isochores

Summary

Summary: Large regions of the GENOME that contain local similarities in BASE COMPOSITION.

Top Publications

  1. Alvarez Valin F, Lamolle G, Bernardi G. Isochores, GC3 and mutation biases in the human genome. Gene. 2002;300:161-8 pubmed
    ..Instead, GC(3)-rich and very GC(3)-rich genes exhibit patterns of mutations that yield expectations of neutral GC(3) content that are much lower than their actual GC(3). ..
  2. Zhang C, Zhang R. An isochore map of the human genome based on the Z curve method. Gene. 2003;317:127-35 pubmed
    ..These domains are thought to be isochores, which usually have sharp boundaries...
  3. Schmegner C, Berger A, Vogel W, Hameister H, Assum G. An isochore transition zone in the NF1 gene region is a conserved landmark of chromosome structure and function. Genomics. 2005;86:439-45 pubmed
    The mammalian genome is organized as a mosaic of isochores, stretches of DNA with a distinct sequence composition...
  4. Clay O, Bernardi G. How not to search for isochores: a reply to Cohen et Al. Mol Biol Evol. 2005;22:2315-7 pubmed
    In a recent paper in these pages, Cohen et al. search for isochores in the human genome, based on a system of attributes that they assign to isochores...
  5. Anuradha S, Tripathi P, Mahajan K, Muniyappa K. Meiosis-specific yeast Hop1 protein promotes pairing of double-stranded DNA helices via G/C isochores. Biochem Biophys Res Commun. 2005;336:934-41 pubmed
    ..To our knowledge, Hop1 is the first protein shown to do so from yeast or any other organism. These results indicate that Hop1 protein is likely to play a direct role in meiotic chromosome pairing and recombination. ..
  6. Vinogradov A. Noncoding DNA, isochores and gene expression: nucleosome formation potential. Nucleic Acids Res. 2005;33:559-63 pubmed
    ..These findings help explain the functional significance of the isochores (regions differing in GC content) in the human genome as a result of optimization of genomic structure for ..
  7. Sun J, Chen M, Xu J, Luo J. Relationships among stop codon usage bias, its context, isochores, and gene expression level in various eukaryotes. J Mol Evol. 2005;61:437-44 pubmed
    ..Our results indicate that stop codons, like synonymous codons, exhibit biases in usage. Additional work will be needed to understand the causes of these biases and their relationship to the mechanism of protein termination. ..
  8. Zhang R, Zhang C. Isochore structures in the genome of the plant Arabidopsis thaliana. J Mol Evol. 2004;59:227-38 pubmed
    ..It is shown that the Arabidopsis genome is organized into a mosaic structure of isochores. All the centromeric regions are located in GC-rich isochores, called centromere-isochores, which are ..
  9. Lipatov M, Arndt P, Hwa T, Petrov D. A novel method distinguishes between mutation rates and fixation biases in patterns of single-nucleotide substitution. J Mol Evol. 2006;62:168-75 pubmed
    ..In addition, we find a small but significant effect that has not been detected in the SNP data-relatively high rates of C:G-->A:T germline mutation in low-GC regions of the genome. ..

More Information

Publications62

  1. Fortes G, Bouza C, Martínez P, Sanchez L. Diversity in isochore structure among cold-blooded vertebrates based on GC content of coding and non-coding sequences. Genetica. 2007;129:281-9 pubmed
    ..coding sequences than of their corresponding introns could aid to understand the discrepancy of sequence analysis with the ultracentrifugation studies in cold-blooded vertebrates that did not predict the existence of GC-rich isochores.
  2. Jabbari K, Bernardi G. Body temperature and evolutionary genomics of vertebrates: a lesson from the genomes of Takifugu rubripes and Tetraodon nigroviridis. Gene. 2004;333:179-81 pubmed
    In this paper, we provide evidence for the body temperature effect on the formation of GC-rich isochores, by analysing genomic sequences from two puffer fishes living at different temperatures...
  3. Press W, Robins H. Isochores exhibit evidence of genes interacting with the large-scale genomic environment. Genetics. 2006;174:1029-40 pubmed
    The genomes of mammals and birds can be partitioned into megabase-long regions, termed isochores, with consistently high, or low, average C + G content...
  4. Schmegner C, Hameister H, Vogel W, Assum G. Isochores and replication time zones: a perfect match. Cytogenet Genome Res. 2007;116:167-72 pubmed
    ..b>Isochores, i.e...
  5. Wen S, Zhang C. Identification of isochore boundaries in the human genome using the technique of wavelet multiresolution analysis. Biochem Biophys Res Commun. 2003;311:215-22 pubmed
    ..of wavelet multiresolution (also known as multiscale) analysis has been proposed to identify the boundaries of isochores in the human genome...
  6. Costantini M, Di Filippo M, Auletta F, Bernardi G. Isochore pattern and gene distribution in the chicken genome. Gene. 2007;400:9-15 pubmed
    ..This raises important questions about genome evolution in vertebrates. ..
  7. Li W, Bernaola Galván P, Carpena P, Oliver J. Isochores merit the prefix 'iso'. Comput Biol Chem. 2003;27:5-10 pubmed
    ..We argue here that a statement in the IHGSC's analysis concerning the existence of isochores is misleading, because the homogeneity was not examined at a large enough length scale and consequently an ..
  8. Duret L, Arndt P. The impact of recombination on nucleotide substitutions in the human genome. PLoS Genet. 2008;4:e1000071 pubmed publisher
    ..Mammalian genomes show large-scale regional variations of GC-content (the isochores), but the substitution processes at the origin of this structure are poorly understood...
  9. Elhaik E, Landan G, Graur D. Can GC content at third-codon positions be used as a proxy for isochore composition?. Mol Biol Evol. 2009;26:1829-33 pubmed publisher
    ..at third-codon positions of protein-coding genes (GC3) was commonly used as a proxy for the GC content of isochores. Oddly, in the postgenomic era, GC3 is still sometimes used as a proxy for the GC composition of isochores...
  10. Clay O, Bernardi G. GC3 of genes can be used as a proxy for isochore base composition: a reply to Elhaik et al. Mol Biol Evol. 2011;28:21-3 pubmed publisher
    ..The answer reasserts that in human and other vertebrates, genes have a strong tendency to reside in compositionally corresponding isochores, which has far-reaching implications for genome structure and evolution.
  11. Belle E, Smith N, Eyre Walker A. Analysis of the phylogenetic distribution of isochores in vertebrates and a test of the thermal stability hypothesis. J Mol Evol. 2002;55:356-63 pubmed
    ..However, we find no correlation between either the mean GC3 or the standard deviation in GC3 and body temperature. ..
  12. Haiminen N, Mannila H. Discovering isochores by least-squares optimal segmentation. Gene. 2007;394:53-60 pubmed
    ..We conclude that the least-squares optimal segmentation method is computationally efficient and yields results close to previous biologically motivated isochore structures. ..
  13. Arhondakis S, Frousios K, Iliopoulos C, Pissis S, Tischler G, Kossida S. Transcriptome map of mouse isochores. BMC Genomics. 2011;12:511 pubmed publisher
    ..We present the transcriptome map of the mouse isochores (DNA segments with a fairly homogeneous base composition) for the three different tissues and the effects of ..
  14. Melodelima C, Gueguen L, Piau D, Gautier C. A computational prediction of isochores based on hidden Markov models. Gene. 2006;385:41-9 pubmed
    ..The G+C content is the basic characteristic of isochores, but they have also been associated with many other biological properties...
  15. Gu J, Li W. Are GC-rich isochores vanishing in mammals?. Gene. 2006;385:50-6 pubmed
    Several studies of nucleotide substitution patterns in mammalian species suggested that GC-rich isochores might be vanishing in mammalian genomes...
  16. Duret L, Eyre Walker A, Galtier N. A new perspective on isochore evolution. Gene. 2006;385:71-4 pubmed
    ..The origin of isochores is still controversial: various neutral and selectionist models have been proposed--and criticized--since the ..
  17. Di Filippo M, Bernardi G. Mapping DNase-I hypersensitive sites on human isochores. Gene. 2008;419:62-5 pubmed publisher
  18. Schmidt T, Frishman D. Assignment of isochores for all completely sequenced vertebrate genomes using a consensus. Genome Biol. 2008;9:R104 pubmed publisher
    ..We present a new consensus isochore assignment method based on majority voting and provide IsoBase, a comprehensive on-line database of isochore maps for all completely sequenced vertebrate genomes. ..
  19. Costantini M, Cammarano R, Bernardi G. The evolution of isochore patterns in vertebrate genomes. BMC Genomics. 2009;10:146 pubmed publisher
    Previous work from our laboratory showed that (i) vertebrate genomes are mosaics of isochores, typically megabase-size DNA segments that are fairly homogeneous in base composition; (ii) isochores belong to a small number of families (..
  20. Varriale A, Bernardi G. Distribution of DNA methylation, CpGs, and CpG islands in human isochores. Genomics. 2010;95:25-8 pubmed publisher
    ..the DNA methylation data that are available in order to establish a map of the levels of GC and methylation in isochores. We also looked for the correlations that hold between GC levels and the distribution of the (1) dinucleotide ..
  21. Fujita M, Edwards S, Ponting C. The Anolis lizard genome: an amniote genome without isochores. Genome Biol Evol. 2011;3:974-84 pubmed publisher
    b>Isochores are large regions of relatively homogeneous nucleotide composition and are present in the genomes of all mammals and birds that have been sequenced to date...
  22. Cohen N, Dagan T, Stone L, Graur D. GC composition of the human genome: in search of isochores. Mol Biol Evol. 2005;22:1260-72 pubmed
    ..Toward this end, we adopt a set of six attributes that are generally claimed to characterize isochores and statistically test their veracity against the available draft sequence of the complete human genome...
  23. Arndt P, Petrov D, Hwa T. Distinct changes of genomic biases in nucleotide substitution at the time of Mammalian radiation. Mol Biol Evol. 2003;20:1887-96 pubmed
    ..patterns in the human genome created patterns of large-scale variation of base composition known as genomic isochores. To gain insight into the origin of the genomic isochores, we develop a maximum-likelihood approach to determine ..
  24. Montoya Burgos J, Boursot P, Galtier N. Recombination explains isochores in mammalian genomes. Trends Genet. 2003;19:128-30 pubmed
    ..These results strongly suggest that recombination is the primary determinant of the isochore organization of mammalian genomes. ..
  25. Duret L, Semon M, Piganeau G, Mouchiroud D, Galtier N. Vanishing GC-rich isochores in mammalian genomes. Genetics. 2002;162:1837-47 pubmed
    To understand the origin and evolution of isochores-the peculiar spatial distribution of GC content within mammalian genomes-we analyzed the synonymous substitution pattern in coding sequences from closely related species in different ..
  26. Lercher M, Smith N, Eyre Walker A, Hurst L. The evolution of isochores: evidence from SNP frequency distributions. Genetics. 2002;162:1805-10 pubmed
    ..The results suggest that mutation biases are not solely responsible for the compositional biases found in noncoding regions. ..
  27. Vinogradov A. Isochores and tissue-specificity. Nucleic Acids Res. 2003;31:5212-20 pubmed
    ..this finding contradicts the biased gene conversion (BGC) explanation for elevated GC content in the heavy isochores of mammal genome...
  28. Paces J, Zika R, Paces V, Pavlicek A, Clay O, Bernardi G. Representing GC variation along eukaryotic chromosomes. Gene. 2004;333:135-41 pubmed
    ..As a complement to a previously published compact view of isochores in the human genome sequence, we include here an analogous map for the recently sequenced mouse genome, and ..
  29. Oliver J, Carpena P, Hackenberg M, Bernaola Galván P. IsoFinder: computational prediction of isochores in genome sequences. Nucleic Acids Res. 2004;32:W287-92 pubmed
    b>Isochores are long genome segments homogeneous in G+C. Here, we describe an algorithm (IsoFinder) running on the web (http://bioinfo2.ugr.es/IsoF/isofinder.html) able to predict isochores at the sequence level...
  30. Belle E, Duret L, Galtier N, Eyre Walker A. The decline of isochores in mammals: an assessment of the GC content variation along the mammalian phylogeny. J Mol Evol. 2004;58:653-60 pubmed
    Whether isochores, the large-scale variation of the GC content in mammalian genomes, are being maintained has recently been questioned...
  31. Hackenberg M, Bernaola Galván P, Carpena P, Oliver J. The biased distribution of Alus in human isochores might be driven by recombination. J Mol Evol. 2005;60:365-77 pubmed
    ..a homogeneous distribution over the human genome but have a higher density in GC-rich (H) than in AT-rich (L) isochores. However, since they preferentially insert into the L isochores, the question arises: What is the evolutionary ..
  32. Arhondakis S, Auletta F, Bernardi G. Isochores and the regulation of gene expression in the human genome. Genome Biol Evol. 2011;3:1080-9 pubmed publisher
    ..the 25-kb gene-flanking regions are representative of the very different patterns already reported for the whole isochores from the L1 and H3 families and, expectedly, identical in upstream and downstream locations; 2) that the ..
  33. D Onofrio G. Expression patterns and gene distribution in the human genome. Gene. 2002;300:155-60 pubmed
    Genes are non-uniformly distributed in the human genome, reaching the highest concentration in GC-rich isochores. This is one of the fundamental aspects of the human genome organization (Gene 241/259 (2000a,b) 3/31, for a review)...
  34. Frenkel Z, Bettecken T, Trifonov E. Nucleosome DNA sequence structure of isochores. BMC Genomics. 2011;12:203 pubmed publisher
    ..in G+C content between different isochore types suggest that the nucleosome positioning patterns in DNA of the isochores should be different as well...
  35. Romiguier J, Ranwez V, Douzery E, Galtier N. Contrasting GC-content dynamics across 33 mammalian genomes: relationship with life-history traits and chromosome sizes. Genome Res. 2010;20:1001-9 pubmed publisher
    ..We showed that the previously reported erosion of GC-rich isochores is not a general trend. Several species (e.g...
  36. Saccone S, Federico C, Bernardi G. Localization of the gene-richest and the gene-poorest isochores in the interphase nuclei of mammals and birds. Gene. 2002;300:169-78 pubmed
    ..This finding has interesting implications for the formation of GC-rich isochores of warm-blooded vertebrates.
  37. Costantini M, Bernardi G. The short-sequence designs of isochores from the human genome. Proc Natl Acad Sci U S A. 2008;105:13971-6 pubmed publisher
    The human genome, a typical mammalian genome, is made up of long (approximately 1-Mb, on average) regions, the isochores, that are fairly homogeneous in base composition and belong in five families characterized by different GC levels...
  38. Vinogradov A. DNA helix: the importance of being GC-rich. Nucleic Acids Res. 2003;31:1838-44 pubmed
    A new explanation for the emergence of heavy (GC-rich) isochores is proposed, based on the study of thermostability, bendability, ability to B-Z transition and curvature of the DNA helix...
  39. Oliver J, Carpena P, Román Roldán R, Mata Balaguer T, Mejías Romero A, Hackenberg M, et al. Isochore chromosome maps of the human genome. Gene. 2002;300:117-27 pubmed
    The human genome is a mosaic of isochores, which are long DNA segments (z.Gt;300 kbp) relatively homogeneous in G+C...
  40. Costantini M, Bernardi G. Replication timing, chromosomal bands, and isochores. Proc Natl Acad Sci U S A. 2008;105:3433-7 pubmed publisher
    ..6, 11q, and 21q, with chromosomal bands as visualized at low (400 bands), high (850 bands), and highest (3,200 isochores) resolution...
  41. Chojnowski J, Franklin J, Katsu Y, Iguchi T, Guillette L, Kimball R, et al. Patterns of vertebrate isochore evolution revealed by comparison of expressed mammalian, avian, and crocodilian genes. J Mol Evol. 2007;65:259-66 pubmed publisher
    Vertebrate genomes are mosaics of isochores, defined as long (>100 kb) regions with relatively homogeneous within-region base composition...
  42. Lercher M, Urrutia A, Pavlicek A, Hurst L. A unification of mosaic structures in the human genome. Hum Mol Genet. 2003;12:2411-5 pubmed
    The human genome is a mosaic structure on many levels: there exist cytogenetic bands, GC composition bands (isochores) and clusters of broadly expressed genes...
  43. Costantini M, Auletta F, Bernardi G. Isochore patterns and gene distributions in fish genomes. Genomics. 2007;90:364-71 pubmed
    ..a large-scale compositional heterogeneity in vertebrate genomes, in which GC-rich and GC-poor regions, the isochores, were found to be characterized by high and low gene densities, respectively...
  44. Bernardi G. The neoselectionist theory of genome evolution. Proc Natl Acad Sci U S A. 2007;104:8385-90 pubmed
    The vertebrate genome is a mosaic of GC-poor and GC-rich isochores, megabase-sized DNA regions of fairly homogeneous base composition that differ in relative amount, gene density, gene expression, replication timing, and recombination ..
  45. Zhang C, Zhang R. Isochore structures in the mouse genome. Genomics. 2004;83:384-94 pubmed
    ..ii). Long domains with relatively homogeneous G+C content (isochores) exist, which usually have sharp boundaries...
  46. Costantini M, Clay O, Federico C, Saccone S, Auletta F, Bernardi G. Human chromosomal bands: nested structure, high-definition map and molecular basis. Chromosoma. 2007;116:29-40 pubmed
    ..We found the rules according to which the approximately 3,200 isochores of the human genome are assembled in high (850-band) resolution bands, and the latter in low (400-band) ..
  47. Tsyba L, Rynditch A, Boeri E, Jabbari K, Bernardi G. Distribution of HIV-1 in the genomes of AIDS patients. Cell Mol Life Sci. 2004;61:721-6 pubmed
    ..1) At low viremia, proviruses are predominantly localized in the GC-richest isochores, which are characterized by an open chromatin structure; this result mimics findings on HIV-1 integration in ..
  48. Alvarez Valin F, Clay O, Cruveiller S, Bernardi G. Inaccurate reconstruction of ancestral GC levels creates a "vanishing isochores" effect. Mol Phylogenet Evol. 2004;31:788-93 pubmed
    ..e., that GC-rich isochores are now vanishing in these lineages...
  49. Semon M, Mouchiroud D, Duret L. Relationship between gene expression and GC-content in mammals: statistical significance and biological relevance. Hum Mol Genet. 2005;14:421-7 pubmed
    Mammalian chromosomes are characterized by large-scale variations of DNA base composition (the so-called isochores). In contradiction with previous studies, Lercher et al. (Hum. Mol. Genet...
  50. Cammarano R, Costantini M, Bernardi G. The isochore patterns of invertebrate genomes. BMC Genomics. 2009;10:538 pubmed publisher
    ..We showed that these genomes are mosaics of isochores, megabase-size DNA sequences that are fairly homogeneous in base composition yet belong to a small number of ..
  51. Bernaola Galván P, Oliver J, Carpena P, Clay O, Bernardi G. Quantifying intrachromosomal GC heterogeneity in prokaryotic genomes. Gene. 2004;333:121-33 pubmed
    ..Supplementary results for all species analyzed are available at our website: http://bioinfo2.ugr.es/prok...
  52. Oliver J, Bernaola Galván P, Hackenberg M, Carpena P. Phylogenetic distribution of large-scale genome patchiness. BMC Evol Biol. 2008;8:107 pubmed publisher
    ..In all these genomes, large-scale patchiness can be associated with the isochore-like regions, as directly detected in silico at the sequence level. ..
  53. Melodelima C, Gautier C. The GC-heterogeneity of teleost fishes. BMC Genomics. 2008;9:632 pubmed publisher
    ..Among other vertebrates the presence of isochores depends upon the taxon; isochore are clearly present in Crocodiles and turtles but fish genome seems very ..