Genetic Interactions Involving Five or More Genes Contribute to a Complex Trait in Yeast
Although it is well known that interactions among genetic variants contribute to many complex traits, the forms of these interactions have not been fully characterized. Most work on this problem to date has focused on relatively simple cases involving two or three loci. However, higher-order interactions involving larger numbers of loci can also occur, and may have significant effects on the relationship between genotype and phenotype. In this paper, we dissect a colony morphology trait that segregates in a cross of two yeast strains and is caused by genetic interactions among five or more loci. Our work demonstrates that higher-order interactions can have major phenotypic effects, and provides novel insights into the genetic and molecular basis of these interactions.
Vyšlo v časopise:
Genetic Interactions Involving Five or More Genes Contribute to a Complex Trait in Yeast. PLoS Genet 10(5): e32767. doi:10.1371/journal.pgen.1004324
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1004324
Souhrn
Although it is well known that interactions among genetic variants contribute to many complex traits, the forms of these interactions have not been fully characterized. Most work on this problem to date has focused on relatively simple cases involving two or three loci. However, higher-order interactions involving larger numbers of loci can also occur, and may have significant effects on the relationship between genotype and phenotype. In this paper, we dissect a colony morphology trait that segregates in a cross of two yeast strains and is caused by genetic interactions among five or more loci. Our work demonstrates that higher-order interactions can have major phenotypic effects, and provides novel insights into the genetic and molecular basis of these interactions.
Zdroje
1. Falconer DS, Mackay TF (1996) Introduction to quantitative genetics (4th edition). Harlow, England: Pearson Education Limited.
2. Lynch M, Walsh B (1998) Genetics and analysis of quantitative traits: Sinauer.
3. MackayTF (2014) Epistasis and quantitative traits: using model organisms to study gene-gene interactions. Nature reviews Genetics 15: 22–33.
4. PhillipsPC (2008) Epistasis–the essential role of gene interactions in the structure and evolution of genetic systems. Nat Rev Genet 9: 855–867.
5. LehnerB (2011) Molecular mechanisms of epistasis within and between genes. Trends Genet 27: 323–331.
6. HuangW, RichardsS, CarboneMA, ZhuD, AnholtRR, et al. (2012) Epistasis dominates the genetic architecture of Drosophila quantitative traits. Proceedings of the National Academy of Sciences of the United States of America 109: 15553–15559.
7. NelsonRM, PetterssonME, CarlborgO (2013) A century after Fisher: time for a new paradigm in quantitative genetics. Trends in genetics: TIG 29: 669–76 doi:10.1016/j.tig.2013.09.006
8. BremRB, StoreyJD, WhittleJ, KruglyakL (2005) Genetic interactions between polymorphisms that affect gene expression in yeast. Nature 436: 701–703.
9. DowellRD, RyanO, JansenA, CheungD, AgarwalaS, et al. (2010) Genotype to phenotype: a complex problem. Science 328: 469.
10. PetterssonM, BesnierF, SiegelPB, CarlborgO (2011) Replication and explorations of high-order epistasis using a large advanced intercross line pedigree. PLoS genetics 7: e1002180.
11. BloomJS, EhrenreichIM, LooWT, LiteTL, KruglyakL (2013) Finding the sources of missing heritability in a yeast cross. Nature 494: 234–237.
12. ManolioTA, CollinsFS, CoxNJ, GoldsteinDB, HindorffLA, et al. (2009) Finding the missing heritability of complex diseases. Nature 461: 747–753.
13. GranekJA, MagwenePM (2010) Environmental and genetic determinants of colony morphology in yeast. PLoS genetics 6: e1000823.
14. GranekJA, MurrayD, KayrkciO, MagwenePM (2013) The genetic architecture of biofilm formation in a clinical isolate of Saccharomyces cerevisiae. Genetics 193: 587–600.
15. HolmesDL, LancasterAK, LindquistS, HalfmannR (2013) Heritable remodeling of yeast multicellularity by an environmentally responsive prion. Cell 153: 153–165.
16. RyanO, ShapiroRS, KuratCF, MayhewD, BaryshnikovaA, et al. (2012) Global gene deletion analysis exploring yeast filamentous growth. Science 337: 1353–1356.
17. TanZ, HaysM, CromieGA, JefferyEW, ScottAC, et al. (2013) Aneuploidy underlies a multicellular phenotypic switch. Proceedings of the National Academy of Sciences of the United States of America 110: 12367–12372.
18. WilkeningS, LinG, FritschES, TekkedilMM, AndersS, et al. (2013) An Evaluation of High-Throughput Approaches to QTL Mapping in Saccharomyces cerevisiae. Genetics 196-: 853–65.
19. HalmeA, BumgarnerS, StylesC, FinkGR (2004) Genetic and epigenetic regulation of the FLO gene family generates cell-surface variation in yeast. Cell 116: 405–415.
20. PirP, GutteridgeA, WuJ, RashB, KellDB, et al. (2012) The genetic control of growth rate: a systems biology study in yeast. BMC systems biology 6: 4.
21. RoopJI, BremRB (2013) Rare variants in hypermutable genes underlie common morphology and growth traits in wild Saccharomyces paradoxus. Genetics 195: 513–525.
22. LiuH, StylesCA, FinkGR (1996) Saccharomyces cerevisiae S288C has a mutation in FLO8, a gene required for filamentous growth. Genetics 144: 967–978.
23. SteinmetzLM, SinhaH, RichardsDR, SpiegelmanJI, OefnerPJ, et al. (2002) Dissecting the architecture of a quantitative trait locus in yeast. Nature 416: 326–330.
24. SinhaH, NicholsonBP, SteinmetzLM, McCuskerJH (2006) Complex genetic interactions in a quantitative trait locus. PLoS genetics 2: e13.
25. LitiG, CarterDM, MosesAM, WarringerJ, PartsL, et al. (2009) Population genomics of domestic and wild yeasts. Nature 458: 337–341.
26. BenedettiH, RathsS, CrausazF, RiezmanH (1994) The END3 gene encodes a protein that is required for the internalization step of endocytosis and for actin cytoskeleton organization in yeast. Mol Biol Cell 5: 1023–1037.
27. TangHY, XuJ, CaiM (2000) Pan1p, End3p, and S1a1p, three yeast proteins required for normal cortical actin cytoskeleton organization, associate with each other and play essential roles in cell wall morphogenesis. Mol Cell Biol 20: 12–25.
28. KobayashiO, SudaH, OhtaniT, SoneH (1996) Molecular cloning and analysis of the dominant flocculation gene FLO8 from Saccharomyces cerevisiae. Molecular & general genetics: MGG 251: 707–715.
29. GagianoM, BesterM, van DykD, FrankenJ, BauerFF, et al. (2003) Mss11p is a transcription factor regulating pseudohyphal differentiation, invasive growth and starch metabolism in Saccharomyces cerevisiae in response to nutrient availability. Molecular microbiology 47: 119–134.
30. TanakaK, NakafukuM, TamanoiF, KaziroY, MatsumotoK, et al. (1990) IRA2, a second gene of Saccharomyces cerevisiae that encodes a protein with a domain homologous to mammalian ras GTPase-activating protein. Molecular and cellular biology 10: 4303–4313.
31. PedrajasJR, KosmidouE, Miranda-VizueteA, GustafssonJA, WrightAP, et al. (1999) Identification and functional characterization of a novel mitochondrial thioredoxin system in Saccharomyces cerevisiae. J Biol Chem 274: 6366–6373.
32. RossSJ, FindlayVJ, MalakasiP, MorganBA (2000) Thioredoxin peroxidase is required for the transcriptional response to oxidative stress in budding yeast. Mol Biol Cell 11: 2631–2642.
33. KimTS, KimHY, YoonJH, KangHS (2004) Recruitment of the Swi/Snf complex by Ste12-Tec1 promotes Flo8-Mss11-mediated activation of STA1 expression. Molecular and cellular biology 24: 9542–9556.
34. HoppinsS, CollinsSR, Cassidy-StoneA, HummelE, DevayRM, et al. (2011) A mitochondrial-focused genetic interaction map reveals a scaffold-like complex required for inner membrane organization in mitochondria. The Journal of cell biology 195: 323–340.
35. TarassovK, MessierV, LandryCR, RadinovicS, Serna MolinaMM, et al. (2008) An in vivo map of the yeast protein interactome. Science 320: 1465–1470.
36. HowardJP, HuttonJL, OlsonJM, PayneGS (2002) Sla1p serves as the targeting signal recognition factor for NPFX(1,2)D-mediated endocytosis. The Journal of cell biology 157: 315–326.
37. TongAH, EvangelistaM, ParsonsAB, XuH, BaderGD, et al. (2001) Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 294: 2364–2368.
38. GuthrieC, FinkGR (1991) Guide to Yeast Genetics and Molecular Biology. Meth Enzymol 194: 429–663.
39. EhrenreichIM, TorabiN, JiaY, KentJ, MartisS, et al. (2010) Dissection of genetically complex traits with extremely large pools of yeast segregants. Nature 464: 1039–1042.
40. LiH, DurbinR (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754–1760.
41. AndolfattoP, DavisonD, ErezyilmazD, HuTT, MastJ, et al. (2011) Multiplexed shotgun genotyping for rapid and efficient genetic mapping. Genome research 21: 610–617.
42. StoriciF, LewisLK, ResnickMA (2001) In vivo site-directed mutagenesis using oligonucleotides. Nature biotechnology 19: 773–776.
43. GietzRD, WoodsRA (2002) Transformation of yeast by lithium acetate/single-stranded carrier DNA/polyethylene glycol method. Methods in enzymology 350: 87–96.
44. ErdenizN, MortensenUH, RothsteinR (1997) Cloning-free PCR-based allele replacement methods. Genome research 7: 1174–1183.
Štítky
Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
2014 Číslo 5
- Je „freeze-all“ pro všechny? Odborníci na fertilitu diskutovali na virtuálním summitu
- Gynekologové a odborníci na reprodukční medicínu se sejdou na prvním virtuálním summitu
Najčítanejšie v tomto čísle
- PINK1-Parkin Pathway Activity Is Regulated by Degradation of PINK1 in the Mitochondrial Matrix
- Phosphorylation of a WRKY Transcription Factor by MAPKs Is Required for Pollen Development and Function in
- Null Mutation in PGAP1 Impairing Gpi-Anchor Maturation in Patients with Intellectual Disability and Encephalopathy
- p53 Requires the Stress Sensor USF1 to Direct Appropriate Cell Fate Decision