scholarly journals Mitotic systemic genomic instability in yeast

2017 ◽  
Author(s):  
Nadia M. V. Sampaio ◽  
Aline Rodrigues-Prause ◽  
V. P. Ajith ◽  
Theodore M. Gurol ◽  
Mary J. Chapman ◽  
...  
Keyword(s):  
Genomic Instability ◽  
Loss Of Heterozygosity ◽  
Chromosomal Instability ◽  
Experimental Approach ◽  
Human Cancer ◽  
Chromosomal Rearrangements ◽  
Point Mutations ◽  
Genomic Variation ◽  
Genomic Disorder ◽  
Structural Genomic

ABSTRACTConventional models of genome evolution generally include the assumption that mutations accumulate gradually and independently over time. We characterized the occurrence of sudden spikes in the accumulation of genome-wide loss-of-heterozygosity (LOH) inSaccharomyces cerevisiae, suggesting the existence of a mitotic systemic genomic instability process (mitSGI). We characterized the emergence of a rough colony morphology phenotype resulting from an LOH event spanning a specific locus (ACE2/ace2-A7). Surprisingly, half of the clones analyzed also carried unselected secondary LOH tracts elsewhere in their genomes. The number of secondary LOH tracts detected was 20-fold higher than expected assuming independence between mutational events. Secondary LOH tracts were not detected in control clones without a primary selected LOH event. We then measured the rates of single and double LOH at different chromosome pairs and found that coincident LOH accumulated at rates 30-100 fold higher than expected if the two underlying single LOH events occurred independently. These results were consistent between two different strain backgrounds, and in mutant strains incapable of entering meiosis. Our results indicate that a subset of mitotic cells within a population experience systemic genomic instability episodes, resulting in multiple chromosomal rearrangements over one or few generations. They are reminiscent of early reports from the classic yeast genetics literature, as well as recent studies in humans, both in the cancer and genomic disorder contexts, all of which challenge the idea of gradual accumulation of structural genomic variation. Our experimental approach provides a model to further dissect the fundamental mechanisms responsible for mitSGI.SIGNIFICANCE STATEMENTPoint mutations and alterations in chromosome structure are generally thought to accumulate gradually and independently over many generations. Here, we combined complementary genetic approaches in budding yeast to track the appearance of chromosomal changes resulting in loss-of-heterozygosity (LOH). Contrary to expectations, our results provided evidence for the occurrence of non-independent accumulation of multiple LOH events over one or a few cell generations. These results are analogous to recent reports of bursts of chromosomal instability in humans. Our experimental approach provides a framework to further dissect the fundamental mechanisms underlying systemic chromosomal instability processes, including in the human cancer and genomic disorder contexts.

scholarly journals Characterization of systemic genomic instability in budding yeast

2020 ◽  
Author(s):  
Nadia M. V. Sampaio ◽  
V. P. Ajith ◽  
Ruth A. Watson ◽  
Lydia R. Heasley ◽  
Parijat Chakraborty ◽  
...  
Keyword(s):  
Experimental Model ◽  
Genomic Instability ◽  
Loss Of Heterozygosity ◽  
Time Window ◽  
Budding Yeast ◽  
Mutation Accumulation ◽  
Genomic Variation ◽  
Biological Processes ◽  
Whole Genome Analysis ◽  
Structural Genomic

ABSTRACTConventional models of genome evolution are centered around the principle that mutations form independently of each other and build up slowly over time. We characterized the occurrence of bursts of genome-wide loss-of-heterozygosity (LOH) in Saccharomyces cerevisiae, providing support for an additional non-independent and faster mode of mutation accumulation. We initially characterized a yeast clone isolated for carrying an LOH event at a specific chromosome site, and surprisingly, found that it also carried multiple unselected rearrangements elsewhere in its genome. Whole genome analysis of over 100 additional clones selected for carrying primary LOH tracts revealed that they too contained unselected structural alterations more often than control clones obtained without any selection. We also measured the rates of coincident LOH at two different chromosomes and found that double LOH formed at rates 14-150 fold higher than expected if the two underlying single LOH events occurred independently of each other. These results were consistent across different strain backgrounds, and in mutants incapable of entering meiosis. Our results indicate that a subset of mitotic cells within a population can experience discrete episodes of systemic genomic instability, when the entire genome becomes vulnerable and multiple chromosomal alterations can form over a narrow time window. They are reminiscent of early reports from the classic yeast genetics literature, as well as recent studies in humans, both in the cancer and genomic disorder contexts. The experimental model we describe provides a system to further dissect the fundamental biological processes responsible for punctuated bursts of structural genomic variation.SIGNIFICANCE STATEMENTMutations are generally thought to accumulate independently and gradually over many generations. Here, we combined complementary experimental approaches in budding yeast to track the appearance of chromosomal changes resulting in loss-of-heterozygosity (LOH). In contrast to the prevailing model, our results provide evidence for the existence of a path for non-independent accumulation of multiple chromosomal alteration events over few generations. These results are analogous to recent reports of bursts of genomic instability in human cells. The experimental model we describe provides a system to further dissect the fundamental biological processes underlying such punctuated bursts of mutation accumulation.

scholarly journals Characterization of systemic genomic instability in budding yeast

2020 ◽  
Vol 117 (45) ◽  
pp. 28221-28231 ◽  
Author(s):  
Nadia M. V. Sampaio ◽  
V. P. Ajith ◽  
Ruth A. Watson ◽  
Lydia R. Heasley ◽  
Parijat Chakraborty ◽  
...  
Keyword(s):  
Genomic Instability ◽  
Time Window ◽  
Genomic Variation ◽  
Genomic Disorder ◽  
Whole Genome Analysis ◽  
Entire Genome ◽  
Structural Genomic ◽  
Genome Wide ◽  
Conventional Models

Conventional models of genome evolution are centered around the principle that mutations form independently of each other and build up slowly over time. We characterized the occurrence of bursts of genome-wide loss-of-heterozygosity (LOH) inSaccharomyces cerevisiae, providing support for an additional nonindependent and faster mode of mutation accumulation. We initially characterized a yeast clone isolated for carrying an LOH event at a specific chromosome site, and surprisingly found that it also carried multiple unselected rearrangements elsewhere in its genome. Whole-genome analysis of over 100 additional clones selected for carrying primary LOH tracts revealed that they too contained unselected structural alterations more often than control clones obtained without any selection. We also measured the rates of coincident LOH at two different chromosomes and found that double LOH formed at rates 14- to 150-fold higher than expected if the two underlying single LOH events occurred independently of each other. These results were consistent across different strain backgrounds and in mutants incapable of entering meiosis. Our results indicate that a subset of mitotic cells within a population can experience discrete episodes of systemic genomic instability, when the entire genome becomes vulnerable and multiple chromosomal alterations can form over a narrow time window. They are reminiscent of early reports from the classic yeast genetics literature, as well as recent studies in humans, both in cancer and genomic disorder contexts. The experimental model we describe provides a system to further dissect the fundamental biological processes responsible for punctuated bursts of structural genomic variation.

scholarly journals SPOP mutation leads to genomic instability in prostate cancer

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Gunther Boysen ◽  
Christopher E Barbieri ◽  
Davide Prandi ◽  
Mirjam Blattner ◽  
Sung-Suk Chae ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Genomic Instability ◽  
Human Cancer ◽  
Chromosomal Rearrangements ◽  
Strand Break ◽  
Common Mechanism ◽  
Dsb Repair ◽  
Structural Genomic ◽  
Prostate Tumorigenesis

Genomic instability is a fundamental feature of human cancer often resulting from impaired genome maintenance. In prostate cancer, structural genomic rearrangements are a common mechanism driving tumorigenesis. However, somatic alterations predisposing to chromosomal rearrangements in prostate cancer remain largely undefined. Here, we show that SPOP, the most commonly mutated gene in primary prostate cancer modulates DNA double strand break (DSB) repair, and that SPOP mutation is associated with genomic instability. In vivo, SPOP mutation results in a transcriptional response consistent with BRCA1 inactivation resulting in impaired homology-directed repair (HDR) of DSB. Furthermore, we found that SPOP mutation sensitizes to DNA damaging therapeutic agents such as PARP inhibitors. These results implicate SPOP as a novel participant in DSB repair, suggest that SPOP mutation drives prostate tumorigenesis in part through genomic instability, and indicate that mutant SPOP may increase response to DNA-damaging therapeutics.

scholarly journals Clonal analysis of delayed karyotypic abnormalities and gene mutations in radiation-induced genetic instability.

1996 ◽  
Vol 16 (11) ◽  
pp. 6252-6262 ◽  
Author(s):  
A J Grosovsky ◽  
K K Parks ◽  
C R Giver ◽  
S L Nelson
Keyword(s):  
Loss Of Heterozygosity ◽  
Genetic Instability ◽  
Chromosomal Instability ◽  
Chromosomal Abnormalities ◽  
Chromosomal Rearrangements ◽  
Marker Locus ◽  
High Rate ◽  
Telomeric Region ◽  
Karyotypic Analysis ◽  
Radiation Induced

Many tumors exhibit extensive chromosomal instability, but karyotypic alterations will be significant in carcinogenesis only by influencing specific oncogenes or tumor suppressor loci within the affected chromosomal segments. In this investigation, the specificity of chromosomal rearrangements attributable to radiation-induced genomic instability is detailed, and a qualitative and quantitative correspondence with mutagenesis is demonstrated. Chromosomal abnormalities preferentially occurred near the site of prior rearrangements, resulting in complex abnormalities, or near the centromere, resulting in deletion or translocation of the entire chromosome arm, but no case of an interstitial chromosomal deletion was observed. Evidence for chromosomal instability in the progeny of irradiated cells also included clonal karyotypic heterogeneity. The persistence of instability was demonstrated for at least 80 generations by elevated mutation rates at the heterozygous, autosomal marker locus tk. Among those TK- mutants that showed a loss of heterozygosity, a statistically significant increase in mutation rate was observed only for those in which the loss of heterozygosity encompasses the telomeric region. This mutational specificity corresponds with the prevalence of terminal deletions, additions, and translocations, and the absence of interstitial deletions, in karyotypic analysis. Surprisingly, the elevated rate of TK- mutations is also partially attributable to intragenic base substitutions and small deletions, and DNA sequence analysis of some of these mutations is presented. Complex chromosomal abnormalities appear to be the most significant indicators of a high rate of persistent genetic instability which correlates with increased rates of both intragenic and chromosomal-scale mutations at tk.

scholarly journals Using Telomeric Length Measurements and Methylation to Understand The Karyotype Diversification of Ctenomys Minutus (A Small Fossorial Mammals)

2021 ◽  
Author(s):  
Cristina A. Matzenbacher ◽  
Juliana Silva ◽  
Ana Leticia H. Garcia ◽  
Rafael Kretschmer ◽  
Mónica Cappetta ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Genomic Instability ◽  
Chromosomal Instability ◽  
Diploid Number ◽  
Karyotype Evolution ◽  
Chromosomal Rearrangements ◽  
Global Dna Methylation ◽  
Methylated Dna ◽  
Significant Difference ◽  
Length Measurements

Abstract The genus Ctenomys has been widely used in karyotype evolution studies due to the variation in their diploid numbers (2n), which range from 2n = 10 to 2n = 70. Ctenomys minutus is characterized by intraspecific variation in diploid number (2n = 42, 46, 48, and 50), which makes it an interesting model to investigate the genomic instability mechanisms that have led to different cytotypes in this species. We aimed to contribute to the knowledge about telomeres’ role in chromosomal instability and global DNA methylation in the genome evolution of C. minutus. This study found that telomere length differs between cytotypes, but only for females (50a<46a,48a,42), although methylation was also higher, no significant difference was shown. It was also shown that young individuals, regardless of cytotype, had the longest telomere and the most methylated DNA, although only the last was statistically significant. Despite this, there is still much to be answered, although new cytotypes seem to have emerged within the distribution of parental cytotypes by the accumulation of different chromosomal rearrangements.

scholarly journals Independent Mechanisms Lead to Genomic Instability in Hodgkin Lymphoma: Microsatellite or Chromosomal Instability

Cancers ◽  
2018 ◽  
Vol 10 (7) ◽  
pp. 233 ◽  
Author(s):  
Corina Cuceu ◽  
Bruno Colicchio ◽  
Eric Jeandidier ◽  
Steffen Junker ◽  
François Plassa ◽  
...  
Keyword(s):  
Dna Repair ◽  
Hodgkin Lymphoma ◽  
Genomic Instability ◽  
Cell Lines ◽  
Chromosomal Instability ◽  
Chromosomal Rearrangements ◽  
Peripheral Blood Lymphocytes ◽  
Small Cells ◽  
Molecular Approaches ◽  
Circulating Lymphocytes

Background: Microsatellite and chromosomal instability have been investigated in Hodgkin lymphoma (HL). Materials and Methods: We studied seven HL cell lines (five Nodular Sclerosis (NS) and two Mixed Cellularity (MC)) and patient peripheral blood lymphocytes (100 NS-HL and 23 MC-HL). Microsatellite instability (MSI) was assessed by PCR. Chromosomal instability and telomere dysfunction were investigated by FISH. DNA repair mechanisms were studied by transcriptomic and molecular approaches. Results: In the cell lines, we observed high MSI in L428 (4/5), KMH2, and HDLM2 (3/5), low MSI in L540, L591, and SUP-HD1, and none in L1236. NS-HL cell lines showed telomere shortening, associated with alterations of nuclear shape. Small cells were characterized by telomere loss and deletion, leading to chromosomal fusion, large nucleoplasmic bridges, and breakage/fusion/bridge (B/F/B) cycles, leading to chromosomal instability. The MC-HL cell lines showed substantial heterogeneity of telomere length. Intrachromosmal double strand breaks induced dicentric chromosome formation, high levels of micronucleus formation, and small nucleoplasmic bridges. B/F/B cycles induced complex chromosomal rearrangements. We observed a similar pattern in circulating lymphocytes of NS-HL and MC-HL patients. Transcriptome analysis confirmed the differences in the DNA repair pathways between the NS and MC cell lines. In addition, the NS-HL cell lines were radiosensitive and the MC-cell lines resistant to apoptosis after radiation exposure. Conclusions: In mononuclear NS-HL cells, loss of telomere integrity may present the first step in the ongoing process of chromosomal instability. Here, we identified, MSI as an additional mechanism for genomic instability in HL.

scholarly journals A novel site of insertion of IS6110 in the moaB3 gene of a clinical isolate of Mycobacterium tuberculosis

2011 ◽  
Vol 2 (1) ◽  
pp. 7
Author(s):  
Suma Sarojini ◽  
GK Madhavilatha ◽  
Smitha Soman ◽  
R Ajay Kumar ◽  
Sathish Mundayoor
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Clinical Isolate ◽  
Biosynthetic Pathway ◽  
Mobile Genetic Element ◽  
Point Mutations ◽  
Tuberculosis H37rv ◽  
Genomic Variation ◽  
Clinical Isolates ◽  
Pcr Analysis ◽  
Genome Plasticity

In Mycobacterium tuberculosis, genomic variation is generated mainly by insertions and deletions rather than by point mutations. RvD5 is one such deletion in M. tuberculosis H37Rv. Previous studies from our laboratory have shown the presence of moaA3 gene in the RvD5 region in a large number of clinical isolates, that is absent in M. tuberculosis H37Rv and H37Ra. The present study was aimed at investigating the RvD5 locus of the clinical isolates by a detailed PCR analysis. Here we report a new point of insertion of the mobile genetic element, IS6110 in the genome of one clinical isolate of M. tuberculosis. The insertion has disrupted the moaB3 gene, one of the ORFs in the RvD5 region, which is involved in the molybdopterin biosynthetic pathway. This insertion of IS6110 in the moaB3 of the clinical isolate is different when compared to the insertion in the moaB3 gene of M. tuberculosis H37Rv where 4kb RvD5 region has been lost by homologous recombination and only a truncated form of the gene is present. This finding is of relevance since IS6110 is a major element determining the genome plasticity of M. tuberculosis and its numerical and positional polymorphism has always been of special interest.

scholarly journals Dormant Replication Origin Firing Links Replication Stress to Whole Chromosomal Instability in Human Cancer

2021 ◽  
Author(s):  
Ann-Kathrin Schmidt ◽  
Nicolas Böhly ◽  
Xiaoxiao Zhang ◽  
Benjamin O. Slusarenko ◽  
Magdalena Hennecke ◽  
...  
Keyword(s):  
Chromosomal Instability ◽  
Replication Origin ◽  
Human Cancer ◽  
Replication Stress ◽  
Origin Firing
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