A Mutation of the Yeast Gene Encoding PCNA Destabilizes Both Microsatellite and Minisatellite DNA Sequences

AbstractThe POL30 gene of the yeast Saccharomyces cerevisiae encodes the proliferating cell nuclear antigen (PCNA), a protein required for processive DNA synthesis by DNA polymerase δ and ϵ. We examined the effects of the pol30-52 mutation on the stability of microsatellite (1- to 8-bp repeat units) and minisatellite (20-bp repeat units) DNA sequences. It had previously been shown that this mutation destabilizes dinucleotide repeats 150-fold and that this effect is primarily due to defects in DNA mismatch repair. From our analysis of the effects of pol30-52 on classes of repetitive DNA with longer repeat unit lengths, we conclude that this mutation may also elevate the rate of DNA polymerase slippage. The effect of pol30-52 on tracts of repetitive DNA with large repeat unit lengths was similar, but not identical, to that observed previously for pol3-t, a temperature-sensitive mutation affecting DNA polymerase δ. Strains with both pol30-52 and pol3-t mutations grew extremely slowly and had minisatellite mutation rates considerably greater than those observed in either single mutant strain.

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Destabilization of Yeast Micro- and Minisatellite DNA Sequences by Mutations Affecting a Nuclease Involved in Okazaki Fragment Processing (rad27) and DNA Polymerase δ (pol3-t)

Molecular and Cellular Biology ◽

10.1128/mcb.18.5.2779 ◽

1998 ◽

Vol 18 (5) ◽

pp. 2779-2788 ◽

Cited By ~ 120

Author(s):

Robert J. Kokoska ◽

Lela Stefanovic ◽

Hiep T. Tran ◽

Michael A. Resnick ◽

Dmitry A. Gordenin ◽

...

Keyword(s):

Dna Polymerase ◽

Dna Sequences ◽

Minisatellite Dna ◽

Dna Polymerase Δ ◽

Repeat Units ◽

Okazaki Fragment Processing ◽

Mutant Strains ◽

Synthetically Lethal ◽

The Stability ◽

Stimulation Of

ABSTRACT We examined the effects of mutations in the Saccharomyces cerevisiae RAD27 (encoding a nuclease involved in the processing of Okazaki fragments) and POL3 (encoding DNA polymerase δ) genes on the stability of a minisatellite sequence (20-bp repeats) and microsatellites (1- to 8-bp repeat units). Both therad27 and pol3-t mutations destabilized both classes of repeats, although the types of tract alterations observed in the two mutant strains were different. The tract alterations observed in rad27 strains were primarily additions, and those observed in pol3-t strains were primarily deletions. Measurements of the rates of repetitive tract alterations in strains with both rad27 and pol3-t indicated that the stimulation of microsatellite instability by rad27 was reduced by the effects of the pol3-t mutation. We also found that rad27 and pol3-01 (an allele carrying a mutation in the “proofreading” exonuclease domain of DNA polymerase δ) mutations were synthetically lethal.

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A MAJOR ROLE FOR BACTERIOPHAGE T4 DNA POLYMERASE IN FRAMESHIFT MUTAGENESIS

Genetics ◽

10.1093/genetics/103.3.353 ◽

1983 ◽

Vol 103 (3) ◽

pp. 353-366

Author(s):

Lynn S Ripley ◽

Nadja B Shoemaker

Keyword(s):

Dna Polymerase ◽

Dna Sequences ◽

Frameshift Mutation ◽

Bacteriophage T4 ◽

Base Substitution ◽

Temperature Sensitive ◽

Polymerase Gene ◽

Frameshift Mutagenesis ◽

Substitution Mutations ◽

Polymerase Mutants

ABSTRACT T4 DNA polymerase strongly influences the frequency and specificity of frameshift mutagenesis. Fifteen of 19 temperature-sensitive alleles of the DNA polymerase gene substantially influenced the reversion frequencies of frameshift mutations measured in the T4 rII genes. Most polymerase mutants increased frameshift frequencies, but a few alleles (previously noted as antimutators for base substitution mutations) decreased the frequencies of certain frameshifts while increasing the frequencies of others. The various patterns of enhanced or decreased frameshift mutation frequencies suggest that T4 DNA polymerase is likely to play a variety of roles in the metabolic events leading to frameshift mutation. A detailed genetic study of the specificity of the mutator properties of three DNA polymerase alleles (tsL56, tsL98 and tsL88) demonstrated that each produces a distinctive frameshift spectrum. Differences in frameshift frequencies at similar DNA sequences within the rII genes, the influence of mutant polymerase alleles on these frequencies, and the presence or absence of the dinucleotide sequence associated with initiation of Okazaki pieces at the frameshift site has led us to suggest that the discontinuities associated with discontinuous DNA replication may contribute to spontaneous frameshift mutation frequencies in T4.

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Isolation of a Pericentromeric Satellite DNA Family in Chnootriba argus (Henosepilachna argus) with an Unusual Short Repeat Unit (TTAAAA) for Beetles

Insects ◽

10.3390/insects10090306 ◽

2019 ◽

Vol 10 (9) ◽

pp. 306 ◽

Cited By ~ 1

Author(s):

Pablo Mora ◽

Jesús Vela ◽

Areli Ruiz-Mena ◽

Teresa Palomeque ◽

Pedro Lorite

Keyword(s):

Repetitive Dna ◽

Satellite Dna ◽

Repeat Unit ◽

Pericentromeric Region ◽

Fish Analysis ◽

Agricultural Pests ◽

Base Pairs ◽

Satellite Dnas ◽

Repeat Units

Ladybird beetles (Coccinellidae) are one of the largest groups of beetles. Among them, some species are of economic interest since they can act as a biological control for some agricultural pests whereas other species are phytophagous and can damage crops. Chnootriba argus (Coccinellidae, Epilachnini) has large heterochromatic pericentromeric blocks on all chromosomes, including both sexual chromosomes. Classical digestion of total genomic DNA using restriction endonucleases failed to find the satellite DNA located on these heterochromatic regions. Cloning of C0t-1 DNA resulted in the isolation of a repetitive DNA with a repeat unit of six base pairs, TTAAAA. The amount of TTAAAA repeat in the C. argus genome was about 20%. Fluorescence in situ hybridization (FISH) analysis and digestion of chromosomes with the endonuclease Tru9I revealed that this repetitive DNA could be considered as the putative pericentromeric satellite DNA (satDNA) in this species. The presence of this satellite DNA was tested in other species of the tribe Epilachnini and it is also present in Epilachna paenulata. In both species, the TTAAAA repeat seems to be the main satellite DNA and it is located on the pericentromeric region on all chromosomes. The size of this satDNA, which has only six base pairs is unusual in Coleoptera satellite DNAs, where satDNAs usually have repeat units of a much larger size. Southern hybridization and FISH proved that this satDNA is conserved in some Epilachnini species but not in others. This result is in concordance with the controversial phylogenetic relationships among the genera of the tribe Epilachnini, where the limits between genera are unclear.

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Distinct pools of proliferating cell nuclear antigen associated to DNA replication sites interact with the p125 subunit of DNA polymerase δ or DNA ligase I

Experimental Cell Research ◽

10.1016/j.yexcr.2003.10.025 ◽

2004 ◽

Vol 293 (2) ◽

pp. 357-367 ◽

Cited By ~ 21

Author(s):

Federica Riva ◽

Monica Savio ◽

Ornella Cazzalini ◽

Lucia A Stivala ◽

Ivana A Scovassi ◽

...

Keyword(s):

Dna Replication ◽

Dna Polymerase ◽

Proliferating Cell Nuclear Antigen ◽

Nuclear Antigen ◽

Dna Ligase ◽

Dna Polymerase Δ ◽

Dna Ligase I ◽

Replication Sites ◽

Proliferating Cell

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Identification of a Novel Protein, PDIP38, That Interacts with the p50 Subunit of DNA Polymerase δ and Proliferating Cell Nuclear Antigen

Journal of Biological Chemistry ◽

10.1074/jbc.m208694200 ◽

2003 ◽

Vol 278 (12) ◽

pp. 10041-10047 ◽

Cited By ~ 66

Author(s):

Li Liu ◽

Esther M. Rodriguez-Belmonte ◽

Nayef Mazloum ◽

Bin Xie ◽

Marietta Y. W. T. Lee

Keyword(s):

Dna Polymerase ◽

Proliferating Cell Nuclear Antigen ◽

Nuclear Antigen ◽

Dna Polymerase Δ ◽

Proliferating Cell ◽

Novel Protein

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Conservation of k-mer Composition and Correlation Contribution between Introns and Intergenic Regions of Animalia Genomes

Genes ◽

10.3390/genes9100482 ◽

2018 ◽

Vol 9 (10) ◽

pp. 482 ◽

Cited By ~ 5

Author(s):

Aaron Sievers ◽

Frederik Wenz ◽

Michael Hausmann ◽

Georg Hildenbrand

Keyword(s):

Dna Sequences ◽

Tandem Repeats ◽

Repeat Unit ◽

Full Range ◽

Correlation Coefficients ◽

Strong Correlations ◽

Sequence Structure ◽

Conserved Sequence ◽

Repeat Units ◽

Intergenic Regions

In this study, we pairwise-compared multiple genome regions, including genes, exons, coding DNA sequences (CDS), introns, and intergenic regions of 39 Animalia genomes, including Deuterostomia (27 species) and Protostomia (12 species), by applying established k-mer-based (alignment-free) comparison methods. We found strong correlations between the sequence structure of introns and intergenic regions, individual organisms, and within wider phylogenetical ranges, indicating the conservation of certain structures over the full range of analyzed organisms. We analyzed these sequence structures by quantifying the contribution of different sets of DNA words to the average correlation value by decomposing the correlation coefficients with respect to these word sets. We found that the conserved structures within introns, intergenic regions, and between the two were mainly a result of conserved tandem repeats with repeat units ≤ 2 bp (e.g., (AT)n), while other conserved sequence structures, such as those found between exons and CDS, were dominated by tandem repeats with repeat unit sizes of 3 bp in length and more complex DNA word patterns. We conclude that the conservation between intron and intergenic regions indicates a shared function of these sequence structures. Also, the similar differences in conserved structures with known origin, especially to the conservation between exons and CDS resulting from DNA codons, indicate that k-mer composition-based functional properties of introns and intergenic regions may differ from those of exons and CDS.

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