Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.64898/2026.05.21.726896

Pharmacological stress exposes hidden allelic background effects in genetic interaction screen normalisation

Islam, R. A.·Xintarakou, O.·Rallis, C.
View original source ↗Export metadata ↓

Abstract

Synthetic Genetic Array (SGA) analysis comprises the high-throughput crossing of a query deletion strain against a genome-wide deletion library to score fitness interactions in thousands of double mutants. SGAs have produced comprehensive genetic interaction maps in yeasts and have emerged as a leading platform for pharmacogenomics: mapping genetic modifiers of drug response, identifying synthetic lethal targets and illuminating mechanisms of drug action and resistance. We have previously demonstrated that in fission yeast, the ade6 mutant is functionally neutral relative to the parental library and can serve as a standard negative control for SGA screens. Here, while we confirm our previous observation, we show that this neutrality fails under pharmacological stress. Using Torin1, an ATP-competitive TOR kinase inhibitor, we demonstrate that the ade6 SGA fitness profile diverges from that of the parental library in a dose-dependent and genomically widespread manner. At 2 M Torin1 only 12.2% of scored genes exceed a 1.5-fold fitness difference between backgrounds; at 3 M this proportion rises to 43.2% -a 3.5-fold increase driven by qualitative reorganisation of the genetic interaction landscape rather than simple scaling of pre-existing differences. Gene ontology analysis of divergent genes implicates autophagy, iron starvation responses, central carbon metabolism, and vesicle trafficking, consistent with TOR-regulated nutrient adaptation being differentially affected by the ade6-M210/M216 point mutations in the library versus the ade6 null in the SGA control. Our results have implications in fission yeast and beyond and we propose solutions towards reliable retrieval of genetic interactions.

Explore related subjects

geneticsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Islam, R. A., Xintarakou, O., Rallis, C.. 2026-05-26. Pharmacological stress exposes hidden allelic background effects in genetic interaction screen normalisation. https://doi.org/10.64898/2026.05.21.726896

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

OPA1 controls mitochondrial dysfunction-driven liver fibrosis in MASLD

Progressive hepatic fibrosis is the principal determinant of morbidity and mortality in metabolic dysfunction-associated steatotic liver disease and steatohepatitis (MASLD/MASH). Mitochondrial dysfunction is a hallmark of MASH, and the release of mitochondrial damage-associated molecular patterns (mito-DAMPs) from injured hepatocytes can promote fibrosis. However, how mitochondrial dynamics and quality control shape the fibrotic response in MASLD/MASH remains unclear. Here, through large-scale genomic analyses of mitochondrial genes governing mitophagy, fusion and fission in human MASLD, with a power-equivalent sample size of approximately 700,000 individuals, we identify a strong association between hepatic fibrosis and the mitochondrial fusion factor dynamin-like GTPase optic atrophy 1 (OPA1). OPA1 transcripts and protein abundance in the liver epithelium were progressively dysregulated with advancing fibrosis. In mice, hepatocyte-specific OPA1 loss alone was sufficient to induce hepatic stellate cell activation and fibrosis in zone 3, promoted the release of mito-DAMPs into the circulation and exacerbated fibrosis in experimental MASH. These findings identify OPA1 as a central regulator of the hepatic fibrotic response and connect defective mitochondrial homeostasis to mito-DAMP release, hepatic stellate cell activation and fibrosis in MASLD.

genetics↗
bioRxiv2026

Mechanism-selective deep mutational scanning distinguishes ERCC2 disease phenotypes

Pathogenic ERCC2 variants cause xeroderma pigmentosum (XP), trichothiodystrophy (TTD) or both, yet variant effect scores are usually interpreted only as measures of pathogenicity rather than of which disease mechanism is disrupted. XPD, the ERCC2-encoded TFIIH subunit, functions in both nucleotide excision repair and transcription. Using yeast complementation deep mutational scanning, we measured the effects of nearly all XPD amino acid substitutions. The assay was mechanism-selective: it preferentially reported transcription-associated function, with pronounced intolerance at the p44 interface, whereas many substitutions affecting DNA binding and helicase activity retained near-wild-type fitness. Accordingly, TTD variants had much lower fitness than XP variants. Computational predictors discriminated pathogenic from benign variants similarly across phenotypes, but the DMS distinguished XP from TTD variants better than all 73 predictors tested. Phenotype-specific ACMG/AMP calibration provided evidence in both directions for TTD but mainly pathogenic evidence for XP. Thus, the selectivity of functional assays, often viewed as a limitation, can reveal disease mechanisms and support phenotype-aware variant interpretation.

genetics↗
bioRxiv2026

Temporal control of mitochondrial mutagenesis reveals the fate of mtDNA mutations with age

Mutations in the mitochondrial genome (mtDNA) play a critical role in the aging process and a wide variety of age-related diseases. However, it remains unclear when the mutations that drive physiological decline arise. To answer this question, we generated a new mouse model in which mitochondrial mutagenesis can be confined to a defined window of time. Surprisingly, we found that mutations that arise during the first two months of life are sufficient to drive a wide variety of age-related pathologies, and that the severity of this pathology is broadly regulated by distinct, tissue-specific selective pressures that control the fate of mtDNA mutations with age. Further, we found that selection against deleterious variants can be modulated by manipulation of mitochondrial fusion in vitro and in vivo. These observations raise the possibility that in some tissues, the pace of aging is pre-determined by events that occur early in life and that interventions targeting mitochondrial fusion may be able to slow down or reverse the expansion of these pathogenic variants. These results carry far-reaching implications for strategies aimed at preventing or delaying age-related decline.

genetics↗