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Chandler CH, Chari S, Kowalski A, Choi L, Tack D, DeNieu M, Pitchers W, Sonnenschein A, Marvin L, Hummel K, Marier C, Victory A, Porter C, Mammel A, Holms J, Sivaratnam G, Dworkin I. How well do you know your mutation? Complex effects of genetic background on expressivity, complementation, and ordering of allelic effects. PLoS Genet 2017; 13:e1007075. [PMID: 29166655 PMCID: PMC5718557 DOI: 10.1371/journal.pgen.1007075] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 12/06/2017] [Accepted: 10/15/2017] [Indexed: 12/16/2022] Open
Abstract
For a given gene, different mutations influence organismal phenotypes to varying degrees. However, the expressivity of these variants not only depends on the DNA lesion associated with the mutation, but also on factors including the genetic background and rearing environment. The degree to which these factors influence related alleles, genes, or pathways similarly, and whether similar developmental mechanisms underlie variation in the expressivity of a single allele across conditions and among alleles is poorly understood. Besides their fundamental biological significance, these questions have important implications for the interpretation of functional genetic analyses, for example, if these factors alter the ordering of allelic series or patterns of complementation. We examined the impact of genetic background and rearing environment for a series of mutations spanning the range of phenotypic effects for both the scalloped and vestigial genes, which influence wing development in Drosophila melanogaster. Genetic background and rearing environment influenced the phenotypic outcome of mutations, including intra-genic interactions, particularly for mutations of moderate expressivity. We examined whether cellular correlates (such as cell proliferation during development) of these phenotypic effects matched the observed phenotypic outcome. While cell proliferation decreased with mutations of increasingly severe effects, surprisingly it did not co-vary strongly with the degree of background dependence. We discuss these findings and propose a phenomenological model to aid in understanding the biology of genes, and how this influences our interpretation of allelic effects in genetic analysis. Different mutations in a gene, or in genes with related functions, can have effects of varying severity. Studying sets of mutations and analyzing how they interact are essential components of a geneticist's toolkit. However, the effects caused by a mutation depend not only on the mutation itself, but on additional genetic variation throughout an organism's genome and on the environment that organism has experienced. Therefore, identifying how the genomic and environmental context alter the expression of mutations is critical for making reliable inferences about how genes function. Yet studies on this context dependence have largely been limited to single mutations in single genes. We examined how the genomic and environmental context influence the expression of multiple mutations in two related genes affecting the fruit fly wing. Our results show that the genetic and environmental context generally affect the expression of related mutations in similar ways. However, the interactions between two different mutations in a single gene sometimes depended strongly on context. In addition, cell proliferation in the developing wing and adult wing size were not affected by the genetic and environmental context in similar ways in mutant flies, suggesting that variation in cell growth cannot fully explain how mutations affect wings. Overall, our findings show that context can have a big impact on the interpretation of genetic experiments, including how we draw conclusions about gene function and cause-and-effect relationships.
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Affiliation(s)
- Christopher H. Chandler
- Department of Integrative Biology, BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, United States of America
| | - Sudarshan Chari
- Department of Integrative Biology, BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, United States of America
| | - Alycia Kowalski
- Department of Integrative Biology, BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, United States of America
| | - Lin Choi
- Department of Integrative Biology, BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, United States of America
| | - David Tack
- Department of Integrative Biology, BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, United States of America
| | - Michael DeNieu
- Department of Integrative Biology, BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, United States of America
| | - William Pitchers
- Department of Integrative Biology, BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, United States of America
| | - Anne Sonnenschein
- Department of Integrative Biology, BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, United States of America
| | - Leslie Marvin
- Department of Integrative Biology, BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, United States of America
| | - Kristen Hummel
- Department of Integrative Biology, BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, United States of America
| | - Christian Marier
- Department of Integrative Biology, BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, United States of America
| | - Andrew Victory
- Department of Integrative Biology, BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, United States of America
| | - Cody Porter
- Department of Integrative Biology, BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, United States of America
| | - Anna Mammel
- Department of Integrative Biology, BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, United States of America
| | - Julie Holms
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | | | - Ian Dworkin
- Department of Integrative Biology, BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, United States of America
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
- * E-mail:
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Hodgetts RB, O'Keefe SL, Anderson KJ. An intact RNA interference pathway is required for expression of the mutant wing phenotype of vg(21-3), a P-element-induced allele of the vestigial gene in Drosophila. Genome 2012; 55:312-26. [PMID: 22452576 DOI: 10.1139/g2012-016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We have determined that two P elements, P[21-3] and P[21r36], residing in the 5'-UTR of the vestigial wing gene, encode functional repressors in eye tissue. However, neither element fits a previous categorization of repressor-making elements as Type I or II. Both elements encode polypeptides that are shorter than the canonical elements they most closely resemble. DNA sequencing reveals that P[21r36] encodes an intact THAP domain that is missing in the P[21] element, which does not encode a functional repressor. Recovery of P[21-3] at sites other than vestigial (where it causes the wing mutant, vg(21-3)) reveals that the element can make repressor in wing tissue of sufficient activity to repress the mutant phenotype of vg(21-3). Why the P[21-3] element fails to produce repressor when located at vestigial may be explained by our observation that three different mutants in the RNA interference pathway cause a partial reversion of vg(21-3). We speculate that the vg and P-initiated transcripts that arise at the vg locus in the vg(21-3) mutant trigger an RNA interference response that results in the mutual degradation of both transcripts.
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Affiliation(s)
- Ross B Hodgetts
- Department of Biological Sciences, University of Alberta, Edmonton, Canada.
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