Evolution of low-copy number and major satellite DNA sequences coexisting in two Pimelia species-groups (Coleoptera)

We have analyzed the organization of the homogeneously staining regions (HSRs) in chromosomes from a methotrexate-resistant mouse melanoma cell line. Fluorescence in situ hybridization techniques were used to localize satellite DNA sequences and the amplified copies of the dihydrofolate reductase (DHFR) gene that confer drug-resistance, in combination with immunofluorescence using antibody probes to differentiate chromatin structure. We show that the major DNA species contained in the HSRs is mouse major satellite, confirming previous reports, and that this is interspersed with DHFR DNA in an alternating tandem array that can be resolved at the cytological level. Mouse minor satellite DNA, which is normally located at centromeres, is also distributed along the HSRs, but does not appear to interfere with centromere function. The blocks of major satellite DNA are coincident with chromatin domains that are labelled by an autoantibody that recognizes a mammalian homologue of Drosophila heterochromatin-associated protein 1, shown previously to be confined to centric heterochromatin in mouse. An antiserum that specifically recognizes acetylated histone H4, a marker for active chromatin, fails to bind to the satellite DNA domains, but labels the intervening segments containing DHFR DNA. We can find no evidence for the spreading of the inactive chromatin domains into adjacent active chromatin, even after extended passaging of cells in the absence of methotrexate selection.

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Detection of Unique or Low Copy Number DNA Sequences in Complex Genomes

New Nucleic Acid Techniques ◽

10.1385/0-89603-127-6:391 ◽

2003 ◽

pp. 391-400

Author(s):

Domingo Gallardo ◽

Albert Boronat

Keyword(s):

Dna Sequences ◽

Copy Number ◽

Low Copy Number Dna ◽

Low Copy Number

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Isolation of low-copy-number sequences that neighbor satellite DNA in mammals

Gene ◽

10.1016/0378-1119(86)90334-3 ◽

1986 ◽

Vol 50 (1-3) ◽

pp. 299-311

Author(s):

Antonella Maresca ◽

Ronald E. Thayer ◽

Chantal Guenet ◽

Maxine F. Singer

Keyword(s):

Satellite Dna ◽

Copy Number ◽

Low Copy Number ◽

Number Sequences

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Comparative study of satellite sequences and phylogeny of five species from the genus Palorus (Insecta, Coleoptera)

Genome ◽

10.1139/g00-035 ◽

2000 ◽

Vol 43 (5) ◽

pp. 776-785 ◽

Cited By ~ 3

Author(s):

Nevenka Meštrovic ◽

Brankica Mravinac ◽

Carlos Juan ◽

Ðurdica Ugarkovic ◽

Miroslav Plohl

Keyword(s):

Cytochrome Oxidase ◽

Satellite Dna ◽

Copy Number ◽

Tertiary Structure ◽

Cytochrome Oxidase I ◽

Dna Curvature ◽

Mitochondrial Cytochrome ◽

Satellite Sequences ◽

Low Copy Number ◽

Mitochondrial Cytochrome Oxidase

Major satellite sequences are analysed in the three tenebrionid beetles Palorus cerylonoides, P. genalis, and P. ficicola, and compared with the ones from P. ratzeburgii and P. subdepressus reported elsewhere. All of them are A+T rich, pericentromerically located, and with lengths of about 150 bp, either in the form of monomers or formed by more complex repeating units. A preliminary phylogenetic analysis of Palorus species using the 3' end of the mitochondrial Cytochrome Oxidase I gene shows that the five Palorus species have been diverging for a considerable amount of evolutionary time, with the pair P. ratzeburgii and P. genalis being the most closely related. Only these two taxa showed some similarity between their respective high-copy-number satellite sequences, while other satellites are mutually unrelated and might have originated independently. However, all the satellites have in common tertiary structure induced by intrinsic DNA curvature, a characteristic which is conserved within the genus. Palorus major satellites were previously detected in the genomes of congeneric species as low-copy-number clusters (Metrovic et al., Mol. Biol. Evol. 15: 1062-1068. 1998). Given the divergences between the analysed species, the substitution rate deduced from high- and low-copy-number repeats is unexpectedly low. The presence of sequence-induced DNA curvature in all Palorus satellites and similar satellite DNAs in the species pair P. ratzeburgii and P. genalis suggest (i) that constraints are at the tertiary structure; and (ii) that the satellite DNA evolutionary turnover can be dependant on the history of the taxa under study, resulting in retention of similar satellites in related taxa.Key words: satellite DNA, evolution, mitochondrial cytochrome oxidase I, DNA curvature.

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Detection of plant species-specific dna (barley and soybean) in blood, muscle tissue, organs and gastrointestinal contents of rabbit.

World Rabbit Science ◽

10.4995/wrs.2010.18.11 ◽

2010 ◽

Vol 18 (2) ◽

pp. 83 ◽

Cited By ~ 5

Author(s):

R. Tudisco ◽

S. Calabrò ◽

F. Bovera ◽

M.I. Cutrignelli ◽

A. Nizza ◽

...

Keyword(s):

Muscle Tissue ◽

Dna Sequences ◽

Soybean Meal ◽

Copy Number ◽

Barley Grain ◽

Melting Curve Analysis ◽

Rrna Gene ◽

Plant Dna ◽

Low Copy Number ◽

Soybean Lectin

The aim of this study was to detect plant DNA sequences from low copy number genes of barley grain and soybean meal, the latter being subjected to solvent extraction process, in blood, liver, kidney, spleen, muscle tissue and digesta (duodenum, caecum and faeces from rectal ampulla) of rabbits. For fattening, Hyla rabbits (20 males and 20 females) were fed a diet including barley grain (15%) and soybean meal (12%). Animals were slaughtered at 74 d of age (2 ± 0.2 kg live weight) and samples collected from each animal. The quality of each DNA sample was verified using the UNIV P/Q primers used to amplify a mammalian specifi c portion of mtDNA 16S rRNA gene. The presence of plant DNA was subsequently ascertained on the same DNA samples, as well as on barley and soybean (control). Two classes of plant DNA sequences were monitored via real-time PCR, using SYBR® Green I Dye: a high copy number chloroplast gene (trnl) and a low copy number specific for barley (metal-dependent hydrolase-like protein) and soybean (lectin) genes. Melting curve analysis was used to identify the PCR products. The chloroplast fragment detection frequency was higher (P<0.01) in muscle (90%), liver (80%), kidney (80%) and spleen (80%) than in blood (40%) and digesta samples. In the latter, chloroplast DNA was found in 40 and 30% of duodenum and caecum contents respectively, and in 30% of faeces. The specificity of the amplicons obtained was checked by sequencing and annotation. In the samples positive for chloroplast fragments, the frequency of detection of barley specific sequence was higher (P<0.01) in liver (62.5%), kidney (62.5%), spleen (62.5%) and digesta (100%) than in blood (25%) and muscle (22.2%) samples. The soybean lectin gene was not detected in animal samples, although it was seen in plant samples. Results confirm that, except for gastrointestinal tract (GIT), plant single copy genes are more difficult to identify in animal samples.

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Quantitative evolution of transposable and satellite DNA sequences in Picea species

Genome ◽

10.1139/g11-007 ◽

2011 ◽

Vol 54 (5) ◽

pp. 431-435 ◽

Cited By ~ 2

Author(s):

V. Sarri ◽

M. Ceccarelli ◽

P.G. Cionini

Keyword(s):

Dna Sequences ◽

Satellite Dna ◽

Copy Number ◽

Genomic Dna ◽

Common Factor ◽

Dot Blot ◽

Dna Library ◽

Picea Pungens ◽

Distinct Sequence ◽

Picea Species

Clones containing tandemly arranged repeats belonging to two distinct sequence families, (i) PAG004P22F (2F) and PAG004E03C (3C) or (ii) Ty3/gypsy- (8R; PAG004B08R) and Ty1/copia-like sequences (9R; PAG007F19R), were selected from a randomly sheared total genomic DNA library of Picea abies . The inserts were used as probes in dot-blot hybridizations to genomic DNA of P. abies, Picea orientalis , Picea pungens , and Picea pungens var. glauca. All these entities are diploid and share the same chromosome number (2n = 24), but the genome sizes differ largely. The redundancy (copy number per 1C DNA) of sequences related to each probe varied greatly between the genomes. No significant correlation was found between the genome size and the copy number of sequences in any family. The quantitative ratios varied greatly (in each genome) between the two families of satellite DNA, between the sequences that represented copia or gypsy retrotransposons, and between tandemly arranged sequences and retroelements as a whole, suggesting that there is no common factor that controls the quantitative evolution of repeats belonging to different sequence families during speciation in Picea.

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CENP-B binds a novel centromeric sequence in the Asian mouse Mus caroli.

Molecular and Cellular Biology ◽

10.1128/mcb.15.8.4009 ◽

1995 ◽

Vol 15 (8) ◽

pp. 4009-4020 ◽

Cited By ~ 59

Author(s):

D Kipling ◽

A R Mitchell ◽

H Masumoto ◽

H E Wilson ◽

L Nicol ◽

...

Keyword(s):

Dna Sequences ◽

Satellite Dna ◽

Binding Sites ◽

Hybrid Cell ◽

Mobility Shift ◽

Major Satellite ◽

Mus Caroli ◽

Centromeric Sequence

Minor satellite DNA, found at Mus musculus centromeres, is not present in the genome of the Asian mouse Mus caroli. This repetitive sequence family is speculated to have a role in centromere function by providing an array of binding sites for the centromere-associated protein CENP-B. The apparent absence of CENP-B binding sites in the M. caroli genome poses a major challenge to this hypothesis. Here we describe two abundant satellite DNA sequences present at M. caroli centromeres. These satellites are organized as tandem repeat arrays, over 1 Mb in size, of either 60- or 79-bp monomers. All autosomes carry both satellites and small amounts of a sequence related to the M. musculus major satellite. The Y chromosome contains small amounts of both major satellite and the 60-bp satellite, whereas the X chromosome carries only major satellite sequences. M. caroli chromosomes segregate in M. caroli x M. musculus interspecific hybrid cell lines, indicating that the two sets of chromosomes can interact with the same mitotic spindle. Using a polyclonal CENP-B antiserum, we demonstrate that M. caroli centromeres can bind murine CENP-B in such an interspecific cell line, despite the absence of canonical 17-bp CENP-B binding sites in the M. caroli genome. Sequence analysis of the 79-bp M. caroli satellite reveals a 17-bp motif that contains all nine bases previously shown to be necessary for in vitro binding of CENP-B. This M. caroli motif binds CENP-B from HeLa cell nuclear extract in vitro, as indicated by gel mobility shift analysis. We therefore suggest that this motif also causes CENP-B to associate with M. caroli centromeres in vivo. Despite the sequence differences, M. caroli presents a third, novel mammalian centromeric sequence producing an array of binding sites for CENP-B.

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