Isochore chromosome maps of the human genome

Oliver, José Luis Tejera; Carpena, Pedro; Román-Roldán, Ramón; Mata-Balaguer, Trinidad; Mejı́as-Romero, Andrés; Hackenberg, Michael; Bernaola‐Galván, Pedro

doi:10.1016/s0378-1119(02)01034-x

Cited by 53 publications

(32 citation statements)

References 50 publications

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“…L1B and L1C do not reside within or close to known or predicted genes, and their immediate surrounding chromatin status is unknown, although they are in regions of low guanosine plus cytosine (GC) content (39.2%) (52). For L1B, our presence͞absence PCRs in three male genomes analyzed suggest that it may have retrotransposed, carrying a 3Ј transduction.…”

Section: Discussionmentioning

confidence: 89%

Extensive individual variation in L1 retrotransposition capability contributes to human genetic diversity

Seleme¹,

Vetter²,

Cordaux

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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Despite being scarce in the human genome, active L1 retrotransposons continue to play a significant role in its evolution. Because of their recent expansion, many L1s are not fixed in humans, and, when present, their mobilization potential can vary among individuals. Previously, we showed that the great majority of retrotransposition events in humans are caused by highly active, or hot, L1s. Here, in four populations of diverse geographic origins (160 haploid genomes), we investigated the degree of sequence polymorphism of three hot L1s and the extent of individual variation in mobilization capability of their allelic variants. For each locus, we found one previously uncharacterized allele in every three to five genomes, including some with nonsense and insertion͞deletion mutations. Single or multiple nucleotide substitutions drastically affected the retrotransposition efficiency of some alleles. Onethird of elements were no longer hot, and these so-called cool alleles substantially increased the range of individual susceptibility to retrotransposition events. Adding the activity of the three elements in each individual resulted in a surprising degree of variation in mobilization capability, ranging from 0% to 390% of a reference L1. These data suggest that individual variation in retrotransposition potential makes an important contribution to human genetic diversity.human variation ͉ population genetics ͉ retrotransposon

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Section: Discussionmentioning

confidence: 89%

Extensive individual variation in L1 retrotransposition capability contributes to human genetic diversity

Seleme¹,

Vetter²,

Cordaux

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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“…CpG rich regions (isochores) are rich in genes and induce lower scale clustering [42][43][44][45][46].…”

Section: Exit and Recurrence Distance Distributionsmentioning

confidence: 99%

DNA viewed as an out-of-equilibrium structure

Provata

Nicolis

2014

Phys. Rev. E

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The complexity of the primary structure of human DNA is explored using methods from nonequilibrium statistical mechanics, dynamical systems theory and information theory. The use of chi-square tests shows that DNA cannot be described as a low order Markov chain of order up to r = 6. Although detailed balance seems to hold at the level of purine-pyrimidine notation it fails when all four basepairs are considered, suggesting spatial asymmetry and irreversibility. Furthermore, the block entropy does not increase linearly with the block size, reflecting the long range nature of the correlations in the human genomic sequences. To probe locally the spatial structure of the chain we study the exit distances from a specific symbol, the distribution of recurrence distances and the Hurst exponent, all of which show power law tails and long range characteristics. These results suggest that human DNA can be viewed as a non-equilibrium structure maintained in its state through interactions with a constantly changing environment. Based solely on the exit distance distribution accounting for the nonequilibrium statistics and using the Monte Carlo rejection sampling method we construct a model DNA sequence. This method allows to keep all long range and short range statistical characteristics of the original sequence. The model sequence presents the same characteristic exponents as the natural DNA but fails to capture point-to-point details. *

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“…The different computational approaches used to disprove or redefine isochores (Eyre-Walker and Hurst 2001;Häring and Kypr 2001;Lander et al 2001;Nekrutenko and Li 2001;Cohen et al 2005) were, however, shown to be inadequate (Bernardi 2001;Bernardi 2001a,b, 2005;Li 2002;Oliver et al 2002Oliver et al , 2004Li et al 2003;Melodelima et al 2005), even if some of them led to a partial identification of isochores. This debate prompted us to map the isochores, as originally defined , in the finished sequence of the human genome (International Human Genome Sequencing Consortium 2004).…”

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confidence: 99%

An isochore map of human chromosomes

Costantini¹,

Clay²,

Auletta³

et al. 2006

Genome Res.

210

300

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Isochores are large DNA segments (≫300 kb on average) that are characterized by an internal variation in GC well below the full variation seen in the mammalian genome. Precisely defining in terms of size and composition as well as mapping the isochores on human chromosomes have, however, remained largely unsolved problems. Here we used a very simple approach to segment the human chromosomes de novo, based on assessments of GC and its variation within and between adjacent regions. We obtain a complete coverage of the human genome (neglecting the remaining gaps) by ∼3200 isochores, which may be visualized as the ultimate chromosomal bands. Isochores visibly belong to five families characterized by different GC levels, as expected from previous investigations. Since we previously showed that isochores are tightly linked to basic biological properties such as gene density, replication timing, and recombination, the new level of detail provided by the isochore map will help the understanding of genome structure, function, and evolution.

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Isochore chromosome maps of the human genome

Cited by 53 publications

References 50 publications

Extensive individual variation in L1 retrotransposition capability contributes to human genetic diversity

Extensive individual variation in L1 retrotransposition capability contributes to human genetic diversity

DNA viewed as an out-of-equilibrium structure

An isochore map of human chromosomes

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