Restriction site periodicities in highly repetitive DNA of primates

Donehower, Larry A.; Gillespie, D. A. F.

doi:10.1016/0022-2836(79)90487-x

Cited by 53 publications

(28 citation statements)

References 33 publications

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“…2. The DNA sequence is in agreement with the known restriction map for this sequence (8). The 343-base-pair fragment is comprised of two wings, denoted "Papio 1" and "Papio 2" in Fig.…”

Section: Resultssupporting

confidence: 60%

“…The similarities among the D)NA sequences in Fig. 3 support the concept that all these highly repeated primate DNA sequences were derived from a common ancestral sequence (8,16,20). Among the primate repeated sequences in Fig.…”

Section: Resultssupporting

confidence: 58%

“…3). These crossovers are hypothesized to have been critical in the formation of the >170-base-pair basic repeats, which characterize various primate highly repeated DNAs (8) and which correspond with the size of a nucleosome in the case of C. aethiops highly repeated DNA (5). Maio et al.…”

Section: Resultsmentioning

confidence: 99%

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DNA sequence of baboon highly repeated DNA: evidence for evolution by nonrandom unequal crossovers.

Donehower¹,

Furlong²,

Gillespie³

et al. 1980

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

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A highly repeated DNA was isolated from the West African baboon (Papio papio) as a 343-base-pair fragment after digestion of total baboon DNA with the restriction endonuclease BamHI. The DNA sequence of this fragment was obtained by chemical cleavage methods and is compared with the DNA sequence of related highly repeated primate DNAs from African green monkey (Cercopithecus aethiops) and man. The 343-base-pair baboon repeat consists of two related but nonidentical wings of 172 and 171 base pairs, respectively. The baboon 172-base-pair wing shares more homology with the African green monkey 172-base-pair repeat than with the baboon 171-base-pair wing. Comparison with the previously published monkey and human DNA sequences indicates that: (i) All the DNA sequences apparently arose from a common ancestral sequence. (ii) Evolution of the primate DNA sequences can be explained by a model involving unequal crossovers at specific points within the repeated DNA, possibly mediated by the sequence 5'-AcC-3' or its invert 5:-CGTA9_3. (iii) There are alternating domains of conserved and divergent DNA sequences within each >170-base-pair wing sequence. Taken together, the DNA sequences of these primates suggest a model whereby highly repeated DNAs are established and evolve as a consequence of unequal nonrandom exchanges of DNA duplexes. These exchanges may be mediated by short repeated nucleotide sequences and involve exchanges within and between the >170-base-pair wings. A significant, but markedly variable, component of the eukaryotic genome is comprised of highly repeated DNA sequences that are localized in constitutive heterochromatin, that are not transcribed, and for which quantitative variation within a species (or among closely related species) is tolerated without major phenotypic effects (1, 2). Nucleic acid hybridization and DNA sequence studies demonstrate that, unlike the remainder of the genome, these highly repeated DNAs tend to be comprised of short simple sequences repeated in tandem with a high degree of quantitative variation both within and among eukaryotic species. Molecular and cytogenetic evidence suggest a model whereby unequal double-strand exchanges associated with mitotic DNA replication result in the creation and amplification of these DNA sequences (1,(3)(4)(5).In this report, the DNA sequence is obtained for a baboon highly repeated DNA. Comparison of this DNA sequence with previously published related DNA sequences from African green monkey (6) and man (7) is consistent with the above unequal exchange model and suggests the additional constraint that the exchanges are nonrandom, possibly mediated by a short specific nucleotide sequence. This model of unequal mitotic exchanges mediated by short specific nucleotide sequences may

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“…2. The DNA sequence is in agreement with the known restriction map for this sequence (8). The 343-base-pair fragment is comprised of two wings, denoted "Papio 1" and "Papio 2" in Fig.…”

Section: Resultssupporting

confidence: 60%

Section: Resultssupporting

confidence: 58%

See 1 more Smart Citation

DNA sequence of baboon highly repeated DNA: evidence for evolution by nonrandom unequal crossovers.

Donehower¹,

Furlong²,

Gillespie³

et al. 1980

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

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“…Alpha satellite DNA is a tandemly repeated DNA family based primarily on a -170-to 172-bp repeat length (4,14,16,19,20,34). This length, the alphoid monomer, is the smallest repetitive unit of alpha satellite and exhibits no recognizable internal redundancy (34).…”

Section: Discussionmentioning

confidence: 99%

“…Although alpha satellite comprises tandem monomers, this unit size does not necessarily correspond to the size of the presumed amplification domain during evolution. Like other tandemly repeated mammalian satellite DNAs, alpha satellite DNA can be characterized by longerrange periodicities marked by the presence of regularly spaced restriction enzyme recognition sites that define a higher-order repeat length (2,4,13,14). Since definition of a higher-order repeat unit is dependent on the adventitious use or availability of a particular (and a priori unknown) restriction enzyme(s), conclusions regarding the equivalence of such operationally defined repeat lengths and repeat lengths of actual evolutionary significance are made with caution.…”

Section: Discussionmentioning

confidence: 99%

Structure, organization, and sequence of alpha satellite DNA from human chromosome 17: evidence for evolution by unequal crossing-over and an ancestral pentamer repeat shared with the human X chromosome.

Waye¹,

Willard²

1986

Mol. Cell. Biol.

205

187

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The centromeric regions of all human chromosomes are characterized by distinct subsets of a diverse tandemly repeated DNA family, alpha satellite. On human chromosome 17, the predominant form of alpha satellite is a 2.7-kilobase-pair higher-order repeat unit consisting of 16 alphoid monomers. We present the complete nucleotide sequence of the 16-monomer repeat, which is present in 500 to 1,000 copies per chromosome 17, as well as that of a less abundant 15-monomer repeat, also from chromosome 17. These repeat units were -98% identical in sequence, differing by the exclusion of precisely 1 monomer from the 15-monomer repeat. Homologous unequal crossing-over is suggested as a probable mechanism by which the different repeat lengths on chromosome 17 were generated, and the putative site of such a recombination event is identified. The monomer organization of the chromosome 17 higher-order repeat unit is based, in part, on tandemly repeated pentamers. A similar pentameric suborganization has been previously demonstrated for alpha satellite of the human X chromosome. Despite the organizational similarities, substantial sequence divergence distinguishes these subsets. Hybridization experiments indicate that the chromosome 17 and X subsets are more similar to each other than to the subsets found on several other human chromosomes. We suggest that the chromosome 17 and X alpha satellite subsets may be related components of a larger alphoid subfamily which have evolved from a common ancestral repeat into the contemporary chromosome-specific subsets.Alpha satellite (alphoid DNA) is a complex family of tandemly repeated DNA found in primate genomes. Long tandem arrays of alpha satellite DNA based on a monomer repeat length of -171 base paiirs (bp) are located principally at the centromeres of primate chromosomes (3,15,16,19,20). In the human genome, these sequences have been identified at the centromeric regions of each human chromosome and constitute some 5% of total human DNA. Human alpha satellite was initially described as a 340-bp EcoRI repeat, comprising two diverged monomer halves of 169 and 171 bp (16,34). However, more recent studies have indicated that this DNA family is substantially more heterogeneous than was once believed. The dimeric EcoRI repeat itself is made up of several distinct subfamilies (11,22), and a number of different molecular configurations in the human genome have been described (7,10,18,28,29,32,33,35). Alpha satellite subsets have been identified on several human chromosomes, and the suggestion has been made that individual human chromosomes may each be characterized by distinct alpha satellite subsets defined by restriction enzyme periodicity and primary sequence (15,18,29).Alpha satellite DNA specific for the human X chromosome (alphaX) has been cloned and extensively characterized (28, 32, 35). The 2.0-kilobase-pair (kb) BamHI higherorder repeat unit from this chromosome consists of 12 tandem but diverged alpha satellite monomers arranged as two adjacent and related pentamer blocks plus ...

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Fractal displays of genomic DNA. I. Eco RI fractal lattice of buffalo rat

Finkel¹

1989

Int J of Quantum Chemistry

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A complex multidimensional DNA structure is obtained when treating the elements of the Eco RI restriction set of buffalo rat as a cascade of self-similar units. Fifteen of the 16 (about 94%) Eco RI repeat families, ranging in length from 2300 to 83 nucleotides and in frequency from 500 to >lo6 units, are sorted into a three-tiered well-ordered fractaliFibonacci lattice. On the first level, 11 fractal dimensions are defined as unique collinear collections of repeat DNA families in a "graph-invariant'' plot of log(fragment length) : log(frequency). On the second level, the individual dimensional arrays are clustered as groups, each sharing, at last, one common vertex. On the third level, the entire display is scaled along a stepwise log to the base 6 expansion. This study represents the first successful attempt to unify an "entire" set of repeat DNAs into a single motif, in effect confirming the contention that select repeat DNAs provide a framework for the discrete packaging and unpackaging of genomic information.

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Restriction site periodicities in highly repetitive DNA of primates

Cited by 53 publications

References 33 publications

DNA sequence of baboon highly repeated DNA: evidence for evolution by nonrandom unequal crossovers.

DNA sequence of baboon highly repeated DNA: evidence for evolution by nonrandom unequal crossovers.

Structure, organization, and sequence of alpha satellite DNA from human chromosome 17: evidence for evolution by unequal crossing-over and an ancestral pentamer repeat shared with the human X chromosome.

Fractal displays of genomic DNA. I. Eco RI fractal lattice of buffalo rat

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