In both prokaryotes and eukaryotes, the transcription of DNA into RNA represents the first stage in the process of gene expression (Chapters 2 and 6) and is the major control point regulating which genes are expressed (Chapters 3 and 7). However, in eukaryotes, the process of transcription is supplemented by a series of post-transcriptional events that are necessary to produce a functional mRNA that is able to be translated into protein ( Figure 8.1 ).
Multiple-choice questions
Questions for Discussion
- Eukaryotic genes often have numerous exons, and accurate splicing relies on the ligation of adjacent exons. Failure of ligating neighboring exons results in exon skipping, which is very rare, despite the similarity of 5ʹ and 3ʹ splice sites. Elaborate the molecular mechanism through which adjacent exons are kept track of and spliced together.
- RNA is a highly unstable molecule and various mechanisms were evolved to regulate its stability. Discuss the process by which the stability of mRNA encoding SPIKE protein in mRNA vaccines was increased.
- The discovery of chemical modifications on mRNA has demonstrated a significant influence on transcription and translation processes, which can affect gene regulation through epigenetic mechanisms. With this in mind, discuss the potential epigenetic impact of mRNA vaccines and the means to minimize it.
- The central dogma of molecular biology states that DNA contains information to code for proteins, and the DNA polymerase enzyme responsible for replicating DNA is itself a protein. This creates a conundrum regarding their interdependence and which came first – DNA or protein? Apply what you’ve learned in this chapter to solve this puzzle.
- The genetic code has a fascinating aspect in that amino acids with comparable properties frequently have comparable codons. For example, codons including U or C as the second nucleotide generally specify hydrophobic amino acids. Can you propose a hypothesis to explain this occurrence about the early evolution of the protein synthesis process?
Further Reading
8.1 Capping
Borden, K., Culjkovic-Kraljacic, B., & Cowling, V. H. (2021). To cap it all off, again: Dynamic capping and recapping of coding and non-coding RNAs to control transcript fate and biological activity. Cell Cycle (Georgetown, Tex.), 20(14), 1347–1360. https://doi.org/10.1080/15384101.2021.1930929
Doamekpor, S. K., Sharma, S., Kiledjian, M., & Tong, L. (2022). Recent insights into noncanonical 5’ capping and decapping of RNA. The Journal of Biological Chemistry, 298(8), 102171. https://doi.org/10.1016/j.jbc.2022.102171
Kachaev, Z. M., Lebedeva, L. A., Kozlov, E. N., & Shidlovskii, Y. V. (2020). Interplay of mRNA capping and transcription machineries. Bioscience Reports, 40(1), BSR20192825. https://doi.org/10.1042/BSR20192825
Kozak M (1986) Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes. Cell 44:283–292.
8.2 Polyadenylation
Blake, D., & Lynch, K. W. (2021). The three as: Alternative splicing, alternative polyadenylation and their impact on apoptosis in immune function. Immunological Reviews, 304(1), 30–50. https://doi.org/10.1111/imr.13018
Mitschka, S., & Mayr, C. (2022). Context-specific regulation and function of mRNA alternative polyadenylation. Nature Reviews. Molecular Cell Biology, 23(12), 779–796. https://doi.org/10.1038/s41580-022-00507-5
Rodríguez-Molina, J. B., & Turtola, M. (2023). Birth of a poly(A) tail: Mechanisms and control of mRNA polyadenylation. FEBS Open Bio, 13(7), 1140–1153. https://doi.org/10.1002/2211-5463.13528 Struhl, K. (2023). How is polyadenylation restricted to 3’-untranslated regions? Yeast (Chichester, England). https://doi.org/10.1002/yea.39156.3
8.3 RNA splicing
Azubel M, Wolf S.G., Sperling J & Sperling R (2004) Three-dimensional structure of the native spliceosome by cryo-electron microscopy. Mol Cell 15:833–839.
Black, C. S., Whelan, T. A., Garside, E. L., MacMillan, A. M., Fast, N. M., & Rader, S. D. (2023). Spliceosome assembly and regulation: Insights from analysis of highly reduced spliceosomes. RNA (New York, N.Y.), 29(5), 531–550. https://doi.org/10.1261/rna.079273.122
De Bortoli, F., Espinosa, S., & Zhao, R. (2021). DEAH-Box RNA Helicases in Pre-mRNA Splicing. Trends in Biochemical Sciences, 46(3), 225–238. https://doi.org/10.1016/j.tibs.2020.10.006
Sharp P.A. (2005) The discovery of split genes and RNA splicing. Trends Biochem Sci 30:279–281.Stark H & Luhrmann R (2006) Cryo-electron microscopy of spliceosomal components. Annu Rev Biophys Biomol Struct 35:435–457.
Tholen, J., & Galej, W. P. (2022). Structural studies of the spliceosome: Bridging the gaps. Current Opinion in Structural Biology, 77, 102461. https://doi.org/10.1016/j.sbi.2022.102461
Wright, C. J., Smith, C. W. J., & Jiggins, C. D. (2022). Alternative splicing as a source of phenotypic diversity. Nature Reviews. Genetics, 23(11), 697–710. https://doi.org/10.1038/s41576-022-00514-4
8.4 Coupling of transcription and RNA processing within the nucleus
Bentley D.L. (2014) Coupling mRNA processing with transcription in time and space. Nat Rev Genet 15:163–175.
Garland, W., & Jensen, T. H. (2020). Nuclear sorting of RNA. Wiley Interdisciplinary Reviews. RNA, 11(2), e1572. https://doi.org/10.1002/wrna.1572
Hsi J-P & Manley J.L. (2012) The RNA polymerase II CTD co-ordinates transcription and RNA processing. Genes Dev 26:2119–2137.Kan, R. L., Chen, J., & Sallam, T. (2022). Crosstalk between epitranscriptomic and epigenetic mechanisms in gene regulation. Trends in Genetics: TIG, 38(2), 182–193. https://doi.org/10.1016/j.tig.2021.06.014
Lee, K.-M., & Tarn, W.-Y. (2013). Coupling pre-mRNA processing to transcription on the RNA factory assembly line. RNA Biology, 10(3), 380–390. https://doi.org/10.4161/rna.23697
Manley, J. L. (2002). Nuclear coupling: RNA processing reaches back to transcription. Nature Structural Biology, 9(11), 790–791. https://doi.org/10.1038/nsb1102-790
Tellier, M., Maudlin, I., & Murphy, S. (2020). Transcription and splicing: A two-way street. Wiley Interdisciplinary Reviews. RNA, 11(5), e1593. https://doi.org/10.1002/wrna.1593
Vorländer, M. K., Pacheco-Fiallos, B., & Plaschka, C. (2022). Structural basis of mRNA maturation: Time to put it together. Current Opinion in Structural Biology, 75, 102431. https://doi.org/10.1016/j.sbi.2022.102431
8.5 RNA transport
Basyuk, E., Rage, F., & Bertrand, E. (2021). RNA transport from transcription to localized translation: A single molecule perspective. RNA Biology, 18(9), 1221–1237. https://doi.org/10.1080/15476286.2020.1842631
Das, S., Vera, M., Gandin, V., Singer, R. H., & Tutucci, E. (2021). Intracellular mRNA transport and localized translation. Nature Reviews. Molecular Cell Biology, 22(7), 483–504. https://doi.org/10.1038/s41580-021-00356-8
De Magistris, P. (2021). The Great Escape: mRNA Export through the Nuclear Pore Complex. International Journal of Molecular Sciences, 22(21), 11767. https://doi.org/10.3390/ijms222111767
Stewart M (2010) Nuclear export of mRNA. Trends Biochem Sci 35:609–614.
8.6 Translation
Andreev, D. E., Loughran, G., Fedorova, A. D., Mikhaylova, M. S., Shatsky, I. N., & Baranov, P. V. (2022). Non-AUG translation initiation in mammals. Genome Biology, 23(1), 111. https://doi.org/10.1186/s13059-022-02674-2
Ben-Shem A, de Loubresse N.G., Melnikov S et al. (2011) The structure of the eukaryotic ribosome at 3.0Å resolution. Science 334:1524–1529.
Bourke, A. M., Schwarz, A., & Schuman, E. M. (2023). De-centralizing the Central Dogma: mRNA translation in space and time. Molecular Cell, 83(3), 452–468. https://doi.org/10.1016/j.molcel.2022.12.030
Farache, D., Antine, S. P., & Lee, A. S. Y. (2022). Moonlighting translation factors: Multifunctionality drives diverse gene regulation. Trends in Cell Biology, 32(9), 762–772. https://doi.org/10.1016/j.tcb.2022.03.006
Guo, X., & Su, M. (2022). The Origin of Translation: Bridging the Nucleotides and Peptides. International Journal of Molecular Sciences, 24(1), 197. https://doi.org/10.3390/ijms24010197
Schmeing T.M. & Ramakrishnan V (2009) What recent ribosome structures have revealed about the mechanism of translation. Nature 461:1234–1242.
Wu, Q., & Bazzini, A. A. (2023). Translation and mRNA Stability Control. Annual Review of Biochemistry, 92, 227–245. https://doi.org/10.1146/annurev-biochem-052621-091808
Anger A.M., Armache J.P., Berninghausen O et al. (2013) Structures of the human and Drosophila 90S ribosome. Nature 497:80–85.
8.7 RNA degradation
Bae, H., & Coller, J. (2022). Codon optimality-mediated mRNA degradation: Linking translational elongation to mRNA stability. Molecular Cell, 82(8), 1467–1476. https://doi.org/10.1016/j.molcel.2022.03.032
Frederick, M. I., & Heinemann, I. U. (2021). Regulation of RNA stability at the 3’ end. Biological Chemistry, 402(4), 425–431. https://doi.org/10.1515/hsz-2020-0325
Passmore, L. A., & Coller, J. (2022). Roles of mRNA poly(A) tails in regulation of eukaryotic gene expression. Nature Reviews. Molecular Cell Biology, 23(2), 93–106. https://doi.org/10.1038/s41580-021-00417-y
Riggs, C. L., Kedersha, N., Ivanov, P., & Anderson, P. (2020). Mammalian stress granules and P bodies at a glance. Journal of Cell Science, 133(16), jcs242487. https://doi.org/10.1242/jcs.242487
Tan, K., Stupack, D. G., & Wilkinson, M. F. (2022). Nonsense-mediated RNA decay: An emerging modulator of malignancy. Nature Reviews. Cancer, 22(8), 437–451. https://doi.org/10.1038/s41568-022-00481-2