Nucleic Acids Research, 2003, Vol. 31, No. 17 5212-5220
© 2003 Oxford University Press
Isochores and tissue-specificity
Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Avenue 4, St Petersburg 194064, Russia
*Tel: +7 812 247 5310; Fax: +7 812 247 0341; Email: aevin{at}mail.cytspb.rssi.ru
The housekeeping (ubiquitously expressed) genes in the mammal genome were shown here to be on average slightly GC-richer than tissue-specific genes. Both housekeeping and tissue-specific genes occupy similar ranges of GC content, but the former tend to concentrate in the upper part of the range. In the human genome, tissue-specific genes show two maxima, GC-poor and GC-rich. The strictly tissue-specific human genes tend to concentrate in the GC-poor region; their distribution is left-skewed and thus reciprocal to the distribution of housekeeping genes. The intermediately tissue-specific genes show an intermediate GC content and the right-skewed distribution. Both in the human and mouse, genes specific for some tissues (e.g., parts of the central nervous system) have a higher average GC content than housekeeping genes. Since they are not transcribed in the germ line (in contrast to housekeeping genes), and therefore have a lower probability of inheritable gene conversion, this finding contradicts the biased gene conversion (BGC) explanation for elevated GC content in the heavy isochores of mammal genome. Genes specific for germ-line tissues (ovary, testes) show a low average GC content, which is also in contradiction to the BGC explanation. Both for the total data set and for the most part of tissues taken separately, a weak positive correlation was found between gene GC content and expression level. The fraction of ubiquitously expressed genes is nearly 1.5-fold higher in the mouse than in the human. This suggests that mouse tissues are comparatively less differentiated (on the molecular level), which can be related to a less pronounced isochoric structure of the mouse genome. In each separate tissue (in both species), tissue-specific genes do not form a clear-cut frequency peak (in contrast to housekeeping genes), but constitute a continuum with a gradually increasing degree of tissue-specificity, which probably reflects the path of cell differentiation and/or an independent use of the same protein in several unrelated tissues.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  H. Robins, M. Krasnitz, and A. J. Levine The Computational Detection of Functional Nucleotide Sequence Motifs in the Coding Regions of Organisms Experimental Biology and Medicine, June 1, 2008; 233(6): 665 - 673. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. Khuu, M. Sandor, J. DeYoung, and P. S. Ho Phylogenomic analysis of the emergence of GC-rich transcription elements PNAS, October 16, 2007; 104(42): 16528 - 16533. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. E. Vinogradov and O. V. Anatskaya Organismal complexity, cell differentiation and gene expression: human over mouse Nucleic Acids Res., October 8, 2007; 35(19): 6350 - 6356. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. R. Dreszer, G. D. Wall, D. Haussler, and K. S. Pollard Biased clustered substitutions in the human genome: The footprints of male-driven biased gene conversion Genome Res., October 1, 2007; 17(10): 1420 - 1430. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. E. Vinogradov 'Genome design' model and multicellular complexity: golden middle Nucleic Acids Res., November 6, 2006; 34(20): 5906 - 5914. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Sinha, X. Ling, C. W. Whitfield, C. Zhai, and G. E. Robinson Genome scan for cis-regulatory DNA motifs associated with social behavior in honey bees PNAS, October 31, 2006; 103(44): 16352 - 16357. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 W. H. Press and H. Robins Isochores Exhibit Evidence of Genes Interacting With the Large-Scale Genomic Environment Genetics, October 1, 2006; 174(2): 1029 - 1040. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Semon, J. R. Lobry, and L. Duret No Evidence for Tissue-Specific Adaptation of Synonymous Codon Usage in Humans Mol. Biol. Evol., March 1, 2006; 23(3): 523 - 529. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Robins, M. Krasnitz, H. Barak, and A. J. Levine A Relative-Entropy Algorithm for Genomic Fingerprinting Captures Host-Phage Similarities J. Bacteriol., December 15, 2005; 187(24): 8370 - 8374. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Robins and W. H. Press Human microRNAs target a functionally distinct population of genes with AT-rich 3' UTRs PNAS, October 25, 2005; 102(43): 15557 - 15562. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Sironi, G. Menozzi, G. P. Comi, R. Cagliani, N. Bresolin, and U. Pozzoli Analysis of intronic conserved elements indicates that functional complexity might represent a major source of negative selection on non-coding sequences Hum. Mol. Genet., September 1, 2005; 14(17): 2533 - 2546. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. T. Webster, N. G. C. Smith, L. Hultin-Rosenberg, P. F. Arndt, and H. Ellegren Male-Driven Biased Gene Conversion Governs the Evolution of Base Composition in Human Alu Repeats Mol. Biol. Evol., June 1, 2005; 22(6): 1468 - 1474. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Cohen, T. Dagan, L. Stone, and D. Graur GC Composition of the Human Genome: In Search of Isochores Mol. Biol. Evol., May 1, 2005; 22(5): 1260 - 1272. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Semon, D. Mouchiroud, and L. Duret Relationship between gene expression and GC-content in mammals: statistical significance and biological relevance Hum. Mol. Genet., February 1, 2005; 14(3): 421 - 427. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. E. Vinogradov Noncoding DNA, isochores and gene expression: nucleosome formation potential Nucleic Acids Res., January 26, 2005; 33(2): 559 - 563. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. T. Webster, N. G.C. Smith, M. J. Lercher, and H. Ellegren Gene Expression, Synteny, and Local Similarity in Human Noncoding Mutation Rates Mol. Biol. Evol., October 1, 2004; 21(10): 1820 - 1830. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. N. Robinson, U. Bohme, R. Lopez, S. Mundlos, and P. Nurnberg Gene-Ontology analysis reveals association of tissue-specific 5' CpG-island genes with development and embryogenesis Hum. Mol. Genet., September 1, 2004; 13(17): 1969 - 1978. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. B. Plotkin, H. Robins, and A. J. Levine Tissue-specific codon usage and the expression of human genes PNAS, August 24, 2004; 101(34): 12588 - 12591. [Abstract] [Full Text] [PDF]
|
|