Engineering protein-responsive mRNA switch in mammalian cells

Methods in Molecular Biology

Volumn 1111, Issue , 2014, Pages 183-196

  Endo, Kei ^a   Saito, Hirohide ^a  

^a KYOTO UNIVERSITY   (Japan)

Author keywords

Mammalian cell; Reporter assay; Riboswitch; RNA module; RNA protein interaction; RNP; Synthetic biology; Transfection; Translation

Indexed keywords

MESSENGER RNA;

ANIMAL CELL; APOPTOSIS; ARTICLE; AUTOREGULATION; CELL DEATH; CONTROLLED STUDY; FLOW CYTOMETRY; GENE EXPRESSION; MAMMAL CELL; NONHUMAN; PRIORITY JOURNAL; PROTEIN ENGINEERING; RIBOSWITCH;

5' UNTRANSLATED REGIONS; ANIMALS; APOPTOSIS; BASE SEQUENCE; CELL CULTURE TECHNIQUES; CELL LINE; CHEMISTRY; FLOW CYTOMETRY; GENES, REPORTER; GENETIC ENGINEERING; GENETICS; HUMANS; METABOLISM; METHODS; PLASMIDS; PROTEIN BIOSYNTHESIS; PROTEINS; RIBOSWITCH; RNA, MESSENGER; TRANSFECTION;

EID: 84934434773     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-755-6_13     Document Type: Article

References (23)

1. Isaacs FJ, Dwyer DJ, Collins JJ (2006) RNA synthetic biology. Nat Biotechnol 24: 545-554
2. Wieland M, Fussenegger M (2010) Ligand-dependent regulatory RNA parts for synthetic biology in eukaryotes. Curr Opin Biotechnol 21:760-765
3. Chang AL, Wolf JJ, Smolke CD (2012) Synthetic RNA switches as a tool for temporal and spatial control over gene expression. Curr Opin Biotechnol 23:679-688
4. Nandagopal N, Elowitz MB (2011) Synthetic biology: integrated gene circuits. Science 333:1244-1248
5. Ruder WC, Lu T, Collins JJ (2011) Synthetic biology moving into the clinic. Science 333:1248-1252
6. Wieland M, Fussenegger M (2012) Engineering molecular circuits using synthetic biology in mammalian cells. Annu Rev Chem Biomol Eng 3:209-234
7. Ausländer S, Ausländer D, Müller M et al (2012) Programmable single-cell mammalian biocomputers. Nature 487:123-127
8. Jackson RJ, Hellen CU, Pestova TV (2010) The mechanism of eukaryotic translation initiation and principles of its regulation. Nat Rev Mol Cell Biol 11:113-127
9. Sonenberg N, Hinnebusch AG (2009) Regulation of translation initiation in eukaryotes: mechanisms and biological targets. Cell 136:731-745
10. Hentze MW, Kühn LC (1996) Molecular control of vertebrate iron metabolism: mRNA-based regulatory circuits operated by iron, nitric oxide, and oxidative stress. Proc Natl Acad Sci U S A 93:8175-8182
11. Stripecke R, Oliveira CC, McCarthy JE et al (1994) Proteins binding to 5 untranslated region sites: A general mechanism for translational regulation of mRNAs in human and yeast cells. Mol Cell Biol 14:5898-5909
12. Paraskeva E, Atzberger A, Hentze MW (1998) A translational repression assay procedure (TRAP) for RNA-protein interactions in vivo. Proc Natl Acad Sci U S A 95:951-956
13. Nie M, Htun H (2006) Different modes and potencies of translational repression by sequence-specific RNA-protein interaction at the 5UTR. Nucleic Acids Res 34:5528-5540
14. Saito H, Kobayashi T, Hara T et al (2010) Synthetic translational regulation by an L7Aekink-turn RNP switch. Nat Chem Biol 6:71-78
15. Werstuck G, Green MR (1998) Controlling gene expression in living cells through small molecule-RNA interactions. Science 282:296-298
16. Endo K, Stapleton JA, Hayashi K et al (2013) Quantitative and simultaneous translational control of distinct mammalian mRNAs. Nucleic Acids Res. 41:e135
17. Imai Y, Matsushima Y, Sugimura T et al (1991) A simple and rapid method for generating a deletion by PCR. Nucleic Acids Res 19:2785
18. Hansson MD, Rzeznicka K, Rosenbäck M et al (2008) PCR-mediated deletion of plasmid DNA. Anal Biochem 375:373-375
19. Saito H, Fujita Y, Kashida S et al (2011) Synthetic human cell fate regulation by protein-driven RNA switches. Nat Commun 2:160
20. Smith AM, Fuchs RT, Grundy FJ et al (2010) Riboswitch RNAs: regulation of gene expression by direct monitoring of a physiological signal. RNA Biol 7:104-110
21. Eisenstein RS (2000) Iron regulatory proteins and the molecular control of mammalian iron metabolism. Annu Rev Nutr 20:627-662
22. Stapleton JA, Endo K, Fujita Y et al (2012) Feedback control of protein expression in mammalian cells by tunable synthetic translational inhibition. ACS Synth Biol 1:83-88
23. Suzuki Y, Ishihara D, Sasaki M et al (2000) Statistical analysis of the 5 untranslated region of human mRNA using 'Oligo-Capped' cDNA libraries. Genomics 64:286-297