Differential expansion of highly repeated DNA sequences in the swine subgenomes

Pita, Miguel; Garcı́a-Casado, Pedro; Toro, M. Á.; Gosálvez, Jaime

doi:10.1111/j.1439-0469.2008.00466.x

Cited by 6 publications

(9 citation statements)

References 11 publications

(21 reference statements)

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“…Distant breeds, as in this case the synthetic hybrid Assaf, chosen for this particular experiment for being such a random breed, tend to show differences. The conclusions reached in this experiment using W-CGH in sheep as well as other recent experiments studying different breeds of pig (Pita et al, 2008a) along with those investigating different species within the same genus as in the grasshopper Arcyptera (Pita et al, 2008b) reinforce the potential use of W-CGH as a simple strategic, informative technique for comparing genomes. W-CGH is of particular interest for performing early studies between breeds and species of which deep molecular studies have yet to be done and only a poor genomic background is available.…”

Section: Discussionmentioning

confidence: 63%

“…The dual hybridization color obtained in the pericentromeric heterochromatin when the Assaf and Castellana or Ojalada breeds were compared revealing quantitative differences proofs that highly repeated DNA sequences of these breeds have not diverged but just accumulated duplications and deletions. According to the 'Model of the Satellite Life History' (Nijman and Lenstra, 2001), the genomes go through different stages of homogenization of their highly repeated DNA sequences, so different species can show different stages that can be detected with W-CGH, not only between chromosomes or genomes but also between subgenomes (Pita et al, 2008a). In this connection, it is important to recall some examples linked to this observation.…”

Section: Discussionmentioning

confidence: 99%

“…If this is the case, W-CGH might be unable to show such differences due to lack of a sequence homology. Using W-CGH to compare different breeds in swine found evidence of a rapid evolution of repetitive DNA sequences associated with the Y chromosome (Pita et al, 2008a).…”

Section: Discussionmentioning

confidence: 99%

“…Whole-comparative genomic hybridization (W-CGH) allows for the rapid identification of chromosomal polymorphisms related to highly repetitive DNA sequences in constitutive heterochromatin that may exist between two genomes of the same species (Pita et al, 2003) or when closely-related individuals from different species are compared (Pita et al, 2008a). As a consequence, the presence/ absence of specific DNA families shared/not shared between the compared genomes as well as differences in the contribution of different chromosomal regions can be detected when differences are of the order of 5 Mb (Forozan et al, 1997).…”

mentioning

confidence: 99%

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Whole-comparative genomic hybridization in domestic sheep <i>(Ovis aries)</i> breeds

Dávila-Rodríguez

Cortés‐Gutiérrez

López‐Fernández

et al. 2009

Cytogenet Genome Res

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Whole-comparative genomic hybridization (W-CGH) allows identification of chromosomal polymorphisms related to highly repetitive DNA sequences localized in constitutive heterochromatin. Such polymorphisms are detected establishing competition between genomic DNAs in an in situ hybridization environment without subtraction of highly repetitive DNA sequences, when comparing two species from closely related taxa (same species, sub-species, or breeds) or somewhat related taxa. This experimental approach was applied to investigating differences in highly repetitive sequences of three sheep breeds (Castellana, Ojalada, and Assaf). To this end, W-CGH was carried out using mouflon (sheep ancestor) chromosomes as a common target to co-hybridize equimolar quantities of two genomic DNAs obtained from either Castellana, Ojalada or Assaf sheep breeds. The results showed that the amount of constitutive heterochromatin is greater in all pericentromeric heterochromatin regions of acrocentric chromosomes than in metacentric or sex chromosomes. Additionally, when W-CGH was performed using DNAs from the Iberian breeds Castellana and Ojalada, chromosomal pericentromeric regions revealed quantitatively and qualitatively a presence of DNA families similar to that obtained from any of the above-cited breeds. On the contrary, when the DNA used in W-CGH experiments was obtained from Assaf, as compared to either Castellana or Ojalada, two different pericentromeric DNA families of highly repetitive sequences could be detected. Lastly, sex chromosomes were shown to be homogeneous among all breeds and thus revealed no detectable constitutive heterochromatin. W-CGH results were confirmed using DNA breakage detection-FISH experiments (DBD-FISH) carried out on lymphocytes. As a whole, the results showed that two different repetitive DNA families are present in the pericentromeric heterochromatin of the sheep breeds studied here. Additionally, they suggest a differential presence of these distinct repetitive DNA families in Castellana and Ojalada breeds as compared to the Assaf breed. Finally, the results of W-CGH after using mouflon as the targeted chromosomes also show that the two DNA families are present in the ancestor.

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Section: Discussionmentioning

confidence: 63%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

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Whole-comparative genomic hybridization in domestic sheep <i>(Ovis aries)</i> breeds

Dávila-Rodríguez

Cortés‐Gutiérrez

López‐Fernández

et al. 2009

Cytogenet Genome Res

Self Cite

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“…In addition, this method permits in a single experiment detection of differences in composition and relative amounts, as well as chromosome mapping of the highly repeated DNAs when comparing 2 different genomes. Therefore, W-CGH provides information on different populations belonging to closely related taxa [same species, sub-species or breeds: see Pita et al, 2003Pita et al, , 2007Pita et al, , 2008aDavila-Rodriguez et al, 2009] or when comparing closely related species. We took advantage of the potential of W-CGH, using human/gorilla genomes to assess whether highly repetitive DNA sequences show similarities and/or differences in the centromeric regions of both chromosome complements.…”

Section: A Highly Conserved Pericentromeric Domain In Human and Gorilmentioning

confidence: 99%

A Highly Conserved Pericentromeric Domain in Human and Gorilla Chromosomes

Pita

Gosálvez²,

Gosálvez³

et al. 2009

Cytogenet Genome Res

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Significant similarity between human and gorilla genomes has been found in all chromosome arms, but not in centromeres, using whole-comparative genomic hybridization (W-CGH). In human chromosomes, centromeric regions, generally containing highly repetitive DNAs, are characterized by the presence of specific human DNA sequences and an absence of homology with gorilla DNA sequences. The only exception is the pericentromeric area of human chromosome 9, which, in addition to a large block of human DNA, also contains a region of homology with gorilla DNA sequences; the localization of these sequences coincides with that of human satellite III. Since highly repetitive DNAs are known for their high mutation frequency, we hypothesized that the chromosome 9 pericentromeric DNA conserved in human chromosomes and deriving from the gorilla genome may thus play some important functional role.

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Nuclear architecture of resting and LPS-stimulated porcine neutrophils by 3D FISH

et al. 2009

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Neutrophils are essential components of the innate immune system due to their ability to kill and phagocytose invading microbes. They possess a lobulated nucleus and are capable of extensive and complex changes in response to bacterial stimulation. The aim of our study was to investigate whether the 3D nuclear organization of porcine neutrophils was modified upon stimulation. The organization of centromeres, telomeres, and chromosome territories (chromosomes 2, 3, 7, 8, 12, 13, and 17) was studied on structurally preserved nuclei using 3D fluorescence in situ hybridization, confocal microscopy, and image analysis. By differential labeling of centromeres of acrocentric and metacentric/submetacentric chromosomes, we showed that centromeres associated to form chromocenters but did so preferentially between chromosomes with the same morphology. Upon activation, some of these chromocenters dispersed. Telomeres were also found to form clusters, but their number remained unchanged in lipopolysaccharide-stimulated neutrophils. The analysis of the position of chromocenters and telomere clusters showed a more internal location of the latter compared to the former. The analysis of chromosome territories revealed that homologs were distributed randomly among lobes whatever the cell's status. The volume of these territories was not proportional to chromosome length, and some chromosomes (chr 3, 12, 13, and 17) were more prone to decondensation when neutrophils were stimulated. Thus, our study demonstrated that activation of neutrophils resulted in several modifications of their nuclear architecture: a decrease in the number of non-acrocentric chromocenters and the decondensation of several chromosomes.

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Differential expansion of highly repeated DNA sequences in the swine subgenomes

Cited by 6 publications

References 11 publications

Whole-comparative genomic hybridization in domestic sheep <i>(Ovis aries)</i> breeds

Whole-comparative genomic hybridization in domestic sheep <i>(Ovis aries)</i> breeds

A Highly Conserved Pericentromeric Domain in Human and Gorilla Chromosomes

Nuclear architecture of resting and LPS-stimulated porcine neutrophils by 3D FISH

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