Protein Kodlanmayan Bölgelerin (UTR) Rolü ve Bu Bölgelerin Haritalanmasında Kullanılan Başlıca Yöntemler
Öz
Virüs genomlarının çevrilmemiş bölgelerinin (UTR'ler), mRNA'ların çekirdek dışına taşınması ve translasyon verimliliği dahil olmak üzere gen ifadesinin transkripsiyon sonrası düzenlenme-sinde önemli roller oynadığı bilinmektedir. Birçok hastalığın moleküler profilinin çıkarılması, mRNA'ların çevrilmemiş bölgelerinin hastalığın ilerlemesinde ve yatkınlığında düşünülenden daha önemli bir rol oynadığını göstermiştir. Bu nedenle, bu bölgelerin haritalanması ve tespitinde kullanılan yöntemler önem kazanmaya devam etmektedir. Dolayısıyla bu bölgelerde meydana gelen mutasyonlar ve bunların hastalık oluşumuna etkileri hakkında daha detaylı bilgi edinilmesi gerekmektedir. Bu çalışmada, çevrilmemiş bölgeleri tespit etmek için kullanılan testler anlatıl-maktadır. Teknoloji gelişimine bağlı olarak, her test yöntemi üniversite araştırmaları ve ticari şir-ketler aracılığıyla önemli ilerlemeler kaydetmektedir. Bu testler Primer Extension Assay, S1 Nuc-lease Assay, RNAse Protection Assay ve Rapid Amplification of cDNA Ends Assay'i içermek-tedir. Bu testler, bir RNA'nın 5' ve 3' terminalini haritalamak ve ters transkriptaz kullanarak bir primeri uzatarak belirli bir RNA miktarını ölçmek için kullanılmaktadır.
Kaynakça
- Bartlett & D. Stirling (Eds.). PCR Protocols, Humana Press., Totowa, NJ. 105-115
- Belin, D. (1996). The RNase protection assay. In Basic DNA and RNA Protocols, Springer, 131-136.
- Berk, A. J. (1989). Characterization of RNA molecules by S1 nuclease analysis. In Methods in Enzymology, Academic Press, 334-347.
- Boorstein, W. R.,Craig, E. A. (1989). Primer extension analysis of RNA. In Methods in En-zymology, Academic Press, 347-369.
- Carey, M. F., Peterson, C. L., Smale, S. T. (2013). The primer extension assay, Cold Spring Harb Protoc, 164-173. doi:10.1101/pdb.prot071902
- Clark, D. P., Pazdernik, N. J. (2013). Chapter 19 - Analysis of Gene Expression. In D. P. Clark,N. J. Pazdernik (Eds.), Molecular Biology (Second Edition), 581-614, Academic Press, Boston.
- Emery, P. (2007). RNase Protection Assay. In E. Rosato (Ed.), Circadian Rhythms: Methods and Protocols, Humana Press, Totowa, NJ, 343-348.
- Frohman, M. A. (1990). RACE: rapid amplification of cDNA ends. PCR protocols. A guide to methods and applications, 28.
- Fromont-Racine, M., Bertrand, E., Pictet, R., Grange, T. (1993). A highly sensitive method for mapping the 5 termini of mRNAs. Nucleic Acids Res 21, 1683–1684.
- Ghosh, P., Reddy, V., Swinscoe, J., Lebowitz, P., Weissman, S. (1978). Heterogeneity and 5′-terminal structures of the late RNAs of simian virus. Journal of molecular biology, 126(4), 813-846.
- Gilman, M. (1993). Ribonuclease protection assay. Current protocols in molecular biology, 24(1), 4.7. 1-4.7. 8.
- Grabowski PJ, Black DL. (2001). Alternative RNA splicing in the nervous system. Prog Ne-urobiol, 65, 289-308.
- Green, M. R.,Sambrook, J. (2021). Mapping RNA with Nuclease S1. Cold Spring Harb Pro-toc, 2021(5). doi:10.1101/pdb.prot101824
- Kozak, M. (1987). An analysis of 5'-noncoding sequences from 699 vertebrate messenger RNAs. Nucleic acids research, 15(20), 8125-8148.
- Kühn, L. C. (2015). Iron regulatory proteins and their role in controlling iron metabo-lism. Metallomics, 7(2), 232-243.
- Liu, X., Gorovsky, M. A. (1993). Mapping the 5' and 3' ends of Tetrahymena thermophila mRNAs using RNA ligase mediated amplification of cDNA ends (RLM-RACE). Nucleic Acids Res, 21, 4954–4960.
- Ma, Y. J., Dissen, G. A., Rage, F., Ojeda, S. R. (1996). RNase protection assay. Methods, 10(3), 273-278.
- Matoulkova, E., Michalova, E., Vojtesek, B., Hrstka, R. (2012). The role of the 3' untranslated region in post-transcriptional regulation of protein expression in mammalian cells. RNA Biology, 9(5), 563-576. doi:10.4161/rna.20231
- Mitschka, S., Fansler, M. M., & Mayr, C. (2021). Chapter Eighteen - Generation of 3′UTR knockout cell lines by CRISPR/Cas9-mediated genome editing. In B. Tian (Ed.), Methods in Enzymology, Vol. 655, pp. 427-457.
- Tessier, D. C., Brousseau, R., Vernet, T. (1986). Ligation of single-stranded oligodeoxyri-bonucleotides by T4 RNA ligase. Anal Biochem, 158, 171–178.
- Pesole G, Mignone F, Gissi C, Grillo G, Licciulli F, Liuni S. (2001). Structural and functio-nal features of eukaryotic mRNA untranslated regions. Gene, 276, 73-81.
- Pesole G, Liuni S, Grillo G, Saccone C. (1997). Structural and compositional features of untranslated regions of eukaryotic mRNAs. Gene, 205, 95-102.
- Schuster, S. L., Hsieh, A. C. (2019). The Untranslated Regions of mRNAs in Cancer. Trends in cancer, 5(4), 245–262.
- Schwanhäusser, B., Busse, D., Li, N., Dittmar, G., Schuchhardt, J., Wolf, J., ... & Selbach, M. (2011). Global quantification of mammalian gene expression control. Nature, 473(7347), 337-342.
- Shumaker, J. M., Metspalu, A.,Caskey, C. T. (1996). Mutation detection by solid phase pri-mer extension. Human mutation, 7(4), 346-354.
- Smith, D. R. (1993). S1 Nuclease Protection Mapping. Transgenesis Techniques: Principles and Protocols, Humana Press, Totowa, NJ., 363-372.
- Venkatesh, L. K., Fasina, O., Pintel, D. J. (2012). RNAse mapping and quantitation of RNA isoforms. RNA Abundance Analysis, Springer, 121-129.
- Volloch, V., Schweitzer, B., Zhang, X., Rits, S. (1991). Identification of negative-strand complements to cytochrome oxidase subunit III RNA in Trypanosoma brucei. Proc Natl Acad Sci USA 88, 10671–10675.
- Yeku, O., Frohman, M. A. (2011). Rapid amplification of cDNA ends (RACE). In RNA, Springer, 107-122.
- Zhao, J., Tang, J., Elfman, J.,Li, H. (2020). RNase Protection Assay. In Chimeric RNA, Springer, 109-116.
- Zhang, Y., Frohman, M. A. (1997). Using rapid amplification of cDNA ends (RACE) to ob-tain full-length cDNAs. In cDNA library protocols, Springer, 61-87.
- Wang, X., Scott Young, W. (2003). Rapid Amplification of cDNA Ends. In J. M. S.
ASSAYS USED IN THE ANALYSIS OF UNTRANSLATED REGIONS OF VIRUSES
Öz
Untranslated regions (UTRs) of virus genomes are known to play crucial roles in the post-
transcriptional regulation of gene expression, including modulation of the transport of mRNAs out of the nucleus and of translation efficiency, subcellular localization and stability. The molecu-lar profiling of many diseases has shown that the untranslated regions of mRNAs play a more significant role in disease progression and susceptibility than previously thought. Therefore, the methods used in the mapping and detection of these regions continue to gain importance. De-pending on technology development, each test method makes significant progress through uni-versity research and commercial companies. Therefore, it provides more detailed information about the mutations that occur in these regions and their effects on the formation of the disease. In this study, the tests used to detect untranslated regions are described. These tests include Pri-mer Extension Assay, S1 Nuclease Assay,RNAse Protection Assay, and Rapid Amplification of cDNA Ends Assay. These assays can be used to map the 5’ and 3’ terminus of an RNA and to quantitate the amount of a given RNA by extending a primer using reverse transcriptase.
Kaynakça
- Bartlett & D. Stirling (Eds.). PCR Protocols, Humana Press., Totowa, NJ. 105-115
- Belin, D. (1996). The RNase protection assay. In Basic DNA and RNA Protocols, Springer, 131-136.
- Berk, A. J. (1989). Characterization of RNA molecules by S1 nuclease analysis. In Methods in Enzymology, Academic Press, 334-347.
- Boorstein, W. R.,Craig, E. A. (1989). Primer extension analysis of RNA. In Methods in En-zymology, Academic Press, 347-369.
- Carey, M. F., Peterson, C. L., Smale, S. T. (2013). The primer extension assay, Cold Spring Harb Protoc, 164-173. doi:10.1101/pdb.prot071902
- Clark, D. P., Pazdernik, N. J. (2013). Chapter 19 - Analysis of Gene Expression. In D. P. Clark,N. J. Pazdernik (Eds.), Molecular Biology (Second Edition), 581-614, Academic Press, Boston.
- Emery, P. (2007). RNase Protection Assay. In E. Rosato (Ed.), Circadian Rhythms: Methods and Protocols, Humana Press, Totowa, NJ, 343-348.
- Frohman, M. A. (1990). RACE: rapid amplification of cDNA ends. PCR protocols. A guide to methods and applications, 28.
- Fromont-Racine, M., Bertrand, E., Pictet, R., Grange, T. (1993). A highly sensitive method for mapping the 5 termini of mRNAs. Nucleic Acids Res 21, 1683–1684.
- Ghosh, P., Reddy, V., Swinscoe, J., Lebowitz, P., Weissman, S. (1978). Heterogeneity and 5′-terminal structures of the late RNAs of simian virus. Journal of molecular biology, 126(4), 813-846.
- Gilman, M. (1993). Ribonuclease protection assay. Current protocols in molecular biology, 24(1), 4.7. 1-4.7. 8.
- Grabowski PJ, Black DL. (2001). Alternative RNA splicing in the nervous system. Prog Ne-urobiol, 65, 289-308.
- Green, M. R.,Sambrook, J. (2021). Mapping RNA with Nuclease S1. Cold Spring Harb Pro-toc, 2021(5). doi:10.1101/pdb.prot101824
- Kozak, M. (1987). An analysis of 5'-noncoding sequences from 699 vertebrate messenger RNAs. Nucleic acids research, 15(20), 8125-8148.
- Kühn, L. C. (2015). Iron regulatory proteins and their role in controlling iron metabo-lism. Metallomics, 7(2), 232-243.
- Liu, X., Gorovsky, M. A. (1993). Mapping the 5' and 3' ends of Tetrahymena thermophila mRNAs using RNA ligase mediated amplification of cDNA ends (RLM-RACE). Nucleic Acids Res, 21, 4954–4960.
- Ma, Y. J., Dissen, G. A., Rage, F., Ojeda, S. R. (1996). RNase protection assay. Methods, 10(3), 273-278.
- Matoulkova, E., Michalova, E., Vojtesek, B., Hrstka, R. (2012). The role of the 3' untranslated region in post-transcriptional regulation of protein expression in mammalian cells. RNA Biology, 9(5), 563-576. doi:10.4161/rna.20231
- Mitschka, S., Fansler, M. M., & Mayr, C. (2021). Chapter Eighteen - Generation of 3′UTR knockout cell lines by CRISPR/Cas9-mediated genome editing. In B. Tian (Ed.), Methods in Enzymology, Vol. 655, pp. 427-457.
- Tessier, D. C., Brousseau, R., Vernet, T. (1986). Ligation of single-stranded oligodeoxyri-bonucleotides by T4 RNA ligase. Anal Biochem, 158, 171–178.
- Pesole G, Mignone F, Gissi C, Grillo G, Licciulli F, Liuni S. (2001). Structural and functio-nal features of eukaryotic mRNA untranslated regions. Gene, 276, 73-81.
- Pesole G, Liuni S, Grillo G, Saccone C. (1997). Structural and compositional features of untranslated regions of eukaryotic mRNAs. Gene, 205, 95-102.
- Schuster, S. L., Hsieh, A. C. (2019). The Untranslated Regions of mRNAs in Cancer. Trends in cancer, 5(4), 245–262.
- Schwanhäusser, B., Busse, D., Li, N., Dittmar, G., Schuchhardt, J., Wolf, J., ... & Selbach, M. (2011). Global quantification of mammalian gene expression control. Nature, 473(7347), 337-342.
- Shumaker, J. M., Metspalu, A.,Caskey, C. T. (1996). Mutation detection by solid phase pri-mer extension. Human mutation, 7(4), 346-354.
- Smith, D. R. (1993). S1 Nuclease Protection Mapping. Transgenesis Techniques: Principles and Protocols, Humana Press, Totowa, NJ., 363-372.
- Venkatesh, L. K., Fasina, O., Pintel, D. J. (2012). RNAse mapping and quantitation of RNA isoforms. RNA Abundance Analysis, Springer, 121-129.
- Volloch, V., Schweitzer, B., Zhang, X., Rits, S. (1991). Identification of negative-strand complements to cytochrome oxidase subunit III RNA in Trypanosoma brucei. Proc Natl Acad Sci USA 88, 10671–10675.
- Yeku, O., Frohman, M. A. (2011). Rapid amplification of cDNA ends (RACE). In RNA, Springer, 107-122.
- Zhao, J., Tang, J., Elfman, J.,Li, H. (2020). RNase Protection Assay. In Chimeric RNA, Springer, 109-116.
- Zhang, Y., Frohman, M. A. (1997). Using rapid amplification of cDNA ends (RACE) to ob-tain full-length cDNAs. In cDNA library protocols, Springer, 61-87.
- Wang, X., Scott Young, W. (2003). Rapid Amplification of cDNA Ends. In J. M. S.