W-Test for Genetic Epistasis Testing

Manganese is an essential, but potentially toxic, trace metal in biological systems. Overexposure to manganese is known to cause neurological deficits in humans, but the pathways that lead to manganese toxicity are largely unknown. We have employed the bakers' yeast Saccharomyces cerevisiae as a model system to identify genes that contribute to manganese-related damage. In a genetic screen for yeast manganese-resistance mutants, we identified S. cerevisiae MAM3 as a gene which, when deleted, would increase cellular tolerance to toxic levels of manganese and also increased the cell's resistance towards cobalt and zinc. By sequence analysis, Mam3p shares strong similarity with the mammalian ACDP (ancient conserved domain protein) family of polypeptides. Mutations in human ACDP1 have been associated with urofacial (Ochoa) syndrome. However, the functions of eukaryotic ACDPs remain unknown. We show here that S. cerevisiae MAM3 encodes an integral membrane protein of the yeast vacuole whose expression levels directly correlate with the degree of manganese toxicity. Surprisingly, Mam3p contributes to manganese toxicity without any obvious changes in vacuolar accumulation of metals. Furthermore, through genetic epistasis studies, we demonstrate that MAM3 operates independently of the well-established manganese-trafficking pathways in yeast, involving the manganese transporters Pmr1p, Smf2p and Pho84p. This is the first report of a eukaryotic ACDP family protein involved in metal homoeostasis.

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The yeast UME5 gene regulates the stability of meiotic mRNAs in response to glucose

Molecular and Cellular Biology ◽

10.1128/mcb.14.5.3446-3458.1994 ◽

1994 ◽

Vol 14 (5) ◽

pp. 3446-3458

Author(s):

R T Surosky ◽

R Strich ◽

R E Esposito

Keyword(s):

Vegetative Growth ◽

Signal Transduction Pathway ◽

Kinase Domain ◽

Specific Protein ◽

Transcript Stability ◽

The Family ◽

Two Factors ◽

Genetic Epistasis ◽

The Stability ◽

Acetate Medium

We reported previously that early meiotic transcripts are highly unstable. These mRNAs exhibit half-lives of approximately 3 min when expressed during vegetative growth in glucose medium and are stabilized twofold during sporulation in acetate medium. Two genes, UME2 and UME5, that regulate the stability of meiosis-specific transcripts have been identified. The wild-type UME5 gene, which has been analyzed in detail, decreases the stability of all meiotic mRNAs tested approximately twofold when expressed during vegetative growth but has no effect on the half-lives of a number of vegetative mRNAs examined. The UME5 gene is dispensable for mitotic and meiotic development. Cells in which the entire UME5 gene has been deleted are viable, although the generation time is slightly longer and sporulation is less efficient. The UME5 transcript is constitutively expressed, and its stability is not autoregulated. The UME5 gene encodes a predicted 63-kDa protein with homology to the family of CDC28 serine/threonine-specific protein kinases. The kinase activity appears to be central to the function of the UME5 protein, since alteration of a highly conserved amino acid in the kinase domain results in a phenotype identical to that of a ume5 deletion. Genetic epistasis studies suggest that the UME2 and UME5 gene products act in the same pathway to regulate meiotic transcript stability. This pathway is independent of deadenylation and translation, two factors known to be important in regulating mRNA turnover. Significantly, the UME5-mediated destabilization of meiotic mRNAs occurs in glucose- but not in acetate-containing medium. Thus, the UME5 gene appears to participate in a glucose signal transduction pathway governing message stability.

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Context-specific regulation of lysosomal lipolysis through network-level diverting of transcription factor interactions

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2104832118 ◽

2021 ◽

Vol 118 (41) ◽

pp. e2104832118

Author(s):

Vinod K. Mony ◽

Anna Drangowska-Way ◽

Reka Albert ◽

Emma Harrison ◽

Abbas Ghaddar ◽

...

Keyword(s):

Oxidative Stress ◽

Target Gene ◽

Specific Nature ◽

C Elegans ◽

Functional Interactions ◽

Genetic Epistasis ◽

Specific Regulation ◽

Context Specific ◽

Factor Interactions ◽

Multicellular Organisms

Plasticity in multicellular organisms involves signaling pathways converting contexts—either natural environmental challenges or laboratory perturbations—into context-specific changes in gene expression. Congruently, the interactions between the signaling molecules and transcription factors (TF) regulating these responses are also context specific. However, when a target gene responds across contexts, the upstream TF identified in one context is often inferred to regulate it across contexts. Reconciling these stable TF–target gene pair inferences with the context-specific nature of homeostatic responses is therefore needed. The induction of the Caenorhabditis elegans genes lipl-3 and lipl-4 is observed in many genetic contexts and is essential to survival during fasting. We find DAF-16/FOXO mediating lipl-4 induction in all contexts tested; hence, lipl-4 regulation seems context independent and compatible with across-context inferences. In contrast, DAF-16–mediated regulation of lipl-3 is context specific. DAF-16 reduces the induction of lipl-3 during fasting, yet it promotes it during oxidative stress. Through discrete dynamic modeling and genetic epistasis, we define that DAF-16 represses HLH-30/TFEB—the main TF activating lipl-3 during fasting. Contrastingly, DAF-16 activates the stress-responsive TF HSF-1 during oxidative stress, which promotes C. elegans survival through induction of lipl-3. Furthermore, the TF MXL-3 contributes to the dominance of HSF-1 at the expense of HLH-30 during oxidative stress but not during fasting. This study shows how context-specific diverting of functional interactions within a molecular network allows cells to specifically respond to a large number of contexts with a limited number of molecular players, a mode of transcriptional regulation we name “contextualized transcription.”

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Evolution and clinical impact of genetic epistasis within EGFR-mutant lung cancers

10.1101/117291 ◽

2017 ◽

Author(s):

Collin M. Blakely ◽

Thomas B.K. Watkins ◽

Wei Wu ◽

Beatrice Gini ◽

Jacob J. Chabon ◽

...

Keyword(s):

Clinical Impact ◽

Lung Cancers ◽

Genetic Epistasis ◽

Egfr Mutant

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Regulation of a dpp target gene in the Drosophila embryo

Development ◽

10.1242/dev.124.2.303 ◽

1997 ◽

Vol 124 (2) ◽

pp. 303-311 ◽

Cited By ~ 3

Author(s):

J. Rusch ◽

M. Levine

Keyword(s):

Target Gene ◽

Fusion Gene ◽

Drosophila Embryo ◽

Specific Expression ◽

Downstream Target ◽

Embryonic Tissues ◽

Posterior Midgut ◽

Downstream Target Gene ◽

Genetic Epistasis ◽

Vp16 Fusion

In Drosophila, two TGF-beta growth factors, dpp and screw, function synergistically to subdivide the dorsal ectoderm into two embryonic tissues, the amnioserosa and dorsal epidermis. Previous studies have shown that peak dpp activity is required for the localized expression of zerknullt (zen), which encodes a homeodomain transcription factor. We present evidence that zen directly activates the amnioserosa-specific expression of a downstream target gene, Race (Related to angiotensin converting enzyme). A 533 bp enhancer from the Race promoter region is shown to mediate selective expression in the amnioserosa, as well as the anterior and posterior midgut rudiments. This enhancer contains three zen protein binding sites, and mutations in these sites virtually abolish the expression of an otherwise normal Race-lacZ fusion gene in the amnioserosa, but not in the gut. Genetic epistasis experiments suggest that zen is not the sole activator of Race, although a hyperactivated form of zen (a zen-VP16 fusion protein) can partially complement reduced levels of dpp activity. These results suggest that dpp regulates multiple transcription factors, which function synergistically to specify the amnioserosa.

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A single frizzled protein has a dual function in tissue polarity

Development ◽

10.1242/dev.120.7.1883 ◽

1994 ◽

Vol 120 (7) ◽

pp. 1883-1893 ◽

Cited By ~ 13

Author(s):

R.E. Krasnow ◽

P.N. Adler

Keyword(s):

Dual Function ◽

Protein Species ◽

Hsp70 Promoter ◽

Tissue Polarity ◽

Genetic Mosaic ◽

Single Protein ◽

Genetic Epistasis ◽

Pupal Wing ◽

Separate Protein ◽

Transgenic Flies

The Drosophila frizzled (fz) gene is required for the development of normal tissue polarity in the epidermis. Genetic epistasis experiments argue that fz is at the top of a regulatory hierarchy that controls the subcellular site for prehair initiation within the cells of the pupal wing (Wong and Adler, 1993; J. Cell Biol. 123, 209–221). Genetic mosaic experiments indicate that fz has both cell autonomous and cell non-autonomous functions that are separately mutable (Vinson and Adler, 1987; Nature 329, 549–551). Two species of fz mRNA have been identified, raising the question as to whether the two functions are provided by a single protein or by two separate protein species. We generated transgenic flies that express each of these mRNAs under the control of an hsp70 promoter. Only one of the transgenes (hsfzI) showed any fz activity. At 29 degrees C, the hsfzI transgene provided almost complete rescue of a null fz mutation, indicating that the protein encoded by this cDNA can fulfill both fz functions. Overexpression of the hsfzI transgene resulted in two distinct tissue polarity phenotypes depending on the time of heat shock.

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Loss of dmrt1 restores zebrafish female fates in the absence of cyp19a1a but not rbpms2a/b

Development ◽

10.1242/dev.190942 ◽

2020 ◽

Vol 147 (18) ◽

pp. dev190942

Author(s):

Shannon Romano ◽

Odelya H. Kaufman ◽

Florence L. Marlow

Keyword(s):

Sex Determination ◽

Somatic Tissue ◽

Male Factor ◽

Fate Specification ◽

Multiple Factors ◽

Apply Genetic ◽

Specific Differentiation ◽

Complex Process ◽

Genetic Epistasis

ABSTRACTSex determination and differentiation is a complex process regulated by multiple factors, including factors from the germline or surrounding somatic tissue. In zebrafish, sex-determination involves establishment of a bipotential ovary that undergoes sex-specific differentiation and maintenance to form the functional adult gonad. However, the relationships among these factors are not fully understood. Here, we identify potential Rbpms2 targets and apply genetic epistasis experiments to decipher the genetic hierarchy of regulators of sex-specific differentiation. We provide genetic evidence that the crucial female factor rbpms2 is epistatic to the male factor dmrt1 in terms of adult sex. Moreover, the role of Rbpms2 in promoting female fates extends beyond repression of Dmrt1, as Rbpms2 is essential for female differentiation even in the absence of Dmrt1. In contrast, female fates can be restored in mutants lacking both cyp19a1a and dmrt1, and prolonged in bmp15 mutants in the absence of dmrt1. Taken together, this work indicates that cyp19a1a-mediated suppression of dmrt1 establishes a bipotential ovary and initiates female fate acquisition. Then, after female fate specification, Cyp19a1a regulates subsequent oocyte maturation and sustains female fates independently of Dmrt1 repression.

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