ArticleJournal of molecular evolution2005
The biased distribution of Alus in human isochores might be driven by recombination.
Article in Journal of molecular evolution, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 44 citations in OpenAlex.
- Compositional Structure of the Genome: A Review.Biology · 2023Review
- A Model-Driven Quantitative Analysis of Retrotransposon Distributions in the Human Genome.Genome biology and evolution · 2020Article
- Population and clinical genetics of human transposable elements in the (post) genomic era.Mobile genetic elements · 2017Review
- Enrichment analysis of Alu elements with different spatial chromatin proximity in the human genome.Protein & cell · 2016Article
- Distribution of segmental duplications in the context of higher order chromatin organisation of human chromosome 7.BMC genomics · 2014Article
- The association between global DNA methylation and telomere length in a longitudinal study of boilermakers.Genetic epidemiology · 2014Article
- Shape-based alignment of genomic landscapes in multi-scale resolution.Nucleic acids research · 2012Article
- Large homogeneous genome regions (isochores) in soybean [glycine max (L.) merr].Frontiers in genetics · 2012Article
- Rescuing Alu: recovery of new inserts shows LINE-1 preserves Alu activity through A-tail expansion.PLoS genetics · 2012Article
- Effect of extreme data loss on long-range correlated and anticorrelated signals quantified by detrended fluctuation analysis.Physical review. E, Statistical, nonlinear, and soft matter physics · 2010Article
- Alu and b1 repeats have been selectively retained in the upstream and intronic regions of genes of specific functional classes.PLoS computational biology · 2009Article
- Effects of L1-ORF2 fragments on green fluorescent protein gene expression.Genetics and molecular biology · 2009Article
- Comparative analysis of distinct non-coding characteristics potentially contributing to the divergence of human tissue-specific genes.Genetica · 2009Article
- The role of LINEs and CpG islands in dosage compensation on the chicken Z chromosome.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2009Article
- Analysis of transposon interruptions suggests selection for L1 elements on the X chromosome.PLoS genetics · 2008Article
- Do Alu repeats drive the evolution of the primate transcriptome?Genome biology · 2008Article
- Assignment of isochores for all completely sequenced vertebrate genomes using a consensus.Genome biology · 2008Article
- Biased distributions and decay of long interspersed nuclear elements in the chicken genome.Genetics · 2008Article
- Alu recombination-mediated structural deletions in the chimpanzee genome.PLoS genetics · 2007Article
- End-sequencing and characterization of silkworm (Bombyx mori) bacterial artificial chromosome libraries.BMC genomics · 2007Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Alu retrotransposons do not show 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 mechanism that shifts the Alu density maximum from L to H isochores? To disclose the role played by each of the potential mechanisms involved in such biased distribution, 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 evolutionary scenario. We consecutively check, and discard, the contributions of the Alu/LINE1 competition for retrotransposase, compositional matching pressure, and Alu overrepresentation in introns. In analyzing the role played by unequal recombination, we scan the genome for Alu trimers, a direct product of Alu-Alu recombination. Through computer simulations, we show that such trimers are much more frequent than expected, the observed/expected ratio being higher in L than in H isochores. This result, together with the known higher selective disadvantage of recombination products in H isochores, points to Alu-Alu recombination as the main agent provoking the density shift of Alus toward the GC-rich parts of the genome. Two independent pieces of evidence-the lower evolutionary divergence shown by recently inserted Alu subfamilies and the higher frequency of old stand-alone Alus in L isochores-support such a conclusion. Other evolutionary factors, such as population bottlenecks during primate speciation, may have accelerated the fast accumulation of Alus in GC-rich isochores.
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