Experts and Doctors on genetic epistasis in United States

Summary

Locale: United States
Topic: genetic epistasis

Top Publications

  1. Desai M, Weissman D, Feldman M. Evolution can favor antagonistic epistasis. Genetics. 2007;177:1001-10 pubmed
    ..This suggests that we should not expect synergistic epistasis to be widespread in nature and hence that the mutational deterministic hypothesis for the advantage of sex may not apply widely. ..
  2. Nichols K, Edo A, Wheeler P, Thorgaard G. The genetic basis of smoltification-related traits in Oncorhynchus mykiss. Genetics. 2008;179:1559-75 pubmed publisher
    ..Dissecting the genetic architecture of this highly complex trait has profound implications for understanding the genetic and evolutionary basis of life-history diversity within and among migratory fishes. ..
  3. Lionikas A, Blizard D, Vandenbergh D, Glover M, Stout J, Vogler G, et al. Genetic architecture of fast- and slow-twitch skeletal muscle weight in 200-day-old mice of the C57BL/6J and DBA/2J lineage. Physiol Genomics. 2003;16:141-52 pubmed
  4. Just B, Santos C, Yandell B, Simon P. Major QTL for carrot color are positionally associated with carotenoid biosynthetic genes and interact epistatically in a domesticated x wild carrot cross. Theor Appl Genet. 2009;119:1155-69 pubmed publisher
    ..These two genes played a major role in carrot domestication and account for the significant role that modern carrot plays in vitamin A nutrition. ..
  5. Merighi M, Majerczak D, Stover E, Coplin D. The HrpX/HrpY two-component system activates hrpS expression, the first step in the regulatory cascade controlling the Hrp regulon in Pantoea stewartii subsp. stewartii. Mol Plant Microbe Interact. 2003;16:238-48 pubmed
    ..These findings suggest that both HrpX and an alternate mechanism are involved in the activation of HrpY in planta. ..
  6. Sucheston L, Chanda P, Zhang A, Tritchler D, Ramanathan M. Comparison of information-theoretic to statistical methods for gene-gene interactions in the presence of genetic heterogeneity. BMC Genomics. 2010;11:487 pubmed publisher
    ..KWII performed similar to logistic regression. Information theoretic models are flexible and have excellent power to detect GGI under a variety of conditions that characterize complex diseases. ..
  7. Maletic V, Raison C. Neurobiology of depression, fibromyalgia and neuropathic pain. Front Biosci (Landmark Ed). 2009;14:5291-338 pubmed
  8. Samuelson D, Aperavich B, Haag J, Gould M. Fine mapping reveals multiple loci and a possible epistatic interaction within the mammary carcinoma susceptibility quantitative trait locus, Mcs5. Cancer Res. 2005;65:9637-42 pubmed
    ..0, 7.5, and 4.5 Mb of rat chromosome 5, and the orthologous regions are on human chromosome 9 and mouse chromosome 4. These loci will provide unbiased candidate gene loci for evaluation in human case-control association studies. ..
  9. Moyle L, Nakazato T. Complex epistasis for Dobzhansky-Muller hybrid incompatibility in solanum. Genetics. 2009;181:347-51 pubmed publisher

More Information

Publications67

  1. Shepherd A, Wesley U, Wesley C. Notch and delta mRNAs in early-stage and mid-stage drosophila embryos exhibit complementary patterns of protein-producing potentials. Dev Dyn. 2010;239:1220-33 pubmed publisher
    ..Our data also raise the possibility that the manner and regulation of Notch signaling change in the course of embryogenesis and that this change is effected by 3' UTR and mRNA 3' processing factors...
  2. Schmitz R, Hong L, Michaels S, Amasino R. FRIGIDA-ESSENTIAL 1 interacts genetically with FRIGIDA and FRIGIDA-LIKE 1 to promote the winter-annual habit of Arabidopsis thaliana. Development. 2005;132:5471-8 pubmed
  3. Krizek B, Lewis M, Fletcher J. RABBIT EARS is a second-whorl repressor of AGAMOUS that maintains spatial boundaries in Arabidopsis flowers. Plant J. 2006;45:369-83 pubmed
    ..RBE thus acts to maintain two different types of spatial boundaries in young flowers: boundaries between organ primordia within a whorl and boundaries of homeotic gene expression between whorls. ..
  4. Bridgham J, Ortlund E, Thornton J. An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Nature. 2009;461:515-9 pubmed publisher
    ..Our findings indicate that even if selection for the ancestral function were imposed, direct reversal would be extremely unlikely, suggesting an important role for historical contingency in protein evolution. ..
  5. Palmer A, Low M, Grandy D, Phillips T. Effects of a Drd2 deletion mutation on ethanol-induced locomotor stimulation and sensitization suggest a role for epistasis. Behav Genet. 2003;33:311-24 pubmed
    ..The impact of the Drd2 null mutation on a subset of ethanol-related behavioral traits is subject to epistatic influences. ..
  6. Grossmann K, Ward A, Matkovic M, Folias A, Moses R. S. cerevisiae has three pathways for DNA interstrand crosslink repair. Mutat Res. 2001;487:73-83 pubmed
  7. Moyle L, Nakazato T. Hybrid incompatibility "snowballs" between Solanum species. Science. 2010;329:1521-3 pubmed publisher
    ..In comparison, loci underlying traits unrelated to hybrid sterility show no evidence for an accelerating rate of accumulation between species. ..
  8. Lu R, Yigit E, Li W, Ding S. An RIG-I-Like RNA helicase mediates antiviral RNAi downstream of viral siRNA biogenesis in Caenorhabditis elegans. PLoS Pathog. 2009;5:e1000286 pubmed publisher
    ..elegans control parallel antiviral RNAi pathways. These findings demonstrate both conserved and unique strategies of C. elegans in antiviral defense. ..
  9. Fredericks C, Shibata S, Aizawa S, Reimann S, Wolfe A. Acetyl phosphate-sensitive regulation of flagellar biogenesis and capsular biosynthesis depends on the Rcs phosphorelay. Mol Microbiol. 2006;61:734-47 pubmed
    ..Temporal control of flagella biogenesis implicates the Rcs phosphorelay (and, by extension, acetyl approximately P) in the transition of motile, planktonic individuals into sessile biofilm communities. ..
  10. Pandey J, Montes Cano M, Aguilar Reina J, Gonzalez Escribano M. Interactive effects of immunoglobulin gamma and human leucocyte antigen genotypes on clearance and persistence of infection with hepatitis C virus. Clin Exp Immunol. 2007;150:518-22 pubmed
    ..80). These results show, for the first time, interactive effects of GM and HLA genotypes in the outcome of HCV infection. ..
  11. Pattin K, White B, Barney N, Gui J, Nelson H, Kelsey K, et al. A computationally efficient hypothesis testing method for epistasis analysis using multifactor dimensionality reduction. Genet Epidemiol. 2009;33:87-94 pubmed publisher
    ..We then demonstrate this new method by applying it to a genetic epidemiology study of bladder cancer susceptibility that was previously analyzed using MDR and assessed using a 1,000-fold permutation test. ..
  12. Jagadeeswaran G, Raina S, Acharya B, Maqbool S, Mosher S, Appel H, et al. Arabidopsis GH3-LIKE DEFENSE GENE 1 is required for accumulation of salicylic acid, activation of defense responses and resistance to Pseudomonas syringae. Plant J. 2007;51:234-46 pubmed
    ..syringae (and possibly other pathogens) by playing a critical role in regulating the levels of pathogen-inducible SA. GDG1 is allelic to the PBS3 (avrPphB susceptible) gene. ..
  13. Rawls J. Analysis of pyrimidine catabolism in Drosophila melanogaster using epistatic interactions with mutations of pyrimidine biosynthesis and beta-alanine metabolism. Genetics. 2006;172:1665-74 pubmed
    ..These results are discussed in the context of similar consequences of 5-fluoropyrimidine toxicity and pyrimidine catabolism mutations in humans. ..
  14. Ratnaparkhi A, Zinn K. The secreted cell signal Folded Gastrulation regulates glial morphogenesis and axon guidance in Drosophila. Dev Biol. 2007;308:158-68 pubmed
    ..We also found that Ptp52F mutants have early VF phenotypes like those seen in fog mutants. ..
  15. Owens K, Santos F, Roberts B, Linbo T, Coffin A, Knisely A, et al. Identification of genetic and chemical modulators of zebrafish mechanosensory hair cell death. PLoS Genet. 2008;4:e1000020 pubmed publisher
    ..The combination of chemical screening with traditional genetic approaches is a new strategy for identifying drugs and drug targets to attenuate hearing and balance disorders. ..
  16. Paulovich A, Margulies R, Garvik B, Hartwell L. RAD9, RAD17, and RAD24 are required for S phase regulation in Saccharomyces cerevisiae in response to DNA damage. Genetics. 1997;145:45-62 pubmed
  17. Pandey J, Prohaszka Z, Veres A, Fust G, Hurme M. Epistatic effects of genes encoding immunoglobulin GM allotypes and interleukin-6 on the production of autoantibodies to 60- and 65-kDa heat-shock proteins. Genes Immun. 2004;5:68-71 pubmed
    ..038) antibody levels. Since these autoantibodies have been implicated in susceptibility to coronary heart disease and carotid atherosclerosis, the associations reported here might be relevant to the etiology of these diseases. ..
  18. Guo J, Tian D, McKinney B, Hartman J. Recursive expectation-maximization clustering: a method for identifying buffering mechanisms composed of phenomic modules. Chaos. 2010;20:026103 pubmed publisher
    ..It facilitates identification of phenomic modules, which contribute to buffering mechanisms that underlie cellular homeostasis and the regulation of phenotypic expression. ..
  19. Abramova N, Cohen B, Sertil O, Kapoor R, Davies K, Lowry C. Regulatory mechanisms controlling expression of the DAN/TIR mannoprotein genes during anaerobic remodeling of the cell wall in Saccharomyces cerevisiae. Genetics. 2001;157:1169-77 pubmed
    ..In addition Rox1, another heme-responsive repressor, and the global repressors Tup1 and Ssn6 are also required for full aerobic repression of these genes. ..
  20. Tran P, Simon J, Liskay R. Interactions of Exo1p with components of MutLalpha in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 2001;98:9760-5 pubmed
    ..Finally, our results show that much of the increase in spontaneous mutation observed in an exo1Delta strain is REV3-dependent, in turn suggesting that Exo1p is also involved in one or more MMR-independent mutation avoidance pathways. ..
  21. Williams B, Mirzoeva O, Morgan W, Lin J, Dunnick W, Petrini J. A murine model of Nijmegen breakage syndrome. Curr Biol. 2002;12:648-53 pubmed
    ..We propose that the ATM-Mre11 complex DNA damage response pathway is essential and that ATM or the Mre11 complex serves as a nexus to additional components of the pathway. ..
  22. Presgraves D, Balagopalan L, Abmayr S, Orr H. Adaptive evolution drives divergence of a hybrid inviability gene between two species of Drosophila. Nature. 2003;423:715-9 pubmed publisher
    ..These results show that a lethal hybrid incompatibility has evolved as a by-product of adaptive protein evolution...
  23. Carter G, Rush C, Uygun F, Sakhanenko N, Galas D, Galitski T. A systems-biology approach to modular genetic complexity. Chaos. 2010;20:026102 pubmed publisher
    ..We further discuss the consequences for genetic interaction networks and propose a framework for the analysis of genetic modularity. ..
  24. Olson J, Goddard K, Dudek D. A second locus for very-late-onset Alzheimer disease: a genome scan reveals linkage to 20p and epistasis between 20p and the amyloid precursor protein region. Am J Hum Genet. 2002;71:154-61 pubmed
    ..We speculate that high-risk polymorphisms in both regions produce a biological interaction between these two proteins that increases susceptibility to a very-late-onset form of AD. ..
  25. Job M, Tang A, Hall F, Sora I, Uhl G, Bergeson S, et al. Mu (mu) opioid receptor regulation of ethanol-induced dopamine response in the ventral striatum: evidence of genotype specific sexual dimorphic epistasis. Biol Psychiatry. 2007;62:627-34 pubmed
    ..This implies that a more complete understanding of the epistatic influences on the MOP receptor and mesolimbic dopamine function may provide more effective pharmacotherapeutic interventions in the treatment of alcoholism. ..
  26. Greene C, Penrod N, Williams S, Moore J. Failure to replicate a genetic association may provide important clues about genetic architecture. PLoS ONE. 2009;4:e5639 pubmed publisher
    ..We recommend that polymorphisms that fail to replicate be checked for interactions with other polymorphisms, particularly when samples are collected from groups with distinct ethnic backgrounds or different geographic regions. ..
  27. Yoon H, McDermott J, Porwollik S, McClelland M, Heffron F. Coordinated regulation of virulence during systemic infection of Salmonella enterica serovar Typhimurium. PLoS Pathog. 2009;5:e1000306 pubmed publisher
    ..Furthermore, experiments to demonstrate epistatic relationships showed that SsrB can replace SlyA and, in some cases, SlyA can replace SsrB for expression of SPI-2 encoded virulence factors...
  28. Tsuchiya T, Eulgem T. The Arabidopsis defense component EDM2 affects the floral transition in an FLC-dependent manner. Plant J. 2010;62:518-28 pubmed publisher
  29. Khatib H, Huang W, Wang X, Tran A, Bindrim A, Schutzkus V, et al. Single gene and gene interaction effects on fertilization and embryonic survival rates in cattle. J Dairy Sci. 2009;92:2238-47 pubmed publisher
    ..Thus, we propose that single genes as well as an entire pathway can be used in selection programs to improve reproduction performance in dairy cattle. ..
  30. Pogorzala L, Mookerjee S, Sia E. Evidence that msh1p plays multiple roles in mitochondrial base excision repair. Genetics. 2009;182:699-709 pubmed publisher
    ..In addition to this separation of function, we also found that the role of Msh1p in BER is unlikely to be involved in the avoidance of large-scale deletions and rearrangements. ..
  31. Gleason J, James R, Wicker Thomas C, Ritchie M. Identification of quantitative trait loci function through analysis of multiple cuticular hydrocarbons differing between Drosophila simulans and Drosophila sechellia females. Heredity (Edinb). 2009;103:416-24 pubmed publisher
    ..simulans is not. Epistatic interactions, only detected for CHCs limited to D. sechellia, imply that complex interactions among loci may also be having a role in these compounds that affect mating isolation. ..
  32. Cuevas H, Staub J, Simon P, Zalapa J. A consensus linkage map identifies genomic regions controlling fruit maturity and beta-carotene-associated flesh color in melon (Cucumis melo L.). Theor Appl Genet. 2009;119:741-56 pubmed publisher
  33. Xu S, Falvey D, Brandriss M. Roles of URE2 and GLN3 in the proline utilization pathway in Saccharomyces cerevisiae. Mol Cell Biol. 1995;15:2321-30 pubmed
    ..URE2 repression appears to be limited to nitrogen assimilatory systems and does not affect genes involved in carbon, inositol, or phosphate metabolism or in mating-type control and sporulation. ..
  34. Lupashin V, Pokrovskaya I, McNew J, Waters M. Characterization of a novel yeast SNARE protein implicated in Golgi retrograde traffic. Mol Biol Cell. 1997;8:2659-76 pubmed
    ..We propose that Vti1p, along with Ykt6p and perhaps Sft1p, acts as a retrograde v-SNARE capable of interacting with the cis-Golgi t-SNARE Sed5p. ..
  35. Demuth J, Wade M. Population differentiation in the beetle Tribolium castaneum. II. Haldane'S rule and incipient speciation. Evolution. 2007;61:694-9 pubmed
  36. Pauli D, Mahowald A. Germ-line sex determination in Drosophila melanogaster. Trends Genet. 1990;6:259-64 pubmed
    ..Only some of the genes involved in somatic sex determination are also needed for germ cell development. Recent genetic studies have identified loci required for germ-line sex determination. ..
  37. Takemaru K, Yamaguchi S, Lee Y, Zhang Y, Carthew R, Moon R. Chibby, a nuclear beta-catenin-associated antagonist of the Wnt/Wingless pathway. Nature. 2003;422:905-9 pubmed
    ..In addition, epistasis experiments indicate that chibby acts downstream of wingless and upstream of armadillo. ..
  38. Tang D, Ade J, Frye C, Innes R. A mutation in the GTP hydrolysis site of Arabidopsis dynamin-related protein 1E confers enhanced cell death in response to powdery mildew infection. Plant J. 2006;47:75-84 pubmed
    ..These observations suggest a mechanistic link between salicylic acid signaling, mitochondria and programmed cell death in plants. ..
  39. Choe C, Miller S, Brown S. A pair-rule gene circuit defines segments sequentially in the short-germ insect Tribolium castaneum. Proc Natl Acad Sci U S A. 2006;103:6560-4 pubmed
    ..This pair-rule gene circuit provides insight into short-germ segmentation in Tribolium that may be more generally applicable to segmentation in other arthropods. ..
  40. Hermann G, Schroeder L, Hieb C, Kershner A, Rabbitts B, Fonarev P, et al. Genetic analysis of lysosomal trafficking in Caenorhabditis elegans. Mol Biol Cell. 2005;16:3273-88 pubmed
    ..The glo mutants thus provide a simple model system for the analysis of lysosome-related organelle biogenesis in animal cells. ..
  41. Kelly J. Epistasis in monkeyflowers. Genetics. 2005;171:1917-31 pubmed
    ..The results for these traits suggest that epistatic effects are variable across genetic backgrounds or sets of interacting loci. ..
  42. Wang S, Hawkins C, Yoo S, Muller H, Hay B. The Drosophila caspase inhibitor DIAP1 is essential for cell survival and is negatively regulated by HID. Cell. 1999;98:453-63 pubmed
  43. Nadeau J. Modifier genes and protective alleles in humans and mice. Curr Opin Genet Dev. 2003;13:290-5 pubmed
    ..Together these modifier genes and protective alleles provide important glimpses into the molecular and cellular basis for the functional networks that provide robustness and homeostasis in complex biological systems. ..
  44. Bergeson S, Kyle Warren R, Crabbe J, Metten P, Gene Erwin V, Belknap J. Chromosomal loci influencing chronic alcohol withdrawal severity. Mamm Genome. 2003;14:454-63 pubmed
  45. Rafalski J. Association genetics in crop improvement. Curr Opin Plant Biol. 2010;13:174-80 pubmed publisher
    ..Classical biparental mapping remains the method of choice for mapping the effects of alleles rare in germplasm collections, such as some disease resistance genes or alleles introgressed from exotic germplasm. ..
  46. Poole E, Hsu L, Xiao L, Kulmacz R, Carlson C, Rabinovitch P, et al. Genetic variation in prostaglandin E2 synthesis and signaling, prostaglandin dehydrogenase, and the risk of colorectal adenoma. Cancer Epidemiol Biomarkers Prev. 2010;19:547-57 pubmed publisher
    ..These data provide little support for associations between adenoma risk and genetic variability related to PGE(2), yet suggest gene-environment interactions with anti-inflammatory exposures. ..
  47. Taga M, Miller S, Bassler B. Lsr-mediated transport and processing of AI-2 in Salmonella typhimurium. Mol Microbiol. 2003;50:1411-27 pubmed
    ..Transport and processing of AI-2 could be required for removing the quorum-sensing signal, conveying the signal to an internal detector and/or scavenging boron...
  48. Bastiani C, Gharib S, Simon M, Sternberg P. Caenorhabditis elegans Galphaq regulates egg-laying behavior via a PLCbeta-independent and serotonin-dependent signaling pathway and likely functions both in the nervous system and in muscle. Genetics. 2003;165:1805-22 pubmed
    ..Our data indicate that there are multiple signaling pathways downstream of EGL-30 and that different pathways could predominate with respect to the regulation of different behaviors. ..
  49. Doebley J. The genetics of maize evolution. Annu Rev Genet. 2004;38:37-59 pubmed
  50. Girgis H, Liu Y, Ryu W, Tavazoie S. A comprehensive genetic characterization of bacterial motility. PLoS Genet. 2007;3:1644-60 pubmed
    ..This unifying framework enables sensitive and comprehensive genetic characterization of complex behaviors across the microbial biosphere. ..
  51. Wu R, Ma C, Hou W, Corva P, Medrano J. Functional mapping of quantitative trait loci that interact with the hg mutation to regulate growth trajectories in mice. Genetics. 2005;171:239-49 pubmed
    ..Our model provides a powerful means for understanding the genetic architecture and regulation of growth rate and body size in mammals. ..
  52. Zhang H, Chatterjee A, Singh K. Saccharomyces cerevisiae polymerase zeta functions in mitochondria. Genetics. 2006;172:2683-8 pubmed
    ..Supporting this evidence, both polymerase zeta and Rev1p were found to be localized in the mitochondria. This is the first report demonstrating that the DNA polymerase zeta and Rev1 proteins function in the mitochondria. ..
  53. Many A, Melki C, Savytskyy O, Maillet D, Acharya S, Zolan M. Meiotic localization of Mre11 and Rad50 in wild type, spo11-1, and MRN complex mutants of Coprinus cinereus. Chromosoma. 2009;118:471-86 pubmed publisher
    ..Independent Mre11 and Rad50 foci might indicate disassociation of the complex during meiosis or could reflect independent structural roles for the two proteins in meiotic chromatin. ..
  54. Zalapa J, Staub J, McCreight J, Chung S, Cuevas H. Detection of QTL for yield-related traits using recombinant inbred lines derived from exotic and elite US Western Shipping melon germplasm. Theor Appl Genet. 2007;114:1185-201 pubmed
    ..positive) of the QTL detected. Results indicate that genes resident in highly branched melon types have potential for increasing yield in US Western Shipping type germplasm via marker-assisted selection...
  55. Lam M, Heaney J, Youngren K, Kawasoe J, Nadeau J. Trans-generational epistasis between Dnd1Ter and other modifier genes controls susceptibility to testicular germ cell tumors. Hum Mol Genet. 2007;16:2233-40 pubmed
  56. Nowacki M, Vijayan V, Zhou Y, Schotanus K, Doak T, Landweber L. RNA-mediated epigenetic programming of a genome-rearrangement pathway. Nature. 2008;451:153-8 pubmed
    ..Injection of artificial templates reprogrammes the DNA rearrangement pathway, suggesting that RNA molecules guide genome rearrangement...
  57. Shao H, Burrage L, Sinasac D, Hill A, Ernest S, O BRIEN W, et al. Genetic architecture of complex traits: large phenotypic effects and pervasive epistasis. Proc Natl Acad Sci U S A. 2008;105:19910-4 pubmed publisher
    ..These results have implications for identification of complex trait genes, developmental and physiological studies of phenotypic variation, and opportunities to engineer phenotypic outcomes in complex biological systems...
  58. Kupchak B, Garitaonandia I, Villa N, Mullen M, Weaver M, Regalla L, et al. Probing the mechanism of FET3 repression by Izh2p overexpression. Biochim Biophys Acta. 2007;1773:1124-32 pubmed
    ..Finally, we show that the mechanism by which PAQR receptors activate signal transduction pathways is likely to be conserved from yeast to humans. ..