Detecting Ribosomal Association with the 5′ Leader of mRNAs by Ribosome Density Mapping (RDM)

Methods in Enzymology

Volumn 431, Issue , 2007, Pages 163-175

  Eldad, Naama ^a   Arava, Yoav ^a  

^a TECHNION ISRAEL INSTITUTE OF TECHNOLOGY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

ANTISENSE OLIGODEOXYNUCLEOTIDE; CYCLOHEXIMIDE; HEPARIN; MESSENGER RNA; RIBONUCLEASE H; RIBONUCLEASE INHIBITOR;

ANIMAL CELL; CONTROLLED STUDY; CROSS LINKING; CYTOLYSIS; ENZYME DEGRADATION; HOUSEKEEPING GENE; INCUBATION TIME; NONHUMAN; NORTHERN BLOTTING; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; REVIEW; RIBOSOME; RNA DEGRADATION; SEDIMENTATION; SUCROSE GRADIENT; TRANSLATION REGULATION; 5' UNTRANSLATED REGION; ANIMAL; BIOLOGICAL MODEL; CHEMISTRY; DENSITY GRADIENT CENTRIFUGATION; EVALUATION; HUMAN; METABOLISM; METHODOLOGY; POLYSOME;

EUKARYOTA;

5' UNTRANSLATED REGIONS; ANIMALS; CENTRIFUGATION, DENSITY GRADIENT; HUMANS; MODELS, BIOLOGICAL; POLYRIBOSOMES; RIBONUCLEASE H; RIBOSOMES;

EID: 38449109263     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(07)31009-4     Document Type: Review

References (19)

1. Abastado J.P., Miller P.F., and Hinnebusch A.G. A quantitative model for translational control of the GCN4 gene of Saccharomyces cerevisiae. New Biol. 3 (1991) 511-524
2. Arava Y. Isolation of polysomal RNA for microarray analysis. Methods Mol. Biol. 224 (2003) 79-87
3. Arava Y., Boas F.E., Brown P.O., and Herschlag D. Dissecting eukaryotic translation and its control by ribosome density mapping. Nucleic Acids Res. 33 (2005) 2421-2432
4. Arava Y., Wang Y., Storey J.D., Liu C.L., Brown P.O., and Herschlag D. Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 100 (2003) 3889-3894
5. Church G.M., and Gilbert W. Genomic sequencing. Proc. Natl. Acad. Sci. USA 81 (1984) 1991-1995
6. Cigan A.M., and Donahue T.F. Sequence and structural features associated with translational initiator regions in yeast-A review. Gene 59 (1987) 1-18
7. Hinnebusch A.G. Translational regulation of GCN4 and the general amino acid control of yeast. Annu. Rev. Microbiol. 59 (2005) 407-450
8. Iacono M., Mignone F., and Pesole G. uAUG and uORFs in human and rodent 5′untranslated mRNAs. Gene 349 (2005) 97-105
9. Kozak M. An analysis of 5′-noncoding sequences from 699 vertebrate messenger RNAs. Nucleic Acids Res. 15 (1987) 8125-8148
10. Kuhn K.M., DeRisi J.L., Brown P.O., and Sarnow P. Global and specific translational regulation in the genomic response of Saccharomyces cerevisiae to a rapid transfer from a fermentable to a nonfermentable carbon source. Mol. Cell Biol. 21 (2001) 916-927
11. Morris D.R., and Geballe A.P. Upstream open reading frames as regulators of mRNA translation. Mol. Cell Biol. 20 (2000) 8635-8642
12. Muhlrad D., and Parker R. Mutations affecting stability and deadenylation of the yeast MFA2 transcript. Genes Dev. 6 (1992) 2100-2111
13. Rickwood D. "Preparative Centrifugation, A Practical Approach,". 2nd Ed. (1992), Oxford, New York
14. Sachs M.S., Wang Z., Gaba A., Fang P., Belk J., Ganesan R., Amrani N., and Jacobson A. Toeprint analysis of the positioning of translation apparatus components at initiation and termination codons of fungal mRNAs. Methods 26 (2002) 105-114
15. Sambrook J., and Russell D.W. "Molecular Cloning-A Laboratory Manual." (2001), CSHL Press, New York
16. Tzamarias D., Roussou I., and Thireos G. Coupling of GCN4 mRNA translational activation with decreased rates of polypeptide chain initiation. Cell 57 (1989) 947-954
17. Vilela C., and McCarthy J.E. Regulation of fungal gene expression via short open reading frames in the mRNA 5′untranslated region. Mol. Microbiol. 49 (2003) 859-867
18. Wang Y., Liu C.L., Storey J.D., Tibshirani R.J., Herschlag D., and Brown P.O. Precision and functional specificity in mRNA decay. Proc. Natl. Acad. Sci. USA 99 (2002) 5860-5865
19. Warner J.R., Knopf P.M., and Rich A. A multiple ribosomal structure in protein synthesis. Proc. Natl. Acad. Sci. USA 49 (1963) 122-129