Efficient 5′ cap-dependent RNA purification use in identifying and studying subsets of RNA

Methods in Molecular Biology

Volumn 419, Issue , 2008, Pages 147-160

  Bajak, Edyta Z ^a   Hagedorn, Curt H ^a  

^a NONE

Author keywords

3 poly(A); 5 RNA cap; Cytoplasmic processing bodies; Deadenylation; EIF4E; M7G cap; Microarray; MRNA; Non coding RNA; RNA purification

Indexed keywords

CAPPED RNA; HYBRID PROTEIN; INITIATION FACTOR 4E; LIGAND; MESSENGER RNA; RNA;

ARTICLE; CHEMISTRY; CLASSIFICATION; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENETIC VARIABILITY; GENETICS; HUMAN; ISOLATION AND PURIFICATION; METABOLISM; PROTEIN BINDING;

EUKARYOTIC INITIATION FACTOR-4E; GENE EXPRESSION PROFILING; HUMANS; LIGANDS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEIN BINDING; RECOMBINANT FUSION PROTEINS; RNA; RNA CAPS; RNA, MESSENGER; VARIATION (GENETICS);

EID: 42949171470     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-59745-033-1_10     Document Type: Article

References (36)

1. Mattick, J. S. and Makunin, I. V. (2006) Non-coding RNA. Hum Mol Genet 15, R17-R29.
2. Herbert, A. and Rich, A. (1999) RNA processing and the evolution of eukaryotes. Nat Genet 21, 265-269.
3. Carninci, P. (2006) Tagging mammalian transcription complexity. Trends Genet 22, 501-510.
4. David, L., Huber, W., Granovskaia, M., Toedling, J., Palm, C. J., Bofkin, L., Jones, T., Davis, R. W., and Steinmetz, L. M. (2006) A high-resolution map of transcription in the yeast genome. Proc Natl Acad Sci USA 103, 5320-5325.
5. Bajak, E. Z. (2005) Genotoxic Stress: Novel Biomarkers and Detection Methods. Uncovering RNAs Role in Epigenetics of Carcinogenesis. Karolinska University Press, Stockholm, Sweden.
6. Calin, G. A., Dumitru, C. D., Shimizu, M., Bichi, R., Zupo, S., Noch, E., Aldler, H., Rattan, S., Keating, M., Rai, K., Rassenti, L., Kipps, T., Negrini, M., Bullrich, F., and Croce, C. M. (2002) Frequent deletions and down-regulation of micro-RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc Natl Acad Sci USA 99, 15524-15529.
7. Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M. C., Maeda, N., et al. (2005) The transcriptional landscape of the mammalian genome. Science 309, 1559-1563.
8. Cai, X., Hagedorn, C. H., and Cullen, B. R. (2004) Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. RNA 10, 1957-1966.
9. Lee, Y., Kim, M., Han., J., Yeom, K. H., Lee, S., Baek, S. H., and Kim, V. N. (2004) MicroRNA genes are transcribed by RNA polymerase II. EMBO J 23, 4051-4060.
10. Houbaviy, H. B., Dennis, L., Jaenisch, R., and Sharp, P. A. (2005) Characterization of a highly variable eutherian microRNA gene. RNA 11, 1245-1257.
11. 7GTP. FEBS Lett 516, 9-14.
12. Choi, Y. H. and Hagedorn, C. H. (2003) Purifying mRNAs with a high-affinity eIF4E mutant identifies the short 3' poly(A) end phenotype. Proc Natl Acad Sci USA 100, 7033-7038.
13. Wang, L., Eckmann, C. R., Kadyk, L. C., Wickens, M., and Kimble, J. (2002) A regulatory cytoplasmic poly(A) polymerase in Caenorhabditis elegans. Nature 419, 312-316.
14. Barnard, D. C., Cao, Q., and Richter, J. D. (2005) Differential phosphorylation controls Maskin association with eukaryotic translation initiation factor 4E and localization on the mitotic apparatus. Mol Cell Biol 25, 7605-7615.
15. Wilusz, C. J. and Wilusz, J. (2004)Bringing the role of mRNA decay in the control of gene expression into focus. Trends Genet 20, 491-497.
16. Coller, J. and Parker, R. (2005) General translational repression by activators of mRNA decapping. Cell 122, 875-886.
17. Mukherjee, D., Gao, M., O'Connor, J. P., Raijmakers, R., Pruijn, G., Lutz, C. S., and Wilusz, J. (2002). The mammalian exosome mediates the efficient degradation of mRNAs that contain AU-rich elements. EMBO 21, 165-174.
18. Newbury, S. F., Mühlemann O., and Stoecklin, G. (2006) Turnover in the Alps: an mRNA perspective. Workshop on mechanisms and regulation of mRNA turnover. EMBO Rep 7, 143-148.
19. Brengues, M., Teixeira, D., and Parker, R. (2005) Movement of eukaryotic mRNAs between polysomes and cytoplasmic processing bodies. Science 310, 486-489.
20. Weber, M., Hagedorn, C. H., Harrison, D. G., and Searles, C. D. (2005) Laminar shear stress and 3' polyadenylation of eNOS mRNA. Circ Res 96, 1161-1168.
21. Engström, P. G., Suzuki, H., Ninomiya, N., Akalin, A., Sessa, L., Lavorgna, G., et al. (2006) Complex loci in human and mouse genomes. PLoS Genet 2, e47.
22. Katayama, S., Tomaru, Y., Kasukawa, T., Waki, K., Nakanishi, M., Nakamura, M., et al. (2005) Antisense transcription in the mammalian transcriptome. Science 309, 1564-1566.
23. Cheng, J., Kapranov, P., Drenkow, J., Dike, S., Brubaker, S., Patel, S., et al. (2005) Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308, 1149-1154.
24. Siddiqui, A. S., Khattra, J., Delaney, A. D., Zhao, Y., Astell, C., Asano, J., et al. (2005) A mouse atlas of gene expression: large-scale digital gene-expression profiles from precisely defined developing C57BL/6J mouse tissues and cells. Proc Natl Acad Sci USA 102, 18485-18490.
25. Hayashizaki, Y. and Carninci, P. (2006) Genome Network and FANTOM3: assessing the complexity of the transcriptome. PLoS Genetics 2, e63.
26. Kiyosawa, H., Mise, N., Iwase, S., Hayashizaki, Y., and Abe, K. (2005) Disclosing hidden transcripts: mouse natural sense-antisense transcripts tend to be poly(A) negative and nuclear localized. Genome Res 15, 463-474.
27. 7G cap analogues and eIF4G peptides. Biochemistry 44, 4546-4550.
28. Salles, F. J., Darrow, A. L., O'Connell, M. L., and Strickland, S. (1992) Isolation of novel murine maternal mRNAs regulated by cytoplasmic polyadenylation. Genes Dev. 6, 1202-1212.
29. Liu X. and 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.
30. Schaefer, B. C. (1995) Revolutions in rapid amplification of cDNA ends: new strategies for polymerase chain reaction cloning of full-length cDNA ends. Anal Biochem 227, 255-273.
31. Friedrich, M., Grahnert, A., and Hauschildt, S. (2005) Analysis of the 3' UTR of the ART3 and ART4 gene by 3' inverse RACE-PCR. DNA Seq 16, 53-57.
32. Bustin, S. A. and Nolan, T. (2004) Template handling, preparation, and quantification, in A-Z of Quantitative PCR (Bustin, S. A., ed.), International University Line, La Jolla, CA, pp. 141-213.
33. human: purification, detailed characterization, and its use in isolating eIF-4E binding proteins. Protein Expr Purif 9, 53-60.
34. Yang Z., Edenberg, H. J., and Davis, R. L. (2005) Isolation of mRNA from specific tissues of Drosophila by mRNA tagging. Nucleic Acids Res 33, e148.
35. 7GDP. Proc Natl Acad Sci USA 76, 4345-4349.
36. Edery, I., Chu, L. L., Sonenberg, N., and Pelletier, J. (1995) An efficient strategy to isolate full-length cDNAs based on an mRNA cap retention procedure (CAPture). Mol Cell Biol 15, 3363-3371.