Isochores and the evolutionary genomics of vertebrates

Bernardi, Giorgio

doi:10.1016/s0378-1119(99)00485-0

Cited by 507 publications

(368 citation statements)

References 94 publications

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“…In general, a good correlation between gene density and high GC content can be expected (Bernardi 2000;Waterston et al 2002). For complete mouse chromosomes, this is indeed the case (R=0.85 for autosomes).…”

Section: Radial Nuclear Positioning Of Gene Loci Does Not Correlate Wmentioning

confidence: 97%

“…However, results from Bernardi and coworkers suggest that a high GC content may be an evolutionary consequence of internal localization rather than the other way round (Federico et al 2006): In warm-blooded vertebrates, GC-rich isochores of the genome were found in central areas of the nucleus (Bernardi 2000;Saccone et al 2002;Federico et al 2004Federico et al , 2005. Compared to cold-blooded vertebrates, warm-blooded vertebrates have an increased GC content in gene-rich regions of the genome, most likely to thermodynamically stabilize the structure of genes transcribed in many tissues by increasing the binding forces between the DNA single strands (Jabbari and Bernardi 2004).…”

Section: Nuclear Positioning and Genomic Propertiesmentioning

confidence: 99%

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Three-dimensional positioning of genes in mouse cell nuclei

et al. 2008

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To understand the regulation of the genome, it is necessary to understand its three-dimensional organization in the nucleus. We investigated the positioning of eight gene loci on four different chromosomes, including the β-globin gene, in mouse embryonic stem cells and in in vitro differentiated macrophages by fluorescence in situ hybridization on structurally preserved nuclei, confocal microscopy, and 3D quantitative image analysis. We found that gene loci on the same chromosome can significantly differ from each other and from their chromosome territory in their average radial nuclear position. Radial distribution of a given gene locus can change significantly between cell types, excluding the possibility that positioning is determined solely by the DNA sequence. For the set of investigated gene loci, we found no relationship between radial distribution and local gene density, as it was described for human cell nuclei. We did find, however, correlation with other genomic properties such as GC content and certain repetitive elements such as long terminal repeats or long interspersed nuclear elements. Our results suggest that gene density itself is not a driving force in nuclear positioning. Instead, we propose that other genomic properties play a role in determining nuclear chromatin distribution.

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Section: Radial Nuclear Positioning Of Gene Loci Does Not Correlate Wmentioning

confidence: 97%

Section: Nuclear Positioning and Genomic Propertiesmentioning

confidence: 99%

Three-dimensional positioning of genes in mouse cell nuclei

et al. 2008

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“…It has been shown that both mammal and bird genomes have an isochore structure, with some regions of very high GC content (Kadi et al 1993;Bernardi 2000). Since both mammals and birds are warm-blooded, Bernardi (1993) proposed that the isochore structure could be an adaptation to homeothermy.…”

Section: Introductionmentioning

confidence: 99%

The Decline of Isochores in Mammals: An Assessment of the GC ContentVariation Along the Mammalian Phylogeny

et al. 2004

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Abstract. Whether isochores, the large-scale variation of the GC content in mammalian genomes, are being maintained has recently been questioned. It has been suggested that GC-rich isochores originated in the ancestral amniote genome but that whatever force gave rise to them is no longer effective and that isochores are now disappearing from mammalian genomes. Here we investigated the evolution of the GC content of 41 coding genes in 6 to 66 species of mammals by estimating the ancestral GC content using a method which allows for different rates of substitution between sites. We found a highly significant decrease in the GC content during early mammalian evolution, as well as a weaker but still significant decrease in the GC content of GC-rich genes later in at least three groups of mammals: primates, rodents, and carnivores. These results are of interest because they confirm the recently suggested disappearance of GC-rich isochores in some mammalian genomes, and more importantly, they suggest that this disappearance started very early in mammalian evolution.

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“…One of the main obstacles to LRC analysis in DNA sequences is the genuine mosaic structure of these sequences which are well known to be formed of 'patches' ('strand bias') of different underlying composition [103,104,105,106]. These patches appear as trends in the reconstructed DNA walk landscape which are likely to introduce some breaking of the scale-invariance [64,68,75,79,82,83,84,107].…”

Section: Introductionmentioning

confidence: 99%

Wavelet Analysis of DNA Bending Profiles reveals Structural Constraints on the Evolution of Genomic Sequences

Audit

Vaillant

Arnéodo

et al. 2004

Journal of Biological Physics

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Abstract. Analyses of genomic DNA sequences have shown in previous works that base pairs are correlated at large distances with scale-invariant statistical properties. We show in the present study that these correlations between nucleotides (letters) result in fact from long-range correlations (LRC) between sequence-dependent DNA structural elements (words) involved in the packaging of DNA in chromatin. Using the wavelet transform technique, we perform a comparative analysis of the DNA text and of the corresponding bending profiles generated with curvature tables based on nucleosome positioning data. This exploration through the optics of the so-called 'wavelet transform microscope' reveals a characteristic scale of 100 − 200 bp that separates two regimes of different LRC. We focus here on the existence of LRC in the small-scale regime ( 200 bp). Analysis of genomes in the three kingdoms reveals that this regime is specifically associated to the presence of nucleosomes. Indeed, small scale LRC are observed in eukaryotic genomes and to a less extent in archaeal genomes, in contrast with their absence in eubacterial genomes. Similarly, this regime is observed in eukaryotic but not in bacterial viral DNA genomes. There is one exception for genomes of Poxviruses, the only animal DNA viruses that do not replicate in the cell nucleus and do not present small scale LRC. Furthermore, no small scale LRC are detected in the genomes of all examined RNA viruses, with one exception in the case of retroviruses. Altogether, these results strongly suggest that small-scale LRC are a signature of the nucleosomal structure. Finally, we discuss possible interpretations of these small-scale LRC in terms of the mechanisms that govern the positioning, the stability and the dynamics of the nucleosomes along the DNA chain. This paper is maily devoted to a pedagogical presentation of the theoretical concepts and physical methods which are well suited to perform a statistical analysis of genomic sequences. We review the results obtained with the so-called waveletbased multifractal analysis when investigating the DNA sequences of various organisms in the three kingdoms. Some of these results have been announced in B. Audit et al. [1,2].

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Isochores and the evolutionary genomics of vertebrates

Cited by 507 publications

References 94 publications

Three-dimensional positioning of genes in mouse cell nuclei

Three-dimensional positioning of genes in mouse cell nuclei

The Decline of Isochores in Mammals: An Assessment of the GC ContentVariation Along the Mammalian Phylogeny

Wavelet Analysis of DNA Bending Profiles reveals Structural Constraints on the Evolution of Genomic Sequences

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