Naturally occurring nucleosome positioning signals in human exons and introns

Journal of Molecular Biology

Volumn 263, Issue 4, 1996, Pages 503-510

  Baldi, Pierre ^a   Brunak, Søren ^b   Chauvin, Yves ^c   Krogh, Anders ^d  

^a CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^b TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^c Net ID Inc   (United States)

^d WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

Bendability; Exon; Intron; Nucleosome; Periodicity

Indexed keywords

NUCLEOTIDE; TRINUCLEOTIDE;

ARTICLE; CODON; DNA STRUCTURE; EXON; GENE SEQUENCE; HUMAN; INTRON; NUCLEOSOME; NUCLEOTIDE SEQUENCE; PERIODICITY; PRIORITY JOURNAL; PROBABILITY; RNA ANALYSIS;

EID: 0030575777     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0592     Document Type: Editorial

References (41)

1. Baldi, P. & Chauvin, Y. (1994). Hidden Markov models of the G-Protein coupled receptor family. J. Comp. Biol. 1, 311-335.
2. Baldi, P., Chauvin, Y., Hunkapiller, T. & McClure, M. A. (1994). Hidden Markov models of biological primary sequence information. Proc. Natl Acad. Sci. USA, 91, 1059-1063.
3. Baldi, P., Brunak, S., Chauvin, Y., Engelbrecht, J. & Krogh, A. (1995). Periodic sequence patterns in human exons. In Proc. Third Int. Conf. on Intelligent Systems for Mol. Biol. (Rawlings, C., Clark, D., Altman, R., Hunter, L., Lengauer, T. & Wodak, S., eds), pp. 30-38. AAAI Press, Menlo Park.
4. Bolshoy, A. (1995). CC dinucleotides contribute to the bending of DNA in chromatin. Nature Struct. Biol. 2, 447-448.
5. Brendel, V., Beckmann, J. S. & Trifonov, E. N. (1986). Linguistics of nucleotide sequences: morphology and comparison of vocabularies. J. Mol. Struct. Dyn. 4, 11-21.
6. Brukner, I., Sánchez, R., Suck, D. & Pongor, S. (1995a). Sequence-dependent bending propensity of DNA as revealed by DNase I: parameters for trinucleotides. EMBO J. 14, 1812-1818.
7. Brukner, I., Sánchez, R., Suck, D. & Pongor, S. (1995b). Trinucleotide models for DNA bending propensity: comparison of models based on DNasel digestion and nucleosome packaging data. J. Biomol. Struct. Dynam. 13, 309-317.
8. Brunak, S. & Engelbrecht, J. (1996). Protein structure and the sequential structure of mRNA: α-helix and β-sheet signals at the nucleotide level. Proteins: Struct. Funct. Genet. 25, 237-252.
9. Brunak, S., Engelbrecht, J. & Knudsen, S. (1991). Prediction of human mRNA donor and acceptor sites from the DNA sequence. J. Mol. Biol. 220, 49-65.
10. Clark, D., Reitman, M., Studitsky, V. & Chung, J. (1993). Chromatin structure of transcriptionally active genes. Cold Spring Harbor Symp. Quant. Biol. 58, 1-6.
11. Crothers, D. M. & Steitz, T. A. (1992). Transriptional activation by Eschericha coli CAP protein. In Transcriptional Regulation (McKnight, S. L. & Yamamoto, K. R., eds.), pp. 501-534, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
12. Drew, H. R. & Travers, A. A. (1985). DNA bending and its relation to nucleosome positioning. J. Mol. Biol. 186, 773-790.
13. Elgin, S. C. R., editor, (1995). Chromatin Structure and Gene Expression, IRL Press, Oxford.
14. Engelbrecht, J., Knudsen, S. & Brunak S. (1992). G + C-rich tract in 5′ end of human introns. J. Mol. Biol. 227, 108-113.
15. Fickett, J. W. (1982). Recognition of protein coding regions in DNA sequences. Nucl. Acids Res. 10, 5303-5318.
16. Fickett, J. W. & Tung, C. S. (1992). Assessment of protein coding measures. Nucl. Acids Res. 20, 6441-6450.
17. Goodman, S. D. & Nash, H. A. (1989). Functional replacement of a protein-induced bend in a DNA recombination site. Nature, 341, 251-254.
18. Goodsell, D. S. & Dickerson, R. E. (1994). Bending and curvature calculations in B-DNA. Nucl. Acids Res. 22, 5497-5503.
19. Haran, T. E., Kahn J. D & Crothers, D. M. (1994). Sequence elements responsible for DNA curvature. J. Mol. Biol. 244, 135-143.
20. Kabsch, W. & Sander, C. (1983). Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical feature. Biopolymers, 22, 2577-2637.
21. Klug, A. & Lutter, L. C. (1981). The helical periodicity of DNA on the nucleosome. Nucl. Acids Res. 9, 4267-4283.
22. Kornberg, R. D. & Lorch, Y. (1992). Chromatin structure and transcription. Annu. Rev. Cell Biol. 8, 563-587.
23. Krogh, A., Brown, M., Mian, I. S., Sjölander, K. & Haussler, D. (1994). Hidden Markov models in computational biology: applications to protein modeling. J. Mol. Biol. 235, 1501-1531.
24. Krogh, A., Mian, I. S. & Haussler, D. (1995). A hidden Markov model that finds genes in E. coli DNA. Nucl. Acids Res. 22, 4768-4778.
25. Lamond, A. I. (1995). Pre-mRNA Processing, R. G. Landes Company, Austin.
26. Levinson, S. E., Rabiner, L. R. & Sondhi, M. M. (1983). An introduction to the application of the theory of probabilistic functions of a Markov process to automatic speech recognition. The Bell Syst. Tech. J. 62, 1035-1074.
27. Lukashin, A. V., Engelbrecht, J. & Brunak, S. (1992). Multiple alignment using simulated annealing: branch point definition in human mRNA splicing. Nucl. Acids Res. 20, 2511-2516.
28. Muyldermans, S. & Travers, A. A. (1994). DNA sequence organization in chromatosomes. J. Mol. Biol. 235, 855-870.
29. Nussinov, R. (1989). Strong patterns in homooligomer tracts occurrences in non-coding and in potential regulatory sites in eukaryotic genomes. J. Biomol. Struct. Dynam. 6, 985-1000.
30. Pehrson, J. R. (1989). Thymine dimer formation as a probe of the path of DNA in and between nucleosomes in intact chromatin. Proc. Natl Acad. Sci. USA, 86, 9149-9153.
31. Rabiner, L. R. (1989). A tutorial on hidden Markov models and selected applications in speech recognition. Proc. IEEE, 77, 257-286.
32. Rumelhart, D. E., Durbin, R., Golden, R. & Chauvin, Y. (1994). Back-propagation: the theory. In Back-propagation: Theory, Architectures and Applications (Chauvin, Y. E. & Rumelhart, D. E., eds), Lawrence Erlbaum Associates, Hillsidle, New Jersey and Hove, UK.
33. Satchwell, S. C., Drew, H. R. & Travers, A. A. (1986). Sequence periodicities in chicken nucleosome core DNA. J. Mol. Biol. 191, 659-675.
34. Sinden, R. R. (1994). DNA Structure and Function, Academic Press, San Diego.
35. Trifonov, E. N. (1987). Translation framing code and frame-monitoring mechanism as suggested by the analysis of mRNA and 16 S rRNA nucleotide sequences. J. Mol. Biol. 194, 643-652.
36. Trifonov, E. N. (1989). The multiple codes of nucleotide sequences. Bull. Math. Biol. 51, 417-432.
37. Trifonov, E. N. & Sussman, J. L. (1980). The pitch of chromatin DNA is reflected in its nucleotide sequence. Proc. Natl Acad. Sci. USA, 77, 3816-3820.
38. VanWye, J. D., Bronson, E. C. & Anderson, J. N. (1991). Species-specific patterns of DNA bending and sequence. Nucl. Acids Res. 19, 5253-5261.
39. Widom, J. (1996). Short-range order in two eukaryotic genomes: relation to chromosome structure. J. Mol. Biol. 259, 579-588.
40. Zhurkin, V. B. (1981). Periodicity in DNA primary structure is defined by secondary structure of the coded protein. Nucl. Acids Res. 9, 1963-1971.
41. Zhurkin, V. B. (1983). Specific alignment of nucleosomes on DNA correlates with periodic distribution of purine-pyrimidine and pyrimidine-purine dimers. FEBS Letters, 158, 293-297.