A palindromic structure in the pericentromeric region of various human chromosomes.

Wöhr, Gudrun; Fink, Thomas; Assum, Günter

doi:10.1101/gr.6.4.267

Cited by 26 publications

(13 citation statements)

References 42 publications

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“…If new seeding events are primarily restricted to the unsequenced p arms of acrocentric chromosomes, we may miss them entirely. There is a small amount of evidence that acrocentric p arms do harbor duplicons (Wohr et al 1996;Eisenbarth et al 1999;Hattori et al 2000;Cserpan et al 2002); however, their sequence identity attributes do not appear to differ significantly from what has been observed for other pericentromeric regions.…”

Section: Discussionmentioning

confidence: 99%

Punctuated duplication seeding events during the evolution of human chromosome 2p11

et al. 2005

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Primate genomic sequence comparisons are becoming increasingly useful for elucidating the evolutionary history and organization of our own genome. Such studies are particularly informative within human pericentromeric regions-areas of particularly rapid change in genomic structure. Here, we present a systematic analysis of the evolutionary history of one ∼700-kb region of 2p11, including the first autosomal transition from pericentromeric sequence to higher-order ␣-satellite DNA. We show that this region is composed of segmental duplications corresponding to 14 ancestral segments ranging in size from 4 kb to ∼115 kb. These duplicons show 94%-98.5% sequence identity to their ancestral loci. Comparative FISH and phylogenetic analysis indicate that these duplicons are differentially distributed in human, chimpanzee, and gorilla genomes, whereas baboon has a single putative ancestral locus for all but one of the duplications. Our analysis supports a model where duplicative transposition events occurred during a narrow window of evolution after the separation of the human/ape lineage from the Old World monkeys (10-20 million years ago). Although dramatic secondary dispersal events occurred during the radiation of the human, chimpanzee, and gorilla lineages, duplicative transposition seeding events of new material to this particular pericentromeric region abruptly ceased after this time period. The multiplicity of initial duplicative transpositions prior to the separation of humans and great-apes suggests a punctuated model for the formation of highly duplicated pericentromeric regions within the human genome. The data further indicate that factors other than sequence are important determinants for such bursts of duplicative transposition from the euchromatin to pericentromeric regions.

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Section: Discussionmentioning

confidence: 99%

Punctuated duplication seeding events during the evolution of human chromosome 2p11

et al. 2005

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“…Although the chromosome 19 organization may be exceptional, large-scale sequence analysis will be required to determine whether similar higher order repeat structures are present in other ␤-satellite chromosomal regions. It is intriguing that large palindromic structures have been identified recently for a different pericentromeric repeat multisequence family, termed chAB4 (Assum et al 1991;Wohr et al 1996). chAB4 repeat units are organized as inverted duplications of 90 kb flanking a ''nonduplicated'' core sequence estimated to be ∼60 kb in length.…”

Section: Discussionmentioning

confidence: 99%

Complex β-Satellite Repeat Structures and the Expansion of the Zinc Finger Gene Cluster in 19p12

et al. 1998

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We investigated the organization, architecture, and evolution of the largest cluster (∼4 Mb) of Krüppel-associated box zinc finger (KRAB-ZNF) genes located in cytogenetic band interval 19p12. A highly integrated physical map (∼700 kb) of overlapping cosmid and BAC clones was developed between genetic STS markers D19S454 and D19S269. Using ZNF91 exon-specific probes to interrogate a detailed EcoRI restriction map of the region, ZNF genes were found to be distributed in a head-to-tail fashion throughout the region with an average density of one ZNF duplicon every 150-180 kb of genomic distance. Sequence analysis of 208,967 bp of this region indicated the presence of two putative ZNF genes: one consisting of a novel member of this gene family (ZNF208) expressed ubiquitously in all tissues examined and the other representing a nonprocessed pseudogene (ZNF209), located 450 kb proximal to ZNF208. Large blocks of (∼25-kb) inverted ␤-satellite repeats with a remarkably symmetrical higher order repeat structure were found to bracket the functional ZNF gene. Hybridization analysis using the ␤-satellite repeat as a probe indicates that ␤-satellite interspersion between ZNF gene cassettes is a general property for 1.5 Mb of the ZNF gene cluster in 19p12. Both molecular clock data as well as a retroposon-mapping molecular fossil approach indicate that this ZNF cluster arose early during primate evolution (∼50 million years ago). We propose an evolutionary model in which heteromorphic pericentromeric repeat structures such as the ␤ satellites have been coopted to accommodate rapid expansion of a large gene family over a short period of evolutionary time.[The sequence data described in this paper have been submitted to GenBank under accession nos. AC003973 and AC004004.] Zinc finger (ZNF) genes represent one of the largest gene families in the human genome with an estimated 500-600 members (Hoovers et al. 1992;Becker et al. 1995;Klug and Schwabe 1995). Although the specific function of the majority of ZNF genes remains largely unknown, as a class they are believed to encode transcriptional regulators that in a few instances have been shown to play critical roles in cellular and developmental differentiation processes (Pieler and Bellefroid 1994). ZNF proteins have been implicated in many diverse eukaryotic developmental processes, such as segment pattern formation in the Drosophila embryo (Rosenberg et al. 1986); cellular proliferation in the cerebellar hindbrain of the mouse (Wilkinson et al. 1989); and hematopoietic differentiation among human myeloid precursor cells (Hromas et al. 1991). DNA binding of the encoded proteins is typically mediated by a ZNF motif that consists either of two cysteines and two histidines (Krüppel family or C 2 /H 2 type) or four cysteines alone (steroid receptor or C 2 / C 2 type). The conserved cysteines and/or histidines form a tetrahedral complex around a zinc metal ion, generating a folded loop or ''finger'' of 30 amino acids that is capable of making contact with DNA (Miller et al. 1985)...

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“…It is possible that DXZ1 sequences may be flanked on one or both sides by a small amount (∼200 kb or less) of other repetitive sequences such as diverged ␣ satellite (e.g., Cooper et al 1993;Bayne et al 1994) or another family of repetitive DNA. In fact, at the centromeres of chromosomes 7 (Wevrick et al 1992), 8 (Lin et al 1993, Y (Cooper et al 1993), and the acrocentric chromosomes (Trowell et al 1993;Wohr et al 1996), there is evidence that small amounts of other tandemly repeated DNA families are located near ␣-satellite sequences.…”

Section: Structural Similarities Between the Two Arrays: Mapping Withmentioning

confidence: 99%

Physical and Genetic Mapping of the Human X Chromosome Centromere: Repression of Recombination

Mahtani¹,

Willard²

1998

Genome Res.

122

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Classical genetic studies in Drosophila and yeast have shown that chromosome centromeres have a cis-acting ability to repress meiotic exchange in adjacent DNA. To determine whether a similar phenomenon exists at human centromeres, we measured the rate of meiotic recombination across the centromere of the human X chromosome. We have constructed a long-range physical map of centromeric ␣-satellite DNA (DXZ1) by pulsed-field gel analysis, as well as detailed meiotic maps of the pericentromeric region of the X chromosome in the CEPH family panel. By comparing these two maps, we determined that, in the proximal region of the X chromosome, a genetic distance of 0.57 cM exists between markers that span the centromere and are separated by at least the average 3600 kb physical distance mapped across the DXZ1 array. Therefore, the rate of meiotic exchange across the X chromosome centromere is <1 cM/6300 kb (and perhaps as low as 1 cM/17,000 kb on the basis of other physical mapping data), at least eightfold lower than the average rate of female recombination on the X chromosome and one of the lowest rates of exchange yet observed in the human genome.Meiotic exchange is not distributed randomly along the length of eukaryotic chromosomes; indeed, much regional variation in recombination frequency has been observed. Perhaps the most conspicuous departure from uniformity is the dramatic repression of exchange found near eukaryotic chromosome centromeres and some telomeres (Mather 1936(Mather , 1939. Repression of meiotic recombination adjacent to the centromere (the centromere effect) is most obvious on the Drosophila X chromosome in which the centric heterochromatin, comprising half of the chromosome's cytogenetic length, barely contributes to its genetic length (Mather 1939;Roberts 1965); a similar centromere-associated repression of recombination is found on the autosomes of Drosophila (Beadle 1932;Painter 1935;Thompson 1963). Some of this repression of exchange is caused by the large blocks of heterochromatin present at the centromeres of higher eukaryotes (Willard 1990;Murphy and Karpen 1995), because heterochromatin, at least in Drosophila, is a poor substrate for recombination regardless of chromosomal location (Baker 1958). Because deletions of centric heterochromatin result in lowered levels of meiotic exchange in centromere-adjacent euchromatin (Yamamoto and Miklos 1978), the presence alone of heterochromatin at Drosophila centromeres does not fully explain the centromere effect. Rather, the centromere seems to exert a suppression of recombination that spreads to adjacent DNA.Studies in yeast support a similar centromeric suppression of meiotic exchange in proximal chromosome regions, although this effect may be less pronounced. In both Saccharomyces cerevisiae and Schizosaccharomyces pombe, mitotic recombination is relatively more frequent than meiotic recombination in the proximity of centromeres (Malone et al. 1980;Minet et al. 1980). Direct evidence for the centromere effect in yeast has come from studies of c...

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A palindromic structure in the pericentromeric region of various human chromosomes.

Cited by 26 publications

References 42 publications

Punctuated duplication seeding events during the evolution of human chromosome 2p11

Punctuated duplication seeding events during the evolution of human chromosome 2p11

Complex β-Satellite Repeat Structures and the Expansion of the Zinc Finger Gene Cluster in 19p12

Physical and Genetic Mapping of the Human X Chromosome Centromere: Repression of Recombination

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