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Welcome to the Pubget Medical Subject Headings (MESH) browser. Click on a topic or subtopic below to explore related papers. In the gold box is the most recent paper about the current MESH term, and below are 20 related papers.
Isochores (0):
Recent article
Isochores
Abstract
1) The positive relationship previously found between the percentage of homoplasy and genome size is a direct consequence of the number of observed bands and the GC content. For the same number of observed bands, the percentage of homoplasy is independent of the genome size of the species. 2) The di...
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PMID: 20056690
PDF is available here.
PDF is available here.
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BMC Genomics (10)1 2009
Abstract
The present availability of a number of fully sequenced genomes ranging from fishes to mammals allowed us to carry out investigations that (i) more precisely quantified our previous conclusions; (ii) showed that the different isochore families of vertebrate genomes are largely conserved in GC levels...
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PMID: 19344507
PDF is available here.
PDF is available here.
BMC Genomics (10)1 2009
Abstract
We applied this methodology between the genome of human and those of five sequenced eutherian mammals which allowed us to delineate evolutionary breakpoint regions along the human genome with a finer resolution (median size 26.6 kb) than obtained before. We investigated the distribution of these bre...
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PMID: 19630943
PDF is available here.
PDF is available here.
BMC Genomics (10)1 2009
Abstract
The present investigation deals with the compositional patterns of the invertebrates for which full genome sequences, or at least scaffolds, are available. We found that (i) a mosaic of isochores is the long-range organization of all the genomes that we investigated; (ii) the isochore families from...
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PMID: 19922632
PDF is available here.
PDF is available here.
Abstract
We sequenced the genome of P. vivax to shed light on its distinctive biological features, and as a means to drive development of new drugs and vaccines. Here we describe the synteny and isochore structure of P. vivax chromosomes, and show that the parasite resembles other malaria parasites in gene c...
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PMID: 18843361
PDF is available here.
PDF is available here.
Abstract
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. An analysis of di- and tri-nucleotide densities in the isochores...
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PMID: 18780784
PDF is available here.
PDF is available here.
Abstract
We found that the ENCODE data lead to an unbalanced representation of the compositional pattern of the human genome, especially for the GC-poorest and GC-richest regions. This unbalanced representativity of ENCODE can, however, be corrected by multiplying ENCODE data by a G/E factor (the ratio of wh...
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PMID: 18378099
PDF is available here.
PDF is available here.
Abstract
We show that HS: (i) are characterized by a much higher GC level (approximately 56%) than the average GC level of the human genome (approximately 41%); (ii) are overwhelmingly located in the GC-richest compartment of the genome, which is predominantly associated with an open chromatin structure; (ii...
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PMID: 18436395
PDF is available here.
PDF is available here.
FEBS Letters (582)16 2008
Abstract
We obtained a complete coverage of the human genome by 3198 isochores with boundaries at single nucleotide resolution. Interestingly, the experimentally confirmed replication timing sites in the regions of 1p36.1, 6p21.32, 17q11.2 and 22q12.1 nearly all coincide with the determined isochore boundari...
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PMID: 18555015
PDF is available here.
PDF is available here.
Abstract
We investigated whether these correlations also hold within the much more homogeneous isochore families. This point was checked not only in the case of mammals, but also in that of phylogenetically distant vertebrates, which are characterized by very different compositional patterns. Indeed, these a...
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PMID: 18252269
PDF is available here.
PDF is available here.
Abstract
We have compared the extended, detailed replication timing maps that are available, namely those of human chromosomes 6, 11q, and 21q, with chromosomal bands as visualized at low (400 bands), high (850 bands), and highest (3,200 isochores) resolution. We have observed that the replicons located in a...
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PMID: 18305168
PDF is available here.
PDF is available here.
Abstract
We identify 620 Mb of the human genome in which the rates of the various types of nucleotide substitutions are the same on both strands. These strand-symmetric regions show an exponential decay of local GC content at a pace determined by local substitution rates. DNA segments subjected to higher rat...
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PMID: 18042807
PDF is available here.
PDF is available here.
Abstract
We re-determined all 79 boundaries of previously identified human isochores at single-nucleotide resolution, and then compared the boundary coordinates with other genome features. We found that 55.7% of isochore boundaries coincide with termini of repeat elements; 45.6% of isochore boundaries coinci...
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PMID: 18092827
PDF is available here.
PDF is available here.
Abstract
Following the development of reliable methods for inferring the direction of mutations of the single nucleotide polymorphism (SNP), and the revealing of the human isochore map, it has become possible to investigate the evolution of the isochore structure in a continuous region. In this study, the re...
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PMID: 18005111
PDF is available here.
PDF is available here.
BMC Genomics (9)1 2008
Abstract
This paper shows in teleost fish genomes the existence of "GC segmentation" sharing some of the characteristics of isochores although teleost fish genomes presenting a particular homogeneity in CG content. The entire genomes of T nigroviridis and D rerio are now available, and this has made it possi...
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PMID: 19108743
PDF is available here.
PDF is available here.
BMC Genomics (9)1 2008
Abstract
For a typical mammal, for example mouse or human, there is a small strand bias throughout the genomic DNA: there is a correlation between (G - C) and (A - T) on the same strand, (that is between the difference in the number of guanine and cytosine bases and the difference in the number of adenine an...
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PMID: 18221531
PDF is available here.
PDF is available here.
Genome Biology (9)6 2008
Abstract
We show that although the currently available isochore mapping methods agree on the isochore classification of about two-thirds of the human DNA, they produce significantly different results with regard to the location of isochore boundaries and isochore length distribution. We present a new consens...
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PMID: 18590563
PDF is available here.
PDF is available here.
Abstract
The local variations in the scaling exponent of the Detrended Fluctuation Analysis are used here to analyze large-scale genome structure and directly uncover the characteristic scales present in genome sequences. Furthermore, through shuffling experiments of selected genome regions, computationally-...
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PMID: 18405379
PDF is available here.
PDF is available here.
Abstract
Here we analyze SNP allele frequencies, retrotransposon insertion polymorphisms (RIPs), as well as fixed substitutions accumulated in the human lineage since its divergence from chimpanzee to indicate that biased gene conversion (BGC) has been playing a role in within-genome GC content variation. Ye...
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PMID: 18371205
PDF is available here.
PDF is available here.
BMC Genomics (9)1 2008
Abstract
Location and quantification of NumtS may be achieved by applying database similarity searching methods: we have applied various methods such as Blastn, MegaBlast and BLAT, changing both parameters and database; the results were compared, further analysed and checked against the already published com...
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PMID: 18522722
PDF is available here.
PDF is available here.
Abstract
We report here investigations on the isochore pattern and the distribution of genes in the chromosomes of chicken. In spite of large differences in genome size and karyotype, the compositional properties and the gene distribution of the chicken genome are very similar to those recently published for...
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PMID: 17629634
PDF is available here.
PDF is available here.
Abstract
We show that HMMs can be used to analyse complex gene structures with bell-shaped length distribution by using convolution of geometric distributions. Thus, we have introduced macros-states to model the distributions of the lengths of the regions. Our study shows that simple HMM could be used to mod...
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PMID: 17486342
PDF is available here.
PDF is available here.
Abstract
We collected more than 6000 expressed sequence tags (ESTs) from the American alligator to overcome sample size limitations suggested to be the fundamental problem in the previous reptilian studies. The alligator ESTs were assembled and aligned with their human, mouse, chicken, and western clawed fro...
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PMID: 17674077
PDF is available here.
PDF is available here.
Abstract
We mapped isochores on fish chromosomes and assessed gene densities in isochore families. Because of the availability of sequence data, we have concentrated our investigations on four species, zebrafish (Brachydanio rerio), medaka (Oryzias latipes), stickleback (Gasterosteus aculeatus), and pufferfi...
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PMID: 17590311
PDF is available here.
PDF is available here.
Abstract
We apply a well-known least-squares optimal segmentation algorithm to isochore discovery. The algorithm finds the best division of the sequence into k pieces, such that the segments are internally as homogeneous as possible. We show how this simple segmentation method can be applied to isochore disc...
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PMID: 17389148
PDF is available here.
PDF is available here.
Abstract
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 frequency. At the emergence of warm-blooded verte...
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PMID: 17494746
PDF is available here.
PDF is available here.
Abstract
We used of the increasing number of genetic sequences, including coding (exons) and non-coding (introns) regions, that have been deposited on the databases throughout last years. The nucleotide distributions of the third codon positions (GC3) have been analyzed in 1510 coding sequences (CDS) of fish...
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PMID: 16897446
PDF is available here.
PDF is available here.
Chromosoma (116)1 2007
Abstract
We report investigations on the nested structure, the high-definition mapping, and the molecular basis of the classical Giemsa and Reverse bands in human chromosomes. We found the rules according to which the approximately 3,200 isochores of the human genome are assembled in high (850-band) resoluti...
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PMID: 17072634
PDF is available here.
PDF is available here.
Abstract
We report here on the spectrum of human SNPs and base pair substitutions between human and chimpanzee. The results show that the mutation rate changes exactly at the GC-content transition zone from low values in the GC-poor sequences to high values in GC-rich ones. The GC content of the GC-poor sequ...
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PMID: 17057231
PDF is available here.
PDF is available here.
Abstract
We demonstrated this interdependency on a molecular level for an abrupt transition from a GC-poor isochore to a GC-rich one in the NF1 gene region; this isochore boundary also separates late from early replicating chromatin. Now, we analyzed another genomic region containing four isochores separated...
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PMID: 17317955
PDF is available here.
PDF is available here.
Abstract
We review the existing support for these two hypotheses, and discuss how they can be combined to provide a new perspective on isochore evolution....
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PMID: 16971063
PDF is available here.
PDF is available here.
Abstract
Mammalian genomes are organised into a mosaic of regions (in general more than 300 kb in length), with differing, relatively homogeneous G+C contents. The G+C content is the basic characteristic of isochores, but they have also been associated with many other biological properties. For instance, the...
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PMID: 17020791
PDF is available here.
PDF is available here.
Abstract
We have applied two maximum likelihood methods to infer the ancestral GC contents of 176 mammalian genes from representative eutherian species and at least one marsupial species. Except for a large GC decrease in marsupial genes, we found no general decreasing trend in GC content in GC-rich genes or...
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PMID: 16987615
PDF is available here.
PDF is available here.
Abstract
We show that approximately 20% of amino acids in proteins are broadly substitutable, without regard to chemical similarity....
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PMID: 16951086
PDF is available here.
PDF is available here.
Nucleic Acids Research (34)Web Server issue 2006
Abstract
We have therefore developed them into GC-Profile, an interactive web-based software system, which can be used to segment prokaryotic and eukaryotic genomes. GC-Profile provides a quantitative and qualitative view of genome organization. Based on the obtained results, the relationships between the G+...
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PMID: 16845098
PDF is available here.
PDF is available here.
Abstract
We have observed a highly significant positive correlation between the recombination rate and GC content (rho = 0.837, p < or = 0.005). Five regions that lie in the distal part of PAR1 are shown to be significantly higher than genomic average divergence. By comparing the intra- and inter-specific AT...
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PMID: 16767166
PDF is available here.
PDF is available here.
Abstract
We describe here a new approach to this problem that utilizes the juxtaposition of forward and reverse substitution rates to determine the relative importance of variability in mutation rates and fixation probabilities in shaping long-term substitutional patterns. We use this approach to demonstrate...
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PMID: 16362483
PDF is available here.
PDF is available here.
Abstract
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. The putative isochores that they find and choose for presentation are almost all below 45% GC and cover only about 41% of the genome. Closer inspect...
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PMID: 16093569
PDF is available here.
PDF is available here.
Abstract
We report that Saccharomyces cerevisiae Hop1 protein, a component of SC, promotes pairing between two double-stranded DNA helices containing a centrally located G/C isochore. Significantly, pairing was rapid and robust, and required four contiguous G/C base pairs. Using a series of truncated DNA dou...
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PMID: 16154534
PDF is available here.
PDF is available here.
Abstract
We systematically investigate stop codon usage bias in various eukaryotes as well as its relationships with its context, GC3 content, gene expression level, and secondary structure. The results show that there is a strong bias for stop codon usage in different eukaryotes, i.e., UAA is overrepresente...
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PMID: 16170455
PDF is available here.
PDF is available here.
Abstract
We have recently demonstrated that the transition from a GC-poor isochore to a GC-rich one in the NF1 gene region occurs within 5 kb and demarcates genomic regions with high and low recombination frequency. We now report that the same transition zone separates early replicating from late replicating...
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PMID: 16081245
PDF is available here.
PDF is available here.
Abstract
We address the question of the validity of the isochore theory through a rigorous sequence-based analysis of the human genome. 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 sequ...
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PMID: 15728737
PDF is available here.
PDF is available here.
Abstract
We carried out a genome-wide analysis of the density of the Alus as a function of their evolutionary age, isochore membership, and intron vs. intergene location. Since Alus depend on the retrotransposase encoded by the LINE1 elements, we also studied the distribution of LINE1 to provide a complete e...
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PMID: 15871047
PDF is available here.
PDF is available here.
Human Molecular Genetics (14)3 2005
Abstract
We reassessed this issue by examining in human and mouse the correlation between gene expression and GC-content, using different measures of gene expression (EST, SAGE and microarray) and different measures of GC-content. We show that correlations between GC-content and expression are very weak, and...
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PMID: 15590696
PDF is available here.
PDF is available here.
Abstract
Fluctuations and increments of both C(3) and G(3) levels along the human coding sequences were investigated comparing two sets of Xenopus/human orthologous genes. The first set of genes shows minor differences of the GC(3) levels, the second shows considerable increments of the GC(3) levels in the h...
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PMID: 15716110
PDF is available here.
PDF is available here.
Chromosome Research (13)8 2005
Abstract
We performed heterologous in-situ hybridizations using chicken GC-richest isochores as probes. Our results clearly show that the gene-rich regions are prevalently located in the few microchromosome pairs and in the telomeric regions of the middle-sized chromosomes, as well as in the interior of the...
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PMID: 16331410
PDF is available here.
PDF is available here.
Nucleic Acids Research (33)2 2005
Abstract
The nucleosome formation potential of introns, intergenic spacers and exons of human genes is shown here to negatively correlate with among-tissues breadth of gene expression. The nucleosome formation potential is also found to negatively correlate with the GC content of genomic sequences; the slope...
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PMID: 15673716
PDF is available here.
PDF is available here.
Abstract
We describe the compositional organization of the pig (Sus scrofa) genome that belongs to the general mammalian pattern. We investigated (i) the compositional distribution of the genes by analysis of their GC3 levels (the GC levels at the third codon positions), and (ii) the correlation between the...
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PMID: 15588579
PDF is available here.
PDF is available here.
Abstract
We report the results of genome-wide analyses suggesting that repositioning may also radically change the evolutionary fate of gene duplicates. As an indicator of these changes, we used the GC content of gene pairs which originated by duplication. This indicator turned out to be duplicate-asymmetric...
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PMID: 15553091
PDF is available here.
PDF is available here.
Abstract
We have analyzed the complete genome sequences of Arabidopsis by using a newly developed windowless method for the GC content computation, the cumulative GC profile. It is shown that the Arabidopsis genome is organized into a mosaic structure of isochores. All the centromeric regions are located in...
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PMID: 15486696
PDF is available here.
PDF is available here.
Nucleic Acids Research (32)Web Server issue 2004
Abstract
We describe an algorithm (IsoFinder) running on the web (http://bioinfo2.ugr.es/IsoF/isofinder.html) able to predict isochores at the sequence level. We move a sliding pointer from left to right along the DNA sequence. At each position of the pointer, we compute the mean G+C values to the left and t...
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PMID: 15215396
PDF is available here.
PDF is available here.
Abstract
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 evolu...
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PMID: 15461422
PDF is available here.
PDF is available here.
Abstract
Abstract
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. The higher body temperature of Tetraodon nigroviridis compared to Takifugu rubripes (DeltaT approximately 15 degrees C) a...
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PMID: 15177693
PDF is available here.
PDF is available here.
Abstract
We present here a brief overview of some methods for visualizing and quantifying GC variation in prokaryotes. We used these methods to examine heterogeneity levels in sequenced prokaryotes, for a range of scales or stringencies. Some species are consistently homogeneous, whereas others are markedly...
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PMID: 15177687
PDF is available here.
PDF is available here.
Abstract
We have devised a simple scheme that combines line plots with color-coded shading of the regions underneath the plots. The scheme can be applied to different eukaryotic genomes to facilitate their comparison, as illustrated here for a sample of chromosomes chosen from seven selected species. As a co...
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PMID: 15177688
PDF is available here.
PDF is available here.
Abstract
We review an artefact of parsimony-based ancestor reconstruction in GC-rich DNA, and show that its magnitude explains the apparent vanishing of the GC-richest regions in cetartiodactyls, even if they are in fact at compositional equilibrium. The presently available data do not allow the disequilibri...
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PMID: 15062812
PDF is available here.
PDF is available here.
Abstract
We have found that: (i). Abrupt variations of the G+C content from a GC-rich region to a GC-poor region, and vice versa, occur frequently at some sites along the sequence of the mouse genome. (ii). Long domains with relatively homogeneous G+C content (isochores) exist, which usually have sharp bound...
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PMID: 14962664
PDF is available here.
PDF is available here.
Abstract
The localization of HIV-1 proviruses in compositional DNA fractions from 27 AIDS patients during the chronic phase of the disease with depletion of CD4+ and different levels of viremia showed the following. (1) At low viremia, proviruses are predominantly localized in the GC-richest isochores, which...
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PMID: 15052414
PDF is available here.
PDF is available here.
Genome Research (13)12 2003
Abstract
We developed a pipeline using features such as intron-absence, frame-disruption, polyadenylation, and truncation. This has enabled us to identify in recent genome drafts approximately 8000 processed pseudogenes (distributed from http://pseudogene.org). Overall, processed pseudogenes are very similar...
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PMID: 14656962
PDF is available here.
PDF is available here.