The human genome in the LINE of fire

Cordaux, Richard

doi:10.1073/pnas.0810202105

Cited by 13 publications

(13 citation statements)

References 20 publications

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“…L1 RMDs are larger on average than Alu RMDs and they occur more frequently in gene-poor regions of the genome than Alu RMDs. These results are suggestive of negative selection against long, deleterious L1 RMDs in gene-rich regions of the genome18,82,83. Thus, Alu and L1 RMD events detectable by comparative genomics approaches largely represent the fraction of all RMDs that have escaped negative selection.…”

Section: Genomic Rearrangementsmentioning

confidence: 92%

“…Altogether, it has been estimated that during primate evolution, as many as ~45,000 insertion-mediated deletions may have removed >30 Mb of genomic sequences18.…”

Section: Genomic Rearrangementsmentioning

confidence: 99%

“…For example, it has long been recognized that recombination between TEs can trigger genomic deletions in humans, as these deletions have caused several genetic disorders8. However, only recently have genome-wide comparisons of human and other primate genomes permitted us to determine the magnitude and significance of TE recombination-mediated deletions at an evolutionary scale16-18.…”

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confidence: 99%

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The impact of retrotransposons on human genome evolution

2009

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Non-LTR retrotransposons – including LINE-1 (or L1), Alu and SVA elements – have proliferated during the past 80 million years of primate evolution and now account for approximately one third of the human genome. These transposable elements are now known to affect the human genome in many different ways: generating insertion mutations, genomic instability, alterations in gene expression and also contributing to genetic innovation. As the sequences of human and other primate genomes are analyzed in increasing detail, we are begining to understand the scale and complexity of the past and current contribution of non-LTR retrotransposons to genomic change in the human lineage.

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Section: Genomic Rearrangementsmentioning

confidence: 92%

“…Altogether, it has been estimated that during primate evolution, as many as ~45,000 insertion-mediated deletions may have removed >30 Mb of genomic sequences18.…”

Section: Genomic Rearrangementsmentioning

confidence: 99%

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confidence: 99%

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The impact of retrotransposons on human genome evolution

2009

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“…The prevalence of non-LTR retrotransposons makes lepidopteran genomes different from that of Drosophila melanogaster, in which LTR retrotransposons are the most abundant (31). Both the rather high repeat coverage and the prevalence of non-LTR retrotransposons make lepidopteran genomes look like mammalian genomes (32,33).…”

Section: Discussionmentioning

confidence: 99%

Extensive synteny conservation of holocentric chromosomes in Lepidoptera despite high rates of local genome rearrangements

d’Alençon

Sezutsu

Legeai³

et al. 2010

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

153

137

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The recent assembly of the silkworm Bombyx mori genome with 432 Mb on 28 holocentric chromosomes has become a reference in the genomic analysis of the very diverse Order of Lepidoptera. We sequenced BACs from two major pests, the noctuid moths Helicoverpa armigera and Spodoptera frugiperda, corresponding to 15 regions distributed on 11 B. mori chromosomes, each BAC/region being anchored by known orthologous gene(s) to analyze syntenic relationships and genome rearrangements among the three species. Nearly 300 genes and numerous transposable elements were identified, with long interspersed nuclear elements and terminal inverted repeats the most abundant transposable element classes. There was a high degree of synteny conservation between B. mori and the two noctuid species. Conserved syntenic blocks of identified genes were very small, however, approximately 1.3 genes per block between B. mori and the two noctuid species and 2.0 genes per block between S. frugiperda and H. armigera. This corresponds to approximately two chromosome breaks per Mb DNA per My. This is a much higher evolution rate than among species of the Drosophila genus and may be related to the holocentric nature of the lepidopteran genomes. We report a large cluster of eight members of the aminopeptidase N gene family that we estimate to have been present since the Jurassic. In contrast, several clusters of cytochrome P450 genes showed multiple lineagespecific duplication events, in particular in the lepidopteran CYP9A subfamily. Our study highlights the value of the silkworm genome as a reference in lepidopteran comparative genomics.comparative genomics | silkworm | Noctuidae | transposable elements | gene clusters

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“…15,16 These repetitive sequences are responsible for creating genetic variation and also human diseases, not only because Alu sequences are known to mediate the occurrence of genetic recombination events as a direct result of their abundance and sequence homology, but also due to the occurrence of insertion mutations as a consequence of Alu retransposition events. 17 We characterized two large deletions involving the BRCA1 gene, which account for about 4% (2/48) of all BRCA1 HBOC families identified in our population. The first rearrangement we here report harbored a deletion comprising exon 7 of the BRCA1 gene to exon 11 of the NBR1 gene (c.441 þ 1724_oNBR1:c.1073 þ 480del).…”

Section: According To Sluiter and Van Rensburg 4 81 And 17 Differentmentioning

confidence: 99%

Genomic characterization of two large Alu-mediated rearrangements of the BRCA1 gene

et al. 2012

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To determine whether a large genomic rearrangement is actually novel and to gain insight about the mutational mechanism responsible for its occurrence, molecular characterization with breakpoint identification is mandatory. We here report the characterization of two large deletions involving the BRCA1 gene. The first rearrangement harbored a 89,664-bp deletion comprising exon 7 of the BRCA1 gene to exon 11 of the NBR1 gene (c.441+1724_oNBR1:c.1073+480del). Two highly homologous Alu elements were found in the genomic sequences flanking the deletion breakpoints. Furthermore, a 20-bp overlapping sequence at the breakpoint junction was observed, suggesting that the most likely mechanism for the occurrence of this rearrangement was nonallelic homologous recombination. The second rearrangement fully characterized at the nucleotide level was a BRCA1 exons 11-15 deletion (c.671-319_4677-578delinsAlu). The case harbored a 23,363-bp deletion with an Alu element inserted at the breakpoints of the deleted region. As the Alu element inserted belongs to a still active AluY family, the observed rearrangement could be due to an insertion-mediated deletion mechanism caused by Alu retrotransposition. To conclude, we describe the breakpoints of two novel large deletions involving the BRCA1 gene and analysis of their genomic context allowed us to gain insight about the respective mutational mechanism.

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The human genome in the LINE of fire

Cited by 13 publications

References 20 publications

The impact of retrotransposons on human genome evolution

The impact of retrotransposons on human genome evolution

Extensive synteny conservation of holocentric chromosomes in Lepidoptera despite high rates of local genome rearrangements

Genomic characterization of two large Alu-mediated rearrangements of the BRCA1 gene

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