Interchromosomal duplications of the adrenoleukodystrophy locus: a phenomenon of pericentromeric plasticity

Eichler, Evan E.; Budarf, Marcia L.; Rocchi, Mariano; Deaven, Larry L.; Doggett, Norman A.; Baldini, Antonio; Nelson, David L.; Mohrenweiser, Harvey W.

doi:10.1093/hmg/6.7.991

Cited by 137 publications

(119 citation statements)

References 42 publications

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“…These larger segments consist of numerous smaller duplication modules of diverse evolutionary origin. Taken together, these findings fit with the proposed two-step model of pericentromeric duplication wherein an initial process of transposition seeding (accumulation of smaller duplications within pericentromeric regions) is followed by pericentromeric exchange (spreading of larger patchwork blocks to pericentromeric regions of nonhomologous chromosomes) (Eichler et al 1997;Horvath et al 2000b;Luijten et al 2000;Samonte and Eichler 2002). In contrast, the most pericentromeric position in the euchromatic island is exclusively present on chromosome 11.…”

Section: Discussionsupporting

confidence: 84%

Interchromosomal segmental duplications of the pericentromeric region on the human Y chromosome

et al. 2005

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Basic medical research critically depends on the finished human genome sequence. Two types of gaps are known to exist in the human genome: those associated with heterochromatic sequences and those embedded within euchromatin. We identified and analyzed a euchromatic island within the pericentromeric repeats of the human Y chromosome. This 450-kb island, although not recalcitrant to subcloning and present in 100 tested males from different ethnic origins, was not detected and is not contained within the published Y chromosomal sequence. The entire 450-kb interval is almost completely duplicated and consists predominantly of interchromosomal rather than intrachromosomal duplication events that are usually prevalent on the Y chromosome. We defined the modular structure of this interval and detected a total of 128 underlying pairwise alignments (Ն90% and Ն1 kb in length) to various autosomal pericentromeric and ancestral pericentromeric regions. We also analyzed the putative gene content of this region by a combination of in silico gene prediction and paralogy analysis. We can show that even in this exceptionally duplicated region of the Y chromosome, eight putative genes with open reading frames reside, including fusion transcripts formed by the splicing of exons from two different duplication modules as well as members of the homeobox gene family DUX.

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Section: Discussionsupporting

confidence: 84%

Interchromosomal segmental duplications of the pericentromeric region on the human Y chromosome

et al. 2005

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“…The repeat structures that demarcate the boundaries of the duplications are unusually GC rich. Similar GC-rich sequences have been reported at the boundaries of other recently duplicated genomic segments including duplications of adrenoleukodystrophy and immunoglobulin variable -chain locus (Borden et al 1990;Eichler et al 1997). The telomere-like elements (HSREP522, TAR, and HSREP286) that define the opposite of end of these repeat structures are likewise composed of GC-rich sequences.…”

Section: Genome Research 1053supporting

confidence: 66%

“…The pericentromericdirected mechanism of gene duplication may be likened to "duplicative transposition." There is, however, no evidence for the production of short direct repeats at the site of integration-suggesting that the process is mechanistically distinct from classically defined transposition (Borden et al 1990;Eichler et al 1996Eichler et al , 1997. Whether the process of pericentromeric-directed gene duplication is an anomaly of primate genome evolution remains to be determined.…”

Section: Genome Research 1053mentioning

confidence: 97%

“…(Pericentromeric DNA, for our purposes, refers to the chromosomal region that begins immediately distal to the ␣-satellite repeat and extends into the first distinguishable cytogenetic Giemsa-stained band on either side of the centromere.) The estimated evolutionary age for a few of these duplications has precluded tetraploidization as a possible mechanism for these duplication events (Eichler et al 1996(Eichler et al , 1997Regnier et al 1997). During our analysis of one such recent (∼10 mya) duplication of the creatine transporter locus, we identified an interspersed CAGGG repeat sequence located at the junction of the duplicated Xq28 genomic segment within 16p11.2.…”

mentioning

confidence: 99%

“…Several independent reports indicate that genic segments, ranging in length from 5 kb to 30 kb, possess duplicate copies within the pericentromeric regions of human autosomes (Borden et al 1990;Wong et al 1990;Eichler et al 1996Eichler et al , 1997Regnier et al 1997;Zimonjic et al 1997;Ritchie et al 1998). (Pericentromeric DNA, for our purposes, refers to the chromosomal region that begins immediately distal to the ␣-satellite repeat and extends into the first distinguishable cytogenetic Giemsa-stained band on either side of the centromere.)…”

mentioning

confidence: 99%

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CAGGG Repeats and the Pericentromeric Duplication of the Hominoid Genome

Eichler¹,

Archidiacono²,

Rocchi³

1999

Genome Res.

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Gene duplication is one of the primary forces of evolutionary change. We present data from three different pericentromeric regions of human chromosomes, which indicate that such regions of the genome have been sites of recent genomic duplication. This form of duplication has involved the evolutionary movement of segments of genomic material, including both intronic and exonic sequence, from diverse regions of the genome toward the pericentromeric regions. Sequence analyses of the target sites of duplication have identified a novel class of interspersed GC-rich repeats located precisely at the boundaries of duplication. Estimates of the evolutionary age of these duplications indicate that they have occurred between 10 and 25 mya. In contrast, comparative analyses confirm that the GC-rich pericentromeric repeats have existed within the pericentromeric regions of primate chromosomes before the divergence of the cercopithecoid and hominoid lineages (∼30 mya). These data provide molecular evidence for considerable interchromosomal duplication of genic segments during the evolution of the hominoid genome and strongly implicate GC-rich repeat elements as playing a direct role in the pericentromeric localization of these events Genome evolution is dependent on the processes of single-base-pair mutation and gene duplication. Duplication of a gene followed by mutation is responsible for the emergence of new genes with specialized functions in an evolving species. Two distinct molecular mechanisms of gene duplication are generally recognized. Tandem duplication of an ancestral gene, vis-à-vis processes of unequal crossover, produces a clustered family of related genes (Smith 1976). In contrast, whole-genome duplication (polyploidy) followed by chromosomal rearrangement and the re-establishment of the disomic state has been proposed as a mechanism for the interchromosomal duplication of large segments of a genome (Ohno 1970). The latter model, put forward originally by Susumu Ohno, explains observations of conserved genic synteny among nonhomologous chromosomes. Because of the genetic consequences of polyploidy, such events, although important in the early expansion of eukaryotic genomes, are rare and ancient (Ohno 1993;Wolfe and Shields 1997). Within the vertebrate lineage, for example, the last tetraploidization event leading to genome duplication is estimated to have occurred >400 mya (Lundin 1993). If polyploidy were the only model by which entire genes could be duplicated among nonhomologous chromosomes, it would then follow that interchromosomal paralogs of recent origin would be unexpected.Recent analyses of data from the Human Genome Project suggest a third form of genomic duplication, which is mechanistically distinct from polyploidy and tandem duplication models of genome evolution. Several independent reports indicate that genic segments, ranging in length from 5 kb to 30 kb, possess duplicate copies within the pericentromeric regions of human autosomes (Borden et

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Determination of 30 X-linked adrenoleukodystrophy mutations, including 15 not previously described

et al. 2000

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Interchromosomal duplications of the adrenoleukodystrophy locus: a phenomenon of pericentromeric plasticity

Cited by 137 publications

References 42 publications

Interchromosomal segmental duplications of the pericentromeric region on the human Y chromosome

Interchromosomal segmental duplications of the pericentromeric region on the human Y chromosome

CAGGG Repeats and the Pericentromeric Duplication of the Hominoid Genome

Determination of 30 X-linked adrenoleukodystrophy mutations, including 15 not previously described

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