Localization of Repetitive DNA Sequences on in vitro Xenopus laevis Chromosomes by Primed in situ Labeling (PRINS)

AbstractThe tetraploid Avena species in the section Pachycarpa Baum, including A. insularis, A. maroccana, and A. murphyi, are thought to be involved in the evolution of hexaploid oats; however, their genome designations are still being debated. Repetitive DNA sequences play an important role in genome structuring and evolution, so understanding the chromosomal organization and distribution of these sequences in Avena species could provide valuable information concerning genome evolution in this genus. In this study, the chromosomal organizations and distributions of six repetitive DNA sequences (including three SSR motifs (TTC, AAC, CAG), one 5S rRNA gene fragment, and two oat A and C genome specific repeats) were investigated using non-denaturing fluorescence in situ hybridization (ND-FISH) in the three tetraploid species mentioned above and in two hexaploid oat species. Preferential distribution of the SSRs in centromeric regions was seen in the A and D genomes, whereas few signals were detected in the C genomes. Some intergenomic translocations were observed in the tetraploids; such translocations were also detected between the C and D genomes in the hexaploids. These results provide robust evidence for the presence of the D genome in all three tetraploids, strongly suggesting that the genomic constitution of these species is DC and not AC, as had been thought previously.

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Response of Sulfolobus solfataricus Dpo4 polymerase in vitro to a DNA G-quadruplex

Mutagenesis ◽

10.1093/mutage/gez010 ◽

2019 ◽

Vol 34 (3) ◽

pp. 289-297 ◽

Cited By ~ 1

Author(s):

Alexandra Berroyer ◽

Gloria Alvarado ◽

Erik D Larson

Keyword(s):

Repetitive Dna ◽

Dna Sequences ◽

Sulfolobus Solfataricus ◽

Repetitive Dna Sequences ◽

Polymerase Eta ◽

G4 Dna ◽

G Quadruplex ◽

Dna Polymerase Iv ◽

Y Family

Abstract Repetitive DNA sequences support the formation of structures that can interrupt replication and repair, leading to breaks and mutagenesis. One particularly stable structure is G-quadruplex (G4) DNA, which is four-stranded and formed from tandemly repetitive guanine bases. When folded within a template, G4 interferes with DNA synthesis. Similar to non-duplex structures, DNA base lesions can also halt an advancing replication fork, but the Y-family polymerases solve this problem by bypassing the damage. In order to better understand how guanine-rich DNA is replicated, we have investigated the activity of the model Y-family polymerase, Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4), on guanine-rich templates in vitro. We find that Dpo4 progression on templates containing either a single GC-rich hairpin or a G4 DNA structure is greatly reduced and synthesis stalls at the structure. Human polymerase eta (hPol eta) showed the same pattern of stalling at G4; however, and in contrast to Klenow, hPol eta and Dpo4 partially synthesise into the guanine repeat. Substitution of the nucleotide selectivity residue in Dpo4 with alanine permitted ribonucleotide incorporation on unstructured templates, but this further reduced the ability of Dpo4 to synthesise across from the guanine repeats. The advancement of Dpo4 on G4 templates was highest when the reaction was supplied with only deoxycytidine triphosphate, suggesting that high-fidelity synthesis is favoured over misincorporation. Our results are consistent with a model where the Y-family polymerases pause upon encountering G4 structures but have an ability to negotiate some synthesis through tetrad-associated guanines. This suggests that the Y-family polymerases reduce mutagenesis by catalysing the accurate replication of repetitive DNA sequences, but most likely in concert with additional replication and structure resolution activities.

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The pachytene chromosomes of maize as revealed by fluorescence in situ hybridization with repetitive DNA sequences

Theoretical and Applied Genetics ◽

10.1007/s001220051445 ◽

2000 ◽

Vol 101 (1-2) ◽

pp. 30-36 ◽

Cited By ~ 32

Author(s):

C. C. Chen ◽

C. M. Chen ◽

F. C. Hsu ◽

C. J. Wang ◽

J. T. Yang ◽

...

Keyword(s):

In Situ Hybridization ◽

Fluorescence In Situ Hybridization ◽

Repetitive Dna ◽

Dna Sequences ◽

Repetitive Dna Sequences

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Genome differentiation in Aegilops. 1. Distribution of highly repetitive DNA sequences on chromosomes of diploid species

Genome ◽

10.1139/g96-040 ◽

1996 ◽

Vol 39 (2) ◽

pp. 293-306 ◽

Cited By ~ 107

Author(s):

Ekaterina D. Badaeva ◽

Bernd Friebe ◽

Bikram S. Gill

Keyword(s):

In Situ Hybridization ◽

Repetitive Dna ◽

Dna Sequences ◽

Repetitive Dna Sequences ◽

Aegilops Species ◽

D Genome ◽

C Banding ◽

Genome Differentiation ◽

Highly Repetitive Dna

Genome differentiation in 12 diploid Aegilops species was analyzed using in situ hybridization with the highly repetitive DNA sequences pSc119 and pAs1 and C-banding. Chromosomes of all these diploid Aegilops species hybridized with the pSc119 probe; however, the level of hybridization and labeling patterns differed among genomes. Only four species (Ae. squarrosa, Ae. comosa, Ae. heldreichii, and Ae. uniaristata) showed distinct hybridization with pAs1. The labeling patterns were species-specific and chromosome-specific. Differences in in situ hybridization (ISH) patterns, also observed by C-banding, exist between the karyotypes of Ae. comosa and Ae. heldreichii, suggesting that they are separate, although closely related, subspecies. The S genome of Ae. spelioides was most similar to the B and G genomes of polyploid wheats on the basis of both C-banding and ISH patterns, but was different from other species of section Sitopsis. These species had different C-banding patterns but they were similar to each other and to Ae. mutica in the distribution of pSc119 hybridization sites. Two types of labeling were detected in Ae. squarrosa with the pAs1 probe. The first resembled that of the D-genome chromosomes of bread wheat, Triticum aestivum L. em. Thell., while the second was similar to the D genome of some of the polyploid Aegilops species. Relationships among diploid Aegilops species and the possible mechanisms of genome differentiation are discussed. Key words : wheat, Triticum, Aegilops, in situ hybridization, C-banding, evolution.

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Flow cytometric quantification of human chromosome specific repetitive DNA sequences by single and bicolor fluorescent in situ hybridization to lymphocyte interphase nuclei

Cytometry ◽

10.1002/cyto.990110118 ◽

1990 ◽

Vol 11 (1) ◽

pp. 153-164 ◽

Cited By ~ 26

Author(s):

H. van Dekken ◽

G. J. A. Arkesteijn ◽

J. W. M. Visser ◽

J. G. J. Bauman

Keyword(s):

In Situ Hybridization ◽

Human Chromosome ◽

Repetitive Dna ◽

Dna Sequences ◽

Fluorescent In Situ Hybridization ◽

Repetitive Dna Sequences ◽

Interphase Nuclei ◽

Flow Cytometric

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New evidence confirming the CD genomic constitutions of the tetraploid Avena species in the section Pachycarpa Baum

PLoS ONE ◽

10.1371/journal.pone.0240703 ◽

2021 ◽

Vol 16 (1) ◽

pp. e0240703

Author(s):

Honghai Yan ◽

Zichao Ren ◽

Di Deng ◽

Kehan Yang ◽

Chuang Yang ◽

...

Keyword(s):

Repetitive Dna ◽

Dna Sequences ◽

Rrna Gene ◽

Repetitive Dna Sequences ◽

D Genome ◽

Intergenomic Translocations ◽

5S Rrna Gene ◽

New Evidence ◽

Robust Evidence

The tetraploid Avena species in the section Pachycarpa Baum, including A. insularis, A. maroccana, and A. murphyi, are thought to be involved in the evolution of hexaploid oats; however, their genome designations are still being debated. Repetitive DNA sequences play an important role in genome structuring and evolution, so understanding the chromosomal organization and distribution of these sequences in Avena species could provide valuable information concerning genome evolution in this genus. In this study, the chromosomal organizations and distributions of six repetitive DNA sequences (including three SSR motifs (TTC, AAC, CAG), one 5S rRNA gene fragment, and two oat A and C genome specific repeats) were investigated using non-denaturing fluorescence in situ hybridization (ND-FISH) in the three tetraploid species mentioned above and in two hexaploid oat species. Preferential distribution of the SSRs in centromeric regions was seen in the A and D genomes, whereas few signals were detected in the C genomes. Some intergenomic translocations were observed in the tetraploids; such translocations were also detected between the C and D genomes in the hexaploids. These results provide robust evidence for the presence of the D genome in all three tetraploids, strongly suggesting that the genomic constitution of these species is DC and not AC, as had been thought previously.

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