Structural elements of dynamic RNA strings

Molecules and Cells

Volumn 16, Issue 2, 2003, Pages 201-210

  Ro Choi, Tae Suk ^a   Choi, Yong Chun ^b  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

^b Dong A University   (South Korea)

Author keywords

Contraction Ratio Rate; RNP Fibril; Stem Loop

Indexed keywords

CALCIDIOL 1 MONOOXYGENASE; INSULIN; MESSENGER RNA;

ARTICLE; GENETIC TRANSCRIPTION; INTRON; RNA ANALYSIS; RNA STRING; RNA STRUCTURE; RNA TRANSCRIPTION; STRUCTURE ANALYSIS; ANIMAL; CHEMISTRY; CONFORMATION; EXON; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; RNA SPLICING;

25-HYDROXYVITAMIN D3 1-ALPHA-HYDROXYLASE; ANIMALS; BASE SEQUENCE; EXONS; INSULIN; INTRONS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA SPLICING; RNA, MESSENGER;

EID: 26444565081     PISSN: 10168478     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (31)

1. Allain, F. H.-T., Bouvet, P., Dieckmann, T., and Feigon, J. (2000) Molecular basis of sequence-specific recognition of pre-ribosomal RNA by nucleolin. EMBO J. 19, 6870-6881.
2. Barnett, S., LeStourgeon, W., and Friedman, D. (1988) Rapid purification of native C protein from nuclear ribonucleoproteinparticles. J. Biochem. Biophys. Meth. 16, 87-98.
3. 3C2. Mol. Cell. Biol. 9, 492-498.
4. Beyer, A. L. and Osheim, Y. N. (1990) Ultrastructural analysis of the ribonucleoprotein substrate for pre-mRNA processing; in The Eukaryotic Nucleus, Strauss, P. R. and Wilson, S. H. (eds.), Vol. 2, pp. 431-451.
5. Beyer, A. L., Christensen, M. E., Walker, B. W., and LeStourgeon, W. M. (1977) Identification and characterization of the packaging proteins of core 40S hnRNP particles. Cell 11, 127-138.
6. Burd, C. G. and Dreyfuss, G. (1994) RNA binding specificity of hnRNP Al, significance of hnRNP A1 high-affinity binding sites in pre-mRNA splicing. EMBO J. 13, 1197-1204.
7. Ding, J., Hayashi, M. K., Zhang, Y., Manche, L., Krainer, A. R., and Xu, R.-M. (1999) Crystal structure of the two-RRM domain of hnRNP A1 complexed with single-stranded telomeric DNA. Genes Dev. 13, 1102-1115.
8. Dreyfuss, G. (1986) Structure and function of nuclear and cytoplasmic ribonucleoprotein particles. Ann. Rev. Cell Biol. 2, 459-498.
9. Dreyfuss, G., Swanson, M. S., and Pinol-Roma, S. (1988) Heterogeneous nuclear ribonucleoprotein particles and the pathway of mRNA formation. Trends Biochem. Sci. 13, 86-91.
10. Eperon, L. P., Graham, I. R., Griffiths, A. D., and Eperon, I. C. (1988) Effects of RNA secondary structure on alternative splicing of pre-mRNA: Is folding limited to a region behind the transcribing RNA polymerase? Cell 54, 393-401.
11. Ford, L. P., Suh, J. M., Wright, W. E., and Shay, J. W. (2000) Heterogeneous nuclear ribonucleoproteins C1 and C2 associate with the RNA component of human telomerase. Mol. Cell. Biol. 20, 9084-9091.
12. Görlach, M., Burd, C. G., and Dreyfuss, G. (1994) The determinants of RNA-binding specificity of the heterogeneous nuclear ribonucleoprotein C proteins. J. Biol. Chem. 269, 23074-23078.
13. Gu, W., Powell, W., Mote, J. Jr., and Reines, D. (1993) Nascent RNA cleavage by arrested RNA polymerae II does not require upstream translocation of the elongation complex on DNA. J. Biol. Chem. 268, 25604-25616.
14. Gu, W., Wind, M., and Reines, D. (1996) Increased accommodation of nascent RNA in a product site on RNA polymerase II during arrest. Proc. Natl. Acad. Sci. USA 93, 6935-6940.
15. Han, K. (2000) A graphical tool for parametric simulation of the RNA structure formation. Mol. Cells 10, 348-355.
16. Jessen, T.-H., Oubridge, C., Teo, C. H., Pritchard, C., and Nagai, K. (1991) Identification of molecular contacts between the U1 A small nuclear ribonucleoprotein and U1 RNA. EMBO J. 10, 3447-3456.
17. Kashlev, M. and Komissarova, N. (2002) Transcription termination: Primary intermediates and secondary adducts. J. Biol. Chem. 277, 14501-14508.
18. Kim, H.-J. and Han, K. (1995) Automated modeling of the RNA folding process. Mol. Cells 5, 406-412.
19. Korzheva, N., Mustaev, A., Kozlov, M., Malhotra, A., Nikiforov, V., Goldfarb, A., and Darst, S. A. (2000) A structural model of transcription elongation. Science 289, 619-625.
20. LeStourgeon, W. M., Barnett, S. F., and Northington, S. J. (1990) Tetramer of the core proteins of 40S nuclear ribonucleoprotein particles assemble to package nascent transcripts into a repeating array of regular particles; in The Eukaryotic Nucleus, Strauss, P. R. and Wilson, S. H. (eds.), Vol. 2, pp. 477-502, The Telford Press, New Jersey.
21. Munroe, S. H. and Pederson, T. (1981) Messenger RNA sequences in nuclear RNP particles are complexed with protein as shown by nuclease protection. J. Mol. Biol. 147, 437-449.
22. Pederson, T. and Davis, N. G. (1980) Messenger RNA processing and nuclear structure: Isolation of nuclear ribonucleoprotein particles containing β-globin mRNA precursors. J. Cell Biol. 87, 47-54.
23. Reeder, T. C. and Hawley, D. K. (1996) Promoter proximal sequences modulate RNA polymerase II elongation by a novel mechanism. Cell 87, 767-777.
24. Samarina, O. P., Lukanidin, E. M., Molnar, J., and Georgiev, G. P. (1968) Structural organization of nuclear complexes containing DNA-like RNA. J. Mol. Biol. 33, 251-263.
25. Skoglund, U., Andersson, K., Björkroth, B., Lamb, M. M., and Daneholt, B. (1983) Visualization of the formation and transport of a specific hnRNP particle. Cell 34, 847-855.
26. Sperling, R. and Sperling, J. (1990) Large nuclear ribonucleoprotein particles of specific RNA polymerase II transcripts; in The Eukaryotic Nucleus, Strauss, P. R. and Wilson, H. S. (eds.), Vol. 2, pp. 453-476, The Telford Press.
27. Steitz, J. A. and Kamen, R. (1981) Arrangement of 30S heterogeneous nuclear ribonucleoprotein on polyoma virus late nuclear transcript. Mol. Cell. Biol. 1, 21-34.
28. Thomas, P. S., Shepherd, J. H., Mulvihill, E. R., and Palmiter, R. D. (1981) Isolation of a nuclear ribonucleoprotein fraction from chick oviduct containing ovalbumin mRNA sequences. J. Mol. Biol. 150, 143-166.
29. Újvári, A., Pal, M., and Luse, D. S. (2002) RNA polymerase II transcription complexes may become arrested if the nascent RNA is shortened to less than 50 nucleotides. J. Biol. Chem. 277, 32527-32537.
30. Wan, L., Kim, J.-K., Pollard, V. W., and Dreyfuss, G. (2001) Mutational definition of RNA-binding and protein-protein interaction domain of heterogeneous nuclear RNP C1. J. Biol. Chem. 276, 7681-7688.
31. Wetterberg, I., Zhao, J., Masich, S., Wieslander, L., and Skoglund, U. (2001) In situ transcription and splicing in the Balbiani ring 3 gene. EMBO J. 20, 2564-2574.