Detection of restriction fragment length polymorphisms at the centromeres of human chromosomes by using chromosome-specific alpha satellite DNA probes: implications for development of centromere-based genetic linkage maps.

Willard, Huntington F.; Waye, John S.; Skolnick, Mark H.; Schwartz, Charles E.; Powers, Vicki E. C.; England, Sarah B.

doi:10.1073/pnas.83.15.5611

Cited by 86 publications

(33 citation statements)

References 32 publications

(50 reference statements)

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“…The predominant alpha satellite repeat unit on chromosome 17 is a 2.7-kb 16-mer higher-order repeat unit (16 171-bp monomers) (44). Chromosome 17 alpha satellite DNA is further characterized by several polymorphic repeat unit variants, ranging in size from 11-to 15-mer repeat units (51), which form the basis for haplotypic analysis of this subset (47). 11-mers are found only in an isolated population of African pygmies and thus define a rare pygmy-specific variant (47).…”

Section: Resultsmentioning

confidence: 99%

Nonrandom localization of recombination events in human alpha satellite repeat unit variants: implications for higher-order structural characteristics within centromeric heterochromatin.

Warburton¹,

Waye²,

Willard³

1993

Mol. Cell. Biol.

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Tandemly repeated DNA families appear to undergo concerted evolution, such that repeat units within a species have a higher degree of sequence similarity than repeat units from even closely related species. While intraspecies homogenization of repeat units can be explained satisfactorily by repeated rounds of genetic exchange processes such as unequal crossing over and/or gene conversion, the parameters controlling these processes remain largely unknown. Alpha satellite DNA is a noncoding tandemly repeated DNA family found at the centromeres of all human and primate chromosomes. We have used sequence analysis to investigate the molecular basis of 13 variant alpha satellite repeat units, allowing comparison of multiple independent recombination events in closely related DNA sequences. The distribution of these events within the 171-bp monomer is nonrandom and clusters in a distinct 20-to 25-bp region, suggesting possible effects of primary sequence and/or chromatin structure. The position of these recombination events may be associated with the location within the higher-order repeat unit of the binding site for the centromere-specific protein CENP-B.These studies have implications for the molecular nature of genetic recombination, mechanisms of concerted evolution, and higher-order structure of centromeric heterochromatin.The complex genomes of eukaryotes contain large amounts of tandemly repeated DNA, often comprising several percent of an organism's genetic complement. These DNA families contain as many as several thousand repeat units at a given location, arranged in a head-to-tail fashion. Noncoding tandemly repeated DNAs are possible candidates for providing some of the structural requirements for proper chromosome function (14,20), while multigene families such as ribosomal DNA (rDNA) and immunoglobulin genes are important for the development and biology of complex organisms (16). One interesting but poorly understood property of these DNA families is the high degree of sequence similarity observed among repeat units within a species compared with the relatively low similarity of repeat units between closely related species (5, 16). Models to explain this phenomenon of concerted evolution invoke repeated rounds of homologous genetic exchange processes such as unequal crossing over and conversion, such that mutations arising in individual repeat units can be duplicated and eventually spread throughout the DNA family within a species (24, 30). Genetic exchange processes are thought to be important in shaping complex genomes, resulting in gene duplication, deletion, or fusion (reviewed in reference 15) and contributing to genetic diversity between populations during evolution (8,32 tinct linear arrangements that form highly homologous chromosome-specific higher-order repeat units (6, 50). These have presumably been homogenized on their particular chromosomes by genetic exchanges between misaligned arrays aligned on the register of the higher-order repeat units (31,38,50). Within a particular chromosomal subse...

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Section: Resultsmentioning

confidence: 99%

Nonrandom localization of recombination events in human alpha satellite repeat unit variants: implications for higher-order structural characteristics within centromeric heterochromatin.

Warburton¹,

Waye²,

Willard³

1993

Mol. Cell. Biol.

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“…According to their sequence homology and array structure, alphoid subsets can be divided into 5 different suprachromosomal families. 21 Because alphoid DNAs typically show extensive polymorphism regarding the number of their tandem repeats, [25][26][27] we had to determine the exact allelic origin of the derivative chromosome before properly evaluating the reduction of the D1Z7 and D7Z1 signals on this chromosome, as the intensity of these FISH signals directly depends on their cluster length.…”

Section: Identification Of the Allelic Chr1 And Chr7 Counterparts Ofmentioning

confidence: 99%

Molecular characterization of the recurrent unbalanced translocation der(1;7)(q10;p10)

Wang

Ogawa²,

Hangaishi³

et al. 2003

Blood

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An unbalanced translocation der(1;7)(q10; p10) is a nonrandom chromosomal aberration commonly observed in myelodysplastic syndrome and acute myeloid leukemia. We molecularly analyzed the breakpoints of der(1;7)(q10;p10) by quantitative fluorescent in situ hybridization (FISH) analyses using centromeric satellite DNAs mapped to chromosomes 1 and 7 as probes. We found that the signal intensities of 2 centromere alphoid probes, D1Z7 on chromosome 1 and D7Z1 on chromosome 7, were almost invariably reduced on the derivative chromosome compared with those on their normal counterparts. These results suggest that this translocation results from the recombination between the 2 alphoids, which was further confirmed by fiber FISH experiments. Because the relative reduction in the intensities of D1Z7 and D7Z1 signals on the derivative chromosomes was highly variable among patients, it was estimated that the breakpoints in these patients were randomly distributed over several megabase pairs within each alphoid cluster except for its extreme end to the short arm. Our results provide a novel insight into the structural basis for generation of this translocation as well as its leukemogenic roles. (Blood. 2003;102: 2597-2604)

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“…tromere regions (Willard et al 1986;Kipling et al 1994). We first identified size polymorphisms in these large fragments between the two common laboratory strains of A. thaliana, Columbia and Landsberg erecta, allowing us to use the Norwich Columbia/Landsberg recombinant inbred (RI) population (Lister and Dean 1993) to map the genetic position of the centromeric repeat arrays.…”

Section: Figurementioning

confidence: 99%

Arabidopsis thaliana Centromere Regions: Genetic Map Positions and Repetitive DNA Structure

Round

Flowers²,

Richards³

1997

Genome Res.

157

103

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The genetic positions of the five Arabidopsis thaliana centromere regions have been identified by mapping size polymorphisms in the centromeric 180-bp repeat arrays. Structural and genetic analysis indicates that 180-bp repeat arrays of up to 1000 kb are found in the centromere region of each chromosome. The genetic behavior of the centromeric arrays suggests that recombination within the arrays is suppressed. These results indicate that the centromere regions of A. thaliana resemble human centromeres in size and genomic organization.Genetic mapping of centromeres is essential for the integration of cytological and genetic maps, and marks an important step toward the molecular characterization of centromeric DNA. Although the centromere is one of the most conspicuous markers on the cytological map, determination of the location of centromeres on genetic maps is frequently difficult to achieve. This is especially true in higher animals and plants where the genetic tools for centromere mapping are limited.We have been pursuing the characterization of centromere regions of the model angiosperm Arabidopsis thaliana. This plant's small genome (∼100 Mb/haploid) (Meyerowitz 1994) and relatively low abundance of repetitive DNA [∼10% of total (Leutwiler et al. 1984)] make it well suited for molecular chromosome studies. Aiding in this analysis is the availability of dense genetic maps that exist for each of A. thaliana's five chromosomes (e.g., Hauge et al. 1993;Lister and Dean 1993). In addition, physical maps are being developed for all A. thaliana chromosomes in the form of overlapping cloned genomic fragments (Schmidt et al. 1995;Zachgo et al. 1996).Considering the generally advanced molecular characterization of the A. thaliana genome, the genomic organization and genetic location of centromeres in this species remain poorly characterized. The A. thaliana centromere regions are heterochromatic (Schweizer et al. 1987) and contain tandem arrays of related repeats (exhibiting ജ80% similarity) that are ∼180 bp in length (Martinez-Zapater et al. 1986;Simoens et al. 1988;Maluszynska and Heslop-Harrison 1991), a genomic organization that resembles the ∼170-bp alphoid repeat arrays at primate centromeres (Willard 1990;Pluta et al. 1995). It is not clear whether the 180-bp repeat arrays flank or span A. thaliana centromeres, but data from mammalian systems suggest that the alphoid repeats are intimately associated with the centromere and are likely to play a role in centromere function (Heartlein et al. 1988;Haaf et al. 1992;Tyler-Smith et al. 1993;Brown et al. 1994;Larin et al. 1994;Harrington et al. 1997). A number of other middlerepetitive sequence elements have been found to be associated with the 180-bp repeats in genomic clones (Richards et al. 1991;Schmidt et al. 1995;Pelissier et al. 1996; Thompson et al. 1996a,b), suggesting that islands of more complex sequence arrangement are located in the A. thaliana centromeric regions.An approximate genetic location of three of the five A. thaliana centromeres (on chromosomes ...

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Detection of restriction fragment length polymorphisms at the centromeres of human chromosomes by using chromosome-specific alpha satellite DNA probes: implications for development of centromere-based genetic linkage maps.

Cited by 86 publications

References 32 publications

Nonrandom localization of recombination events in human alpha satellite repeat unit variants: implications for higher-order structural characteristics within centromeric heterochromatin.

Nonrandom localization of recombination events in human alpha satellite repeat unit variants: implications for higher-order structural characteristics within centromeric heterochromatin.

Molecular characterization of the recurrent unbalanced translocation der(1;7)(q10;p10)

Arabidopsis thaliana Centromere Regions: Genetic Map Positions and Repetitive DNA Structure

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