MutantHuntWGS: A Pipeline for Identifying <i>Saccharomyces cerevisiae</i> Mutations

Ellison, Mitchell A.; Walker, Jennifer L.; Ropp, Patrick J.; Durrant, Jacob D.; Arndt, Karen M.

doi:10.1534/g3.120.401396

Cited by 6 publications

(2 citation statements)

References 34 publications

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“…SAMtools were used to calculate genotype likelihoods before calling sequence variants using BCFtools ( Li et al 2009 ; Li 2011 ). Using VCFtools ( Danecek et al 2011 ), VCF files for mutant and wild-type segregants were compared and only the mutations found in the suppressor pool were selected from the output text ( Ellison et al 2020 ). Variants with a quality score > 50 and found within coding regions were retained, leaving three variants.…”

Section: Methodsmentioning

confidence: 99%

Opposing functions of the Hda1 complex and histone H2B mono-ubiquitylation in regulating cryptic transcription inSaccharomyces cerevisiae

Shirra

Kocik

Ellison

et al. 2021

G3 Genes|Genomes|Genetics

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Maintenance of chromatin structure under the disruptive force of transcription requires cooperation among numerous regulatory factors. Histone post-translational modifications can regulate nucleosome stability and influence the disassembly and reassembly of nucleosomes during transcription elongation. The Paf1 transcription elongation complex, Paf1C, is required for several transcription-coupled histone modifications, including the mono-ubiquitylation of H2B. In Saccharomyces cerevisiae, amino acid substitutions in the Rtf1 subunit of Paf1C greatly diminish H2B ubiquitylation and cause transcription to initiate at a cryptic promoter within the coding region of the FLO8 gene, an indicator of chromatin disruption. In a genetic screen to identify factors that functionally interact with Paf1C, we identified mutations in HDA3, a gene encoding a subunit of the Hda1C histone deacetylase, as suppressors of an rtf1 mutation. Absence of Hda1C also suppresses the cryptic initiation phenotype of other mutants defective in H2B ubiquitylation. The genetic interactions between Hda1C and the H2B ubiquitylation pathway appear specific: loss of Hda1C does not suppress the cryptic initiation phenotypes of other chromatin mutants and absence of other histone deacetylases does not suppress the absence of H2B ubiquitylation. Providing further support for an appropriate balance of histone acetylation in regulating cryptic initiation, absence of the Sas3 histone acetyltransferase elevates cryptic initiation in rtf1 mutants. Our data suggest that the H2B ubiquitylation pathway and Hda1C coordinately regulate chromatin structure during transcription elongation and point to a potential role for a histone deacetylase in supporting chromatin accessibility.

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Section: Methodsmentioning

confidence: 99%

Opposing functions of the Hda1 complex and histone H2B mono-ubiquitylation in regulating cryptic transcription inSaccharomyces cerevisiae

Shirra

Kocik

Ellison

et al. 2021

G3 Genes|Genomes|Genetics

Self Cite

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“…To identify potential resistance-conferring mutations, we followed the protocol described in Ellison et al [131]. In brief, we used the Bowtie 2 software [132] to align the sequence reads to the S288C reference yeast genome.…”

Section: In Vitro Evolution and Whole Genome Sequencing Analysismentioning

confidence: 99%

Novel mutation in hexokinase 2 confers resistance to 2-deoxyglucose by altering protein dynamics

et al. 2022

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Glucose is central to many biological processes, serving as an energy source and a building block for biosynthesis. After glucose enters the cell, hexokinases convert it to glucose-6-phosphate (Glc-6P) for use in anaerobic fermentation, aerobic oxidative phosphorylation, and the pentose-phosphate pathway. We here describe a genetic screen in Saccharomyces cerevisiae that generated a novel spontaneous mutation in hexokinase-2, hxk2G238V, that confers resistance to the toxic glucose analog 2-deoxyglucose (2DG). Wild-type hexokinases convert 2DG to 2-deoxyglucose-6-phosphate (2DG-6P), but 2DG-6P cannot support downstream glycolysis, resulting in a cellular starvation-like response. Curiously, though the hxk2G238V mutation encodes a loss-of-function allele, the affected amino acid does not interact directly with bound glucose, 2DG, or ATP. Molecular dynamics simulations suggest that Hxk2G238V impedes sugar binding by altering the protein dynamics of the glucose-binding cleft, as well as the large-scale domain-closure motions required for catalysis. These findings shed new light on Hxk2 dynamics and highlight how allosteric changes can influence catalysis, providing new structural insights into this critical regulator of carbohydrate metabolism. Given that hexokinases are upregulated in some cancers and that 2DG and its derivatives have been studied in anti-cancer trials, the present work also provides insights that may apply to cancer biology and drug resistance.

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GIP: an open-source computational pipeline for mapping genomic instability from protists to cancer cells

Späth

Bussotti

2021

Nucleic Acids Research

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Genome instability has been recognized as a key driver for microbial and cancer adaptation and thus plays a central role in many diseases. Genome instability encompasses different types of genomic alterations, yet most available genome analysis software are limited to just one type of mutation. To overcome this limitation and better understand the role of genetic changes in enhancing pathogenicity we established GIP, a novel, powerful bioinformatic pipeline for comparative genome analysis. Here, we show its application to whole genome sequencing datasets of Leishmania, Plasmodium, Candida and cancer. Applying GIP on available data sets validated our pipeline and demonstrated the power of our tool to drive biological discovery. Applied to Plasmodium vivax genomes, our pipeline uncovered the convergent amplification of erythrocyte binding proteins and identified a nullisomic strain. Re-analyzing genomes of drug adapted Candida albicans strains revealed correlated copy number variations of functionally related genes, strongly supporting a mechanism of epistatic adaptation through interacting gene-dosage changes. Our results illustrate how GIP can be used for the identification of aneuploidy, gene copy number variations, changes in nucleic acid sequences, and chromosomal rearrangements. Altogether, GIP can shed light on the genetic bases of cell adaptation and drive disease biomarker discovery.

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MutantHuntWGS: A Pipeline for Identifying Saccharomyces cerevisiae Mutations

Cited by 6 publications

References 34 publications

Opposing functions of the Hda1 complex and histone H2B mono-ubiquitylation in regulating cryptic transcription inSaccharomyces cerevisiae

Opposing functions of the Hda1 complex and histone H2B mono-ubiquitylation in regulating cryptic transcription inSaccharomyces cerevisiae

Novel mutation in hexokinase 2 confers resistance to 2-deoxyglucose by altering protein dynamics

GIP: an open-source computational pipeline for mapping genomic instability from protists to cancer cells

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