Noncoding DNA, isochores and gene expression: Nucleosome formation potential

Nucleic Acids Research

Volumn 33, Issue 2, 2005, Pages 559-563

  Vinogradov, Alexander E ^a  

^a INSTITUTE OF CYTOLOGY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; GUANINE; SPACER DNA;

ARTICLE; CHROMATIN CONDENSATION; COMPARATIVE STUDY; CONTROLLED STUDY; CORRELATION FUNCTION; DNA CONTENT; EPIGENETICS; EXON; GENE EXPRESSION; GENE FUNCTION; GENE REPRESSION; GENE SEQUENCE; GENE STRUCTURE; GENETIC CODE; HUMAN; HUMAN CELL; HUMAN GENOME; INTRON; ISOCHORE; NUCLEOSOME; PRIORITY JOURNAL; REGRESSION ANALYSIS; SEQUENCE ANALYSIS; TISSUE SPECIFICITY; CHEMISTRY; GC RICH SEQUENCE; GENOME;

DNA, INTERGENIC; EXONS; GC RICH SEQUENCE; GENE EXPRESSION; GENOME, HUMAN; HUMANS; INTRONS; ISOCHORES; NUCLEOSOMES;

EID: 13744263543     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gki184     Document Type: Article

References (62)

1. Bernardi,G. (2000) Isochores and the evolutionary genomics of vertebrates. Gene, 241, 3-17.
2. Bernardi,G. (2000) The compositional evolution of vertebrate genomes. Gene, 259, 31-43.
3. Bernardi,G. (2004) Structural and Evolutionary Genomics. Natural Selection in Genome Evolution. Elsevier, Amsterdam.
4. Eyre-Walker,A. and Hurst,L.D. (2001) The evolution of isochores. Nature Rev. Genet., 2, 549-555.
5. Eyre-Walker,A. (1999) Evidence of selection on silent site base composition in mammals: potential implications for the evolution of isochores and junk DNA. Genetics, 152, 675-683.
6. Fryxell,K.J. and Zuckerkandl,E. (2000) Cytosine deamination plays xa primary role in the evolution of mammalian isochores. Mol. Biol. Evol., 17, 1371-1383.
7. Galtier,N., Piganeau,G., Mouchiroud,D. and Duret,L. (2001) GC content evolution in mammalian genomes, the biased gene conversion hypothesis. Genetics, 159, 907-911.
8. Smith,N.G. and Eyre-Walker,A. (2001) Synonymous codon bias is not caused by mutation bias in human. Mol. Biol. Evol., 18, 982-986.
9. Duret,L., Semon,M., Piganeau,G., Mouchiroud,D. and Galtier,N. (2002) Vanishing GC-rich isochores in mammalian genomes. Genetics, 162, 1837-1847.
10. Lercher,M.J., Smith,N.G., Eyre-Walker,A. and Hurst,L.D. (2002) The evolution of isochores: evidence from SNP frequency distributions. Genetics, 162, 1805-1810.
11. Arndt,P.F., Petrov,D.A. and Hwa,T. (2003) Distinct changes of genomic biases in nucleotide substitution at the time of Mammalian radiation. Mol. Biol. Evol., 20, 1887-1896.
12. Galtier,N. (2003) Gene conversion drives GC content evolution in mammalian histones. Trends Genet., 19, 65-68.
13. Meunier,J. and Duret,L. (2004) Recombination drives the evolution of GC-content in the human genome. Mol. Biol. Evol., 21, 984-990.
14. Bernardi,G. and Bernardi,G. (1986) Compositional constraints and genome evolution. J. Mol. Evol., 24, 1-11.
15. Vinogradov,A.E. (2001) Bendable genes of warm-blooded vertebrates. Mol. Biol. Evol., 18, 2195-2200.
16. Vinogradov,A.E. (2003) DNA helix: the importance of being GC-rich. Nucleic Acids Res., 31, 1838-1844.
17. Vinogradov,A.E. (2003) Isochores and tissue-specificity. Nucleic Acids Res., 31, 5212-5220.
18. Galtier,N. and Lobry,JR. (1997) Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes. J. Mol. Evol., 44, 632-636.
19. Hurst,L.D. and Merchant,A.R. (2001) High guanine-cytosine content is not an adaptation to high temperature, a comparative analysis amongst prokaryotes. Proc. R. Soc. Lond., B., Biol. Sci, 268, 493-497.
20. Belle,E.M., Smith,N. and Eyre-Walker,A. (2002) Analysis of the phylogenetic distribution of isochores in vertebrates and a test of the thermal stability hypothesis. J. Mol. Evol., 55, 356-363.
21. Ream,R.A., Johns,G.C. and Somero,G.N. (2003) Base compositions of genes encoding alpha-actin and lactate dehydrogenase-A from differently adapted vertebrates show no temperature-adaptive variation in G + C content. Mol. Biol. Evol., 20, 105-110.
22. Radic,M.Z., Lundgren,K. and Hamkalo,B.A. (1987) Curvature of mouse satellite DNA and condensation of heterochromatin. Cell, 50, 1101-1108.
23. Blomquist,P., Belikov,S. and Wrange,O. (1999) Increased nuclear factor 1 binding to its nucleosomal site mediated by sequence-dependent DNA structure. Nucleic Acids Res., 27, 517-525.
24. Anselmi,C., Bocchinfuso,G., De Santis,P., Savino,M. and Scipioni,A. (1999) Dual role of DNA intrinsic curvature and flexibility in determining nucleosome stability. J. Mol. Biol., 286, 1293-1301.
25. Anselmi,C., Bocchinfuso,G., De Santis,P., Savino,M. and Scipioni,A. (2000) A theoretical model for the prediction of sequence-dependent nucleosome thermodynamic stability. Biophys. J., 79, 601-613.
26. Kiyama,R. and Trifonov,E.N. (2002) What positions nucleosomes? - A model. FEBS Lett., 523, 7-11.
27. Vinogradov,A.E. (2003) Silent DNA: speaking RNA language?. Bioinformatics, 9, 2167-2170.
28. Saccone,S., Federico,C. and Bernardi,G. (2002) Localization of the gene-richest and the gene-poorest isochores in the interphase nuclei of mammals and birds. Gene, 300, 169-178.
29. Mouchiroud,D., Fichant,G. and Bernardi,G. (1987) Compositional compartmentalization and gene composition in the genome of vertebrates. J. Mol. Evol., 26, 198-204.
30. Pesole,G., Bernardi,G. and Saccone,C. (1999) Isochore specificity of AUG initiator context of human genes. FEBS Lett., 464, 60-62.
31. Castillo-Davis,C.I., Mekhedov,S.L., Hartl,D.L., Koonin,E.V. and Kondrashov,F.A. (2002) Selection for short introns in highly expressed genes. Nature Genet., 31, 415-418.
32. Eisenberg,E. and Levanon,E.Y. (2003) Human housekeeping genes are compact. Trends Genet., 19, 362-365.
33. Urrutia,A.O. and Hurst,L.D. (2003) The signature of selection mediated by expression on human genes. Genome Res., 13, 2260-2264.
34. Vinogradov,A.E. (2004) Compactness of human housekeeping genes: selection for economy or genomic design? Trends Genet., 20, 248-253.
35. Su,A.I., Cooke,M.P., Ching,K.A., Hakak,Y., Walker,J.R., Wiltshire,T., Orth,A.P., Vega,R.G., Sapinoso,L.M., Moqrich,A. et al. (2002) Large-scale analysis of the human and mouse transcriptomes. Proc. Natl Acad. Sci. USA, 99, 4465-4470.
36. Pruitt,K.D., Tatusova,T. and Maglott,D.R. (2003) NCBI Reference Sequence project: update and current status. Nucleic Acids Res., 31, 34-37.
37. Levitsky,V.G., Podkolodnaya,O.A., Kolchanov,N.A. and Podkolodny,N.L. (2001) Nucleosome formation potential of eukaryotic DNA: calculation and promoters analysis. Bioinformatics, 17, 998-1010.
38. Levitsky,V.G., Podkolodnaya,O.A., Kolchanov,N.A. and Podkolodny,N.L. (2001) Nucleosome formation potential of exons, introns, and Alu repeats. Bioinformatics, 17, 1062-1064.
39. Levitsky,V.G. (2004) RECON: a program for prediction of nucleosome formation potential. Nucleic Acids Res., 32, W346-W349.
40. Ioshikhes,I. and Trifonov,E.N. (1993) Nucleosomal DNA sequence database. Nucleic Acids Res., 21, 4857-4859.
41. Widlund,H.R., Cao,H., Simonsson,S., Magnusson,E., Simonsson,T., Nielsen,P.E., Kahn,J.D., Crothers,D.M. and Kubista,M. (1997) Identification and characterization of genomic nucleosome-positioning sequences. J. Mol. Biol., 267, 807-817.
42. Cao,H., Widlund,H.R., Simonsson,T. and Kubista,M. (1998) TGGA repeats impair nucleosome formation. J. Mol. Biol., 281, 253-260.
43. Farkas,G., Leibovitch,B.A. and Elgin,S.C.R. (2000) Chromatin organization and transcriptional control of gene expressionin Drosophila. Gene, 253, 117-136.
44. Horn,P.J. and Peterson,C.L. (2002) Molecular biology. Chromatin higher order folding - wrapping up transcription. Science 297, 1824-1827.
45. Jenuwein,T. and Allis,C.D. (2001) Translating the histone code. Science, 293, 1074-1080.
46. Aerts,S., Thijs,G., Coessens,B., Staes,M., Moreau,Y. and De Moor,B. (2003) Toucan: deciphering the cis-regulatory logic of coregulated genes. Nucleic Acids Res., 31, 1753-1764.
47. Zuckerkandl,E. (1981) A general function of noncoding polynucleotide sequences. Mass binding of transconformational proteins. Mol. Biol. Rep., 7, 149-158.
48. Zuckerkandl,E. (1997) Junk DNA and sectorial gene repression. Gene, 205, 323-343.
49. Trifonov,E.N. (1993) Spatial separation of overlapping messages. Comput. Chem., 117, 27-31.
50. Lauderdale,J.D. and Stein,A. (1992) Introns of the chicken ovalbumin gene promote nucleosome alignment in vitro. Nucleic Acids Res., 20, 6589-6596.
51. Liu,K., Sandgren,E.P., Palmiter,R.D. and Stein,A. (1995) Rat growth hormone gene introns stimulate nucleosome alignment in vitro and in transgenic mice. Proc. Natl Acad. Sci. USA, 92, 7724-7728.
52. International Human Genome Sequencing Consortium (2001), Initial sequencing and analysis of the human genome. Nature, 409 860-921.
53. Bernardi,G. (2001) Misunderstandings about isochores. Part 1. Gene, 276, 3-13.
54. Li,W., Bernaola-Galvan,P., Carpena,P. and Oliver,J.L. (2003) Isochores merit the prefix 'iso'. Comput. Biol. Chem., 27, 5-10.
55. Wen,S.Y. and Zhang,C.T. (2003) Identification of isochore boundaries in the human genome using the technique of wavelet multiresolution analysis. Biochem. Biophys. Res. Commun., 311 215-222.
56. Vinogradov,A.E. (2001) Within-intron correlation with base composition of adjacent exons in different genomes. Gene, 276 143-151.
57. Vinogradov,A.E. (1998) Buffering: a possible passive-homeostasis role for redundant DNA. J. Theor. Biol., 193 197-199.
58. Vinogradov,A.E. (2005) Genome size and chromatin condensation in vertebrates. Chromosoma, in press.
59. Thastrom,A., Lowary,P.T. and Widom,J. (2004) Measurement of histone-DNA interaction free energy in nucleosomes. Methods, 33 33-44.
60. Bird,A.P. (1995) Gene number, noise reduction and biological complexity. Trends Genet., 11, 94-100.
61. Hurst,L.D. (1995) Evolutionary genetics. The silence of the genes. Curr. Biol., 5, 459-461.
62. Droge,P. and Muller-Hill,B. (2001) High local protein concentrations at promoters: strategies in prokaryotic and eukaryotic cells. Bioessays, 23, 179-183.