Method for quantitative analysis of nonsense-mediated mRNA decay at the single cell level

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Pereverzev, Anton P ^a   Gurskaya, Nadya G ^a   Ermakova, Galina V ^a   Kudryavtseva, Elena I ^a   Markina, Nadezhda M ^a   Kotlobay, Alexey A ^a   Lukyanov, Sergey A ^a,b   Zaraisky, Andrey G ^a   Lukyanov, Konstantin A ^a,b  

^a SHEMYAKIN OVCHINNIKOV INSTITUTE OF BIOORGANIC CHEMISTRY   (Russian Federation)

^b PRIVOLZHSKY RESEARCH MEDICAL UNIVERSITY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

3' UNTRANSLATED REGION; GREEN FLUORESCENT PROTEIN;

3' UNTRANSLATED REGION; ANIMAL; ANIMAL EMBRYO; FLOW CYTOMETRY; FLUORESCENCE MICROSCOPY; GENE VECTOR; GENETICS; HEK293 CELL LINE; HELA CELL LINE; HUMAN; METABOLISM; MOUSE; NONSENSE MEDIATED MRNA DECAY; PROCEDURES; REPORTER GENE; RNA SPLICING; SINGLE CELL ANALYSIS; XENOPUS LAEVIS;

3' UNTRANSLATED REGIONS; ANIMALS; EMBRYO, NONMAMMALIAN; FLOW CYTOMETRY; GENES, REPORTER; GENETIC VECTORS; GREEN FLUORESCENT PROTEINS; HEK293 CELLS; HELA CELLS; HUMANS; MICE; MICROSCOPY, FLUORESCENCE; NONSENSE MEDIATED MRNA DECAY; RNA SPLICING; SINGLE-CELL ANALYSIS; XENOPUS LAEVIS;

EID: 84930205194     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep07729     Document Type: Article

References (37)

1. Behm-Ansmant, I. et al. mRNA quality control: an ancient machinery recognizes and degrades mRNAs with nonsense codons. FEBS Lett. 581, 2845-2853 (2007).
2. Bhuvanagiri, M., Schlitter, A. M., Hentze, M. W., Kulozik, A. E. NMD: RNA biology meets human genetic medicine. Biochem. J. 430, 365-377 (2010).
3. Huang, L., Wilkinson, M. F. Regulation of nonsense-mediated mRNA decay. Wiley Interdiscip. Rev. RNA 3, 807-828 (2012).
4. Mendell, J. T., Sharifi, N. A., Meyers, J. L., Martinez-Murillo, F., Dietz, H. C. Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise. Nat. Genet. 36, 1073-1078 (2004).
5. Rehwinkel, J., Letunic, I., Raes, J., Bork, P., Izaurralde, E. Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets. RNA 11, 1530-1544 (2005).
6. Bruno, I. G. et al. Identification of a microRNA that activates gene expression by repressing nonsense-mediated RNA decay. Mol. Cell 42, 500-510 (2011).
7. Nicholson, P., Mühlemann, O. Cutting the nonsense: the degradation of PTCcontaining mRNAs. Biochem. Soc. Trans. 38, 1615-1620 (2010).
8. Rebbapragada, I., Lykke-Andersen, J. Execution of nonsense-mediated mRNA decay: what defines a substrate Curr. Opin. Cell Biol. 21, 394-402 (2009).
9. Schweingruber, C., Rufener, S. C., Zünd, D., Yamashita, A., Mühlemann, O. Nonsense-mediated mRNA decay-mechanisms of substrate mRNA recognition and degradation in mammalian cells. Biochim. Biophys. Acta. 1829, 612-623 (2013).
10. Shyu, A. B., Wilkinson, M. F., van Hoof, A. Messenger RNA regulation: to translate or to degrade. EMBO J. 27, 471-481 (2008).
11. Gudikote, J. P., Imam, J. S., Garcia, R. F., Wilkinson, M. F. RNA splicing promotes translation and RNA surveillance. Nat. Struct. Mol. Biol. 12, 801-809 (2005).
12. Usuki, F. et al. Inhibition of nonsense-mediated mRNA decay rescues the phenotype in Ullrich's disease. Ann. Neurol. 55, 740-744 (2004).
13. Boelz, S., Neu-Yilik, G., Gehring, N. H., Hentze, M. W., Kulozik, A. E. A chemiluminescence-based reporter system to monitor nonsense-mediated mRNA decay. Biochem. Biophys. Res. Commun. 349, 186-191 (2006).
14. Nickless, A. et al. Intracellular calcium regulates nonsense-mediated mRNA decay. Nat. Med. 20, 961-966 (2014).
15. Paillusson, A., Hirschi, N., Vallan, C., Azzalin, C. M., Mühlemann, O. A GFPbased reporter system to monitor nonsense-mediatedmRNAdecay. Nucleic Acids Res. 33, e54 (2005).
16. Tessarollo, L. Manipulating mouse embryonic stem cells. in Gene knockout protocols Tymms, M. J., Kola, I. (eds.) 47-63 (Humana Press, Totowa, , NJ, 2000).
17. Martynova, N. et al. Patterning the forebrain: FoxA4a/Pintallavis and Xvent2 determine the posterior limit of Xanf1 expression in the neural plate. Development 131, 2329-2338 (2004).
18. Bayramov, A. V. et al. Novel functions of Noggin proteins: inhibition of Activin/Nodal and Wnt signaling. Development 138, 5345-5356 (2011).
19. Shcherbo, D. et al. Bright far-red fluorescent protein for whole-body imaging. Nat. Methods 4, 741-746 (2007).
20. Gurskaya, N. G. et al.Analysis of alternative splicing of cassette exons at single-cell level using two fluorescent proteins. Nucleic Acids Res. 40, e57 (2012).
21. Noensie, E. N., Dietz, H. C. A strategy for disease gene identification through nonsense-mediatedmRNAdecay inhibition. Nat. Biotechnol. 19, 434-439 (2001).
22. Yamashita, A., Ohnishi, T., Kashima, I., Taya, Y., Ohno, S. Human SMG-1, a novel phosphatidylinositol 3-kinase-related protein kinase, associates with components of the mRNA surveillance complex and is involved in the regulation of nonsense-mediated mRNA decay. Genes Dev. 15, 2215-2228 (2001).
23. Mendell, J. T., Sharifi, N. A., Meyers, J. L., Martinez-Murillo, F., Dietz, H. C. Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise. Nat. Genet.,36, 1073-1078 (2004).
24. Singh, G., Rebbapragada, I., Lykke-Andersen, J. A competition between stimulators and antagonists of Upf complex recruitment governs human nonsense-mediated mRNA decay. PLoS Biol. 6, e111 (2008).
25. Hogg, J. R., Goff, S. P. Upf1 senses 3'UTR length to potentiate mRNA decay. Cell 143, 379-389 (2010).
26. Summerton, J.,Weller, D. Morpholino antisense oligomers: design, preparation, and properties. Antisense Nucl. Acid Drug Dev. 7, 187-195 (1997).
27. Heasman, J., Kofron, M., Wylie, C. Beta-catenin signaling activity dissected in the early Xenopus embryo: a novel antisense approach. Dev. Biol. 222, 124-134 (2000).
28. Wittkopp, N. et al. Nonsense-mediated mRNA decay effectors are essential for zebrafish embryonic development and survival. Mol Cell Biol. 29, 3517-3528 (2009).
29. Gardner, L. B. Hypoxic inhibition of nonsense-mediated RNA decay regulates gene expression and the integrated stress response. Mol. Cell. Biol. 28, 3729-3741 (2008).
30. Gardner, L. B. Nonsense-mediated RNA decay regulation by cellular stress: implications for tumorigenesis. Mol. Cancer Res. 8, 295-308 (2010).
31. Wang, D. et al. Inhibition of nonsense-mediated RNA decay by the tumor microenvironment promotes tumorigenesis. Mol. Cell Biol. 31, 3670-3680 (2011).
32. Huang, L. et al. RNA homeostasis governed by cell type-specific and branched feedback loops acting on NMD. Mol. Cell 43, 950-961 (2011).
33. Hwang, J., Maquat, L. E. Nonsense-mediated mRNA decay (NMD) in animal embryogenesis: to die or not to die, that is the question. Curr. Opin. Genet. Dev. 21, 422-430 (2011).
34. Schoenberg, D. R., Maquat, L. E. Regulation of cytoplasmic mRNA decay. Nat. Rev. Genet. 13, 246-259 (2012).
35. Linde, L., Boelz, S., Neu-Yilik, G., Kulozik, A. E., Kerem, B. The efficiency of nonsense-mediated mRNA decay is an inherent character and varies among different cells. Eur. J. Hum. Genet. 15, 1156-1162 (2007).
36. Gehring, N. H. et al. Exon-junction complex components specify distinct routes of nonsense-mediated mRNA decay with differential cofactor requirements. Mol. Cell 20, 65-75 (2005).
37. Chan, W. K. et al. An alternative branch of the nonsense-mediated decay pathway. EMBO J. 26, 1820-1830 (2007).