TE and mRNA levels. Moreover, the authors demonstrated that mRNA levels cannot regulate TE directly by the BPP examination. In contrast, they used both bioinformatics analysis and experiments to show that transcription rate positively affects TE. The chemical compound © XXXX American Chemical Society
Special Issue: Regulating the Central Dogma Received: August 29, 2018
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DOI: 10.1021/acs.biochem.8b00903 Biochemistry XXXX, XXX, XXX−XXX
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Biochemistry in vitro with different m6A/A incorporation ratios. The TE of Rluc was significantly reduced when the incorporation of m6A increased. In summary, the work by Slobodin et al. demonstrated a global link between transcription and translation; unexpectedly, the cotranscriptional m6A modification on mRNAs bridges these two processes. mRNAs produced with a slow transcription rate contain a relatively higher content of m6A modification, which, in turn, reduces the translation efficiency. The impact of m6A on translation has been subjected to intensive examination in recent years. Several studies have demonstrated a stimulatory effect of m6A on translation, whereas other studies, including this work, have reported an inhibitory effect. It is apparent that many factors (including the mRNA sequence context, the location of the modification, and the presence of various reader proteins, among others) can impact the effect of m6A on translation.4 In addition, the question of whether other mRNA marks could influence transcription and translation remains to be answered in the future.5 Nevertheless, this work provides a new angle to directly link transcription and translation.
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AUTHOR INFORMATION
Corresponding Author
*E-mail:
[email protected]. ORCID
Kun Wang: 0000-0001-9034-9203 Chengqi Yi: 0000-0003-2540-9729 Funding
C.Y. is supported by the National Natural Science Foundation of China (21522201 and 91740112). Notes
The authors declare no competing financial interest.
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REFERENCES
(1) Bhat, M., Robichaud, N., Hulea, L., Sonenberg, N., Pelletier, J., and Topisirovic, I. (2015) Targeting the translation machinery in cancer. Nat. Rev. Drug Discovery 14, 261−278. (2) Slobodin, B., Han, R., Calderone, V., Vrielink, J. A. F. O., LoayzaPuch, F., Elkon, R., and Agami, R. (2017) Transcription Impacts the Efficiency of mRNA Translation via Co-transcriptional N6-adenosine Methylation. Cell 169, 326−337. (3) Roundtree, I. A., Evans, M. E., Pan, T., and He, C. (2017) Dynamic RNA Modifications in Gene Expression Regulation. Cell 169, 1187−1200. (4) Hoernes, T. P., Huttenhofer, A., and Erlacher, M. D. (2016) mRNA modifications: Dynamic regulators of gene expression? RNA Biol. 13, 760−765. (5) Li, X., Xiong, X., and Yi, C. (2017) Epitranscriptome sequencing technologies: decoding RNA modifications. Nat. Methods 14, 23−31.
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DOI: 10.1021/acs.biochem.8b00903 Biochemistry XXXX, XXX, XXX−XXX
