The Biased Distribution of Alus in Human Isochores Might Be Driven by Recombination

Hackenberg, Michael; Bernaola‐Galván, Pedro; Carpena, Pedro; Oliver, José Luis Tejera

doi:10.1007/s00239-004-0197-2

Cited by 42 publications

(39 citation statements)

References 48 publications

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“…The trend persists, although less clearly, if we take into account the fact that AT-rich regions represent 58% of the genome (Lander et al, 2001). These results suggesting a slight preferential insertion of the youngest Alu elements in AT-rich regions therefore concur with previously published results (Lander et al, 2001;Chimpanzee Sequencing and Analysis Consortium, 2005;Hackenberg et al, 2005).…”

Section: Genomic Distribution Of the Youngest Human Alu Elementssupporting

confidence: 94%

“…This is consistent with an analysis of the distribution of recently integrated Alu elements inserted in human chromosome 19 (Arcot et al, 1998). By contrast, it a priori seems at odds with genome-wide analyses that suggested that young Alu elements are preferentially inserted in AT-rich regions (Lander et al, 2001;Chimpanzee Sequencing and Analysis Consortium, 2005;Hackenberg et al, 2005), although we note that the statistical significance of this observation has not been tested in any of the studies. Even though our data are consistent with the previously reported apparent insertion bias towards AT-rich regions, we show that it is not statistically different from a random insertion model.…”

Section: Recently Integrated Alu Elements and Selectionsupporting

confidence: 79%

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Recently integrated Alu retrotransposons are essentially neutral residents of the human genome

Cordaux

Lee

Dinoso

et al. 2006

Gene

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Alu elements represent the largest family of human mobile elements in copy number. A controversial issue with implications for both Alu biology and human genome evolution is whether selective pressures are affecting Alu elements on a large scale. To address this issue, we analyzed the genomic distribution of the three youngest known human Alu subfamilies (Ya5a2, Ya8 and Yb9) in conjunction with their insertion polymorphism status in the human population, since selection can only act on polymorphic elements. Our results indicate that: (i) polymorphic and fixed recently integrated Alu elements are found in genomic regions whose GC contents are statistically indistinguishable, and (ii) recently integrated Alu elements are inserted randomly, regardless of the GC content of the surrounding genomic DNA. These results provide strong evidence that recently integrated "young" Alu elements are not subject to positive or negative selection on a large scale. Therefore, young Alu elements can be regarded as essentially neutral residents of the human genome. These results also imply that selective processes specifically targeting Alu elements can be ruled out as explanations for the accumulation of Alu elements in GC-rich regions of the human genome.

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Section: Genomic Distribution Of the Youngest Human Alu Elementssupporting

confidence: 94%

Section: Recently Integrated Alu Elements and Selectionsupporting

confidence: 79%

Recently integrated Alu retrotransposons are essentially neutral residents of the human genome

Cordaux

Lee

Dinoso

et al. 2006

Gene

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“…This selection scenario allows us to avoid invoking a mechanism whereby the LINE-1 transposition machinery leads to Alu elements being inserted in different regions from LINE-1 elements. It would also account for why all of the youngest Alu and LINE-1 subfamilies are more randomly distributed than the older subfamilies as not enough time would have passed to select for the favored distributions (Gu et al, 2000;Pavlícek et al, 2001;Medstrand et al, 2002;Belle et al, 2005;Hackenberg et al, 2005).…”

Section: Non-random Repeat Distributions Via Natural Selectionmentioning

confidence: 99%

Repetitive sequence environment distinguishes housekeeping genes

Eller¹,

Regelson²,

Merriman³

et al. 2007

Gene

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Housekeeping genes are expressed across a wide variety of tissues. Since repetitive sequences have been reported to influence the expression of individual genes, we employed a novel approach to determine whether housekeeping genes can be distinguished from tissue-specific genes their repetitive sequence context. We show that Alu elements are more highly concentrated around housekeeping genes while various longer (>400-bp) repetitive sequences ("repeats"), including Long Interspersed Nuclear Element 1 (LINE-1) elements, are excluded from these regions. We further show that isochore membership does not distinguish housekeeping genes from tissue-specific genes and that repetitive sequence environment distinguishes housekeeping genes from tissue-specific genes in every isochore. The distinct repetitive sequence environment, in combination with other previously published sequence properties of housekeeping genes, were used to develop a method of predicting housekeeping genes on the basis of DNA sequence alone. Using expression across tissue types as a measure of success, we demonstrate that repetitive sequence environment is by far the most important sequence feature identified to date for distinguishing housekeeping genes.

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“…SINEs use the enzymatic machinery of LINEs for replication and insertion (Smit et al 1995;Jurka 1997;Dewannieux et al 2003;Dewannieux and Heidmann 2005), and therefore the two classes of TEs might be expected to have similar distributions in the genome. However, their distributions are very different; in primates and rodents, SINEs insert into AT-rich regions of the genome and accumulate in gene-rich regions with high GC content, while LINEs reside in AT-rich regions (Soriano et al 1983;Lander et al 2001;Pavlicek et al 2001;Yang et al 2004;Hackenberg et al 2005) and show only modest GC enrichment over time. This pattern has received considerable attention in recent years, but there is still no consensus on the mechanism causing it.…”

mentioning

confidence: 99%

“…However, the accumulation of Alu's in gene-rich regions is still slower than the time necessary for the fixation of neutral alleles (Brookfield 2001), which seems to question this possibility. An alternative hypothesis is that deletions (most likely by ectopic exchange between repeats) drive the accumulation of repeats in gene-rich regions (Lobachev et al 2000;Brookfield 2001;Lander et al 2001;Stenger et al 2001;Batzer and Deininger 2002;Hackenberg et al 2005;Abrusan and Krambeck 2006). According to this theory, deletions are more deleterious in gene-and GCrich regions of the genome than in the gene-poor, ATrich regions, because they may result in loss of selectively important sequences.…”

mentioning

confidence: 99%

Biased Distributions and Decay of Long Interspersed Nuclear Elements in the Chicken Genome

et al. 2008

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The genomes of birds are much smaller than mammalian genomes, and transposable elements (TEs) make up only 10% of the chicken genome, compared with the 45% of the human genome. To study the mechanisms that constrain the copy numbers of TEs, and as a consequence the genome size of birds, we analyzed the distributions of LINEs (CR1's) and SINEs (MIRs) on the chicken autosomes and Z chromosome. We show that (1) CR1 repeats are longest on the Z chromosome and their length is negatively correlated with the local GC content; (2) the decay of CR1 elements is highly biased, and the 59-ends of the insertions are lost much faster than their 39-ends; (3) the GC distribution of CR1 repeats shows a bimodal pattern with repeats enriched in both AT-rich and GC-rich regions of the genome, but the CR1 families show large differences in their GC distribution; and (4) the few MIRs in the chicken are most abundant in regions with intermediate GC content. Our results indicate that the primary mechanism that removes repeats from the chicken genome is ectopic exchange and that the low abundance of repeats in avian genomes is likely to be the consequence of their high recombination rates.

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The Biased Distribution of Alus in Human Isochores Might Be Driven by Recombination

Cited by 42 publications

References 48 publications

Recently integrated Alu retrotransposons are essentially neutral residents of the human genome

Recently integrated Alu retrotransposons are essentially neutral residents of the human genome

Repetitive sequence environment distinguishes housekeeping genes

Biased Distributions and Decay of Long Interspersed Nuclear Elements in the Chicken Genome

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