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 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.

Rescaling Biology: Increasing Integration Across Biological Scales and Subdisciplines to Enhance Understanding and Prediction

2021 ◽  
Author(s):  
Colette St. Mary ◽  
Thomas H Q Powell ◽  
John S Kominoski ◽  
Emily Weinert
Keyword(s):  
Multiple Scales ◽  
Genomic Variation ◽  
Biological Processes ◽  
Explicit Integration ◽  
Fully Integrated ◽  
Community Or ◽  
Complex Processes ◽  
Spatiotemporal Scales ◽  
Patterns And Processes ◽  
Vast Range

Synopsis The organization of the living world covers a vast range of spatiotemporal scales, from molecules to the biosphere, seconds to centuries. Biologists working within specialized subdisciplines tend to focus on different ranges of scales. Therefore, developing frameworks that enable testing questions and predictions of scaling requires sufficient understanding of complex processes across biological subdisciplines and spatiotemporal scales. Frameworks that enable scaling across subdisciplines would ideally allow us to test hypotheses about the degree to which explicit integration across spatiotemporal scales is needed for predicting the outcome of biological processes. For instance, how does genomic variation within populations allow us to explain community structure? How do the dynamics of cellular metabolism translate to our understanding of whole-ecosystem metabolism? Do patterns and processes operate seamlessly across biological scales, or are there fundamental laws of biological scaling that limit our ability to make predictions from one scale to another? Similarly, can sub-organismal structures and processes be sufficiently understood in isolation of potential feedbacks from the population, community, or ecosystem levels? And can we infer the sub-organismal processes from data on the population, community, or ecosystem scale? Concerted efforts to develop more cross-disciplinary frameworks will open doors to a more fully integrated field of biology. In this paper, we discuss how we might integrate across scales, specifically by (1) identifying scales and boundaries, (2) determining analogous units and processes across scales, (3) developing frameworks to unite multiple scales, and (4) extending frameworks to new empirical systems.

scholarly journals Structural genome analysis in cultivated potato taxa

2019 ◽  
Vol 133 (3) ◽  
pp. 951-966 ◽  
Author(s):  
Maria Kyriakidou ◽  
Sai Reddy Achakkagari ◽  
José Héctor Gálvez López ◽  
Xinyi Zhu ◽  
Chen Yu Tang ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Agronomic Traits ◽  
Genomic Variation ◽  
Sequencing Data ◽  
Structural Variations ◽  
Structural Genomic ◽  
Ploidy Levels ◽  
Cultivated Potato ◽  
Number Variation

Abstract Key message Twelve potato accessions were selected to represent two principal views on potato taxonomy. The genomes were sequenced and analyzed for structural variation (copy number variation) against three published potato genomes. Abstract The common potato (Solanum tuberosum L.) is an important staple crop with a highly heterozygous and complex tetraploid genome. The other taxa of cultivated potato contain varying ploidy levels (2X–5X), and structural variations are common in the genomes of these species, likely contributing to the diversification or agronomic traits during domestication. Increased understanding of the genomes and genomic variation will aid in the exploration of novel agronomic traits. Thus, sequencing data from twelve potato landraces, representing the four ploidy levels, were used to identify structural genomic variation compared to the two currently available reference genomes, a double monoploid potato genome and a diploid inbred clone of S. chacoense. The results of a copy number variation analysis showed that in the majority of the genomes, while the number of deletions is greater than the number of duplications, the number of duplicated genes is greater than the number of deleted ones. Specific regions in the twelve potato genomes have a high density of CNV events. Further, the auxin-induced SAUR genes (involved in abiotic stress), disease resistance genes and the 2-oxoglutarate/Fe(II)-dependent oxygenase superfamily proteins, among others, had increased copy numbers in these sequenced genomes relative to the references.

scholarly journals Punctuated Aneuploidization of the Budding Yeast Genome

Genetics ◽  
2020 ◽  
Vol 216 (1) ◽  
pp. 43-50 ◽  
Author(s):  
Lydia R. Heasley ◽  
Ruth A. Watson ◽  
Juan Lucas Argueso
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Tumor Cells ◽  
Genomic Instability ◽  
High Frequency ◽  
Budding Yeast ◽  
Cell Types ◽  
Eukaryotic Cell ◽  
Yeast Genome ◽  
Single Chromosome ◽  
Brewing Yeasts

Remarkably complex patterns of aneuploidy have been observed in the genomes of many eukaryotic cell types, ranging from brewing yeasts to tumor cells. Such aberrant karyotypes are generally thought to take shape progressively over many generations, but evidence also suggests that genomes may undergo faster modes of evolution. Here, we used diploid Saccharomyces cerevisiae cells to investigate the dynamics with which aneuploidies arise. We found that cells selected for the loss of a single chromosome often acquired additional unselected aneuploidies concomitantly. The degrees to which these genomes were altered fell along a spectrum, ranging from simple events affecting just a single chromosome, to systemic events involving many. The striking complexity of karyotypes arising from systemic events, combined with the high frequency at which we detected them, demonstrates that cells can rapidly achieve highly altered genomic configurations during temporally restricted episodes of genomic instability.

A Whole Genome Analysis Identifies SLCO1B1 as a Determinant of Methotrexate Pharmacokinetics and Adverse Effects

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 214-214
Author(s):  
Lisa R Trevino ◽  
Noriko Shimasaki ◽  
Wenjian Yang ◽  
John C. Panetta ◽  
Cheng Cheng ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Lymphoblastic Leukemia ◽  
Organic Anion ◽  
Linear Regression Analysis ◽  
Treatment Protocol ◽  
Genomic Variation ◽  
Organic Anion Transporter ◽  
Strong Impact ◽  
Whole Genome Analysis ◽  
Anion Transporter

Abstract Methotrexate is a major component in every treatment protocol for childhood acute lymphoblastic leukemia (ALL). Both beneficial and detrimental effects of methotrexate in ALL have been clearly related to methotrexate plasma pharmacokinetics, which vary substantially among patients. However the genetic basis of such variability remains largely unknown. Herein, we surveyed 600,000 germline single nucleotide polymorphisms (SNPs) to determine how inherited genetic variation affects the disposition of methotrexate among 434 children with ALL who received 3014 courses of methotrexate at 2 to 5 g/m2. Adjusting for age, race, gender and methotrexate regimen, the most significant SNPs associated with methotrexate clearance were annotated to a plausible gene, the organic anion transporter polypeptide, SLCO1B1. The three top SNPs included rs11045879 (P = 1.7 × 10−10), rs4149081 (P = 1.7 × 10−9), and rs2900478 (P = 2.8 × 10−8). Linkage disequilibrium (LD) was observed among these three SLCO1B1 SNPs (r2=1) and with a known functional polymorphism in SLCO1B1, T521C (rs4149056, r2 = 0.86). The top two SLCO1B1 SNPs rs11045879 and rs4149081 were further validated (P = 0.018 and P = 0.017) in an independent cohort of 206 patients with ALL. Additional SNPs annotated to SLCO1B1 were identified and further validated. In a stepwise multiple linear regression analysis, SLCO1B1 genetic variation remained significant and explained clearance variability comparable to that of other non-genetic factors including treatment regimen. SNPs in SLCO1B1 were also associated with methotrexate-related gastrointestinal toxicity (P= 0.03 to 0.0005, odds ratio 8.3 to 16.4). In summary, we have identified a candidate gene, SLCO1B1, which is strongly associated with the pharmacokinetics of methotrexate, an anticancer drug with a low therapeutic index in multiple treatment regimens. Although SLCO1B1 is widely recognized as having a strong impact on the disposition of many drugs in clinical use, based on in vitro data, it was not thought to have a major role in methotrexate transport or disposition. Our study demonstrates proof of principle that genome-wide tools in clinical pharmacologic problems can lead to the discovery of important and novel pharmacogenetic links between inherited genomic variation and drug response in humans.

Identification of Novel Recurrent Copy Number Variations and Regions of Copy-Neutral Loss of Heterozygosity by High Resolution Genomic Array in Pre-Treatment and Relapsed B-CLL.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 1098-1098
Author(s):  
Samantha JL Knight ◽  
Elham Sadighi Akha ◽  
Adele Timbs ◽  
Tariq Enver ◽  
Andrew R Pettitt ◽  
...  
Keyword(s):  
High Resolution ◽  
Copy Number Variation ◽  
B Cell ◽  
Genomic Instability ◽  
Loss Of Heterozygosity ◽  
Copy Number ◽  
Neutral Loss ◽  
Single Gene ◽  
Number Variation ◽  
Pre Treatment

Abstract Abstract 1098 Poster Board I-120 Background B-cell chronic lymphocytic leukaemia (B-CLL) is the most common form of adult leukaemia in the Western World. It is a heterogeneous disease and important biological and clinical differences have been identified. However, the molecular mechanisms underlying emergence and maintenance of B-CLL after treatment remain elusive. Array based comparative genomic hybridization (aCGH) has revolutionized our ability to perform genome wide analyses of copy number variation (CNV) within cancer genomes. Single Nucleotide Polymorphism arrays (aSNP) provide genotyping and copy number variation data and detect regions of copy neutral Loss of Heterozygosity (cnLOH) with the potential to indicate genes involved in leukaemia pathogenesis. Both technologies are evolving rapidly and emerging platforms are thought to allow high resolution (HR) of abnormalities down to a single gene level. Aim The aim of the current study was therefore to test a HR-aCGH and a HR-aSNP platform for their ability to detect large and small CNVs and regions of cnLOH in B-CLL. More specifically, we wanted to: Method We used a high resolution 244K aCGH platform and a 1Mio SNP array in parallel to test and characterize enriched B-CLL peripheral blood samples (>80% CD19+;CD5+) from 44 clinically annotated patients collected at our institution. To distinguish CNVs seen commonly in the general population the results were compared with ‘in house’ control data sets and the Database of Genomic Variants (http://projects.tcag.ca/variation/). Results Our results show that large abnormalities, already noted by FISH, were reliably identified and the boundaries of abnormalities at 11q22.3, 13q14.2 and 17p could be defined more precisely. In addition, novel and recurrent CNVs within the sample set were identified (1p33; 3p24.3; 3p14.2; 4q12; 4q13.3; 6q21; 6q27; 8p22; 10q24; 11p15.4; 11q12; 11q13.4; 11q14.1; 11q22.1; 11q23.3; 13q14.11; 14q21.1; 15q15.1; 15q25.3; 17p13.3; 17q22; 18p11.32; 18p23; 19p13.13; 19p13.12; 19p13.32; 22q11.21; 22q11.22). Interestingly, some of these abnormalities contain single gene alterations involving oncogenes, chemokine receptors, kinases and transcription factors important in B cell development and differentiation. Assessment of smaller CNVs (less then 10 consecutive oligonucleotides) also revealed recurrent CNVs involving single genes that were clustered according to function and pathways. Comparison of paired pre-treatment and relapse samples showed differences in large CNVs in 6 out of the 14 pairs with the majority being losses within the relapse sample. In particular, relapse samples contained new losses within 2q33.1-2q37.1; 4q13.2-4q13.3; 5q31.3-5q34; 7q36.3; 10q23.1-10q25.1 11q12.3 and multiple losses within 13q14.1-13q14.3. Taken together, these data indicates that genomic instability plays a role in clonal evolution and selection after treatment in at least some patients. Analysis of a bigger cohort of matched pre-treatment and relapse samples is on-going. The importance of copy neutral LOH in B-CLL has been a subject of debate. Using the 1Mio HR-aSNP, we were able to detect multiple regions of cnLOH throughout the genome. Examination of the four regions that are known to have prognostic significance when deleted identified cnLOH involving 13q11-13q34(ter) and cnLOH of 13q21.1-q34(ter) outside the FISH region. Deletions of the 17p13.1 locus including the p53 gene confer poor prognosis in B-CLL and direct treatment decisions. Interestingly, we were able to identify cnLOH involving this region in 5% of samples. In addition, we also noticed cnLOH in 17p13.2 containing genes previously implicated in cancer. The exact pathogenetic and prognostic implications of these findings remain to be established. Conclusion Using HR-aCGH and HR-aSNP we have identified novel recurrent CNVs and regions of cnLOH in patients with B-CLL. Sequential analysis of the same patients over time suggests that at least in some patients, clonal complexity and dynamics are driven by genomic instability. Disclosures No relevant conflicts of interest to declare.

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