P J Wittkopp

Summary

Affiliation: University of Michigan
Country: USA

Publications

  1. pmc Contrasting properties of gene-specific regulatory, coding, and copy number mutations in Saccharomyces cerevisiae: frequency, effects, and dominance
    Jonathan D Gruber
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
    PLoS Genet 8:e1002497. 2012
  2. pmc Nomadic enhancers: tissue-specific cis-regulatory elements of yellow have divergent genomic positions among Drosophila species
    Gizem Kalay
    Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
    PLoS Genet 6:e1001222. 2010
  3. pmc Sources of bias in measures of allele-specific expression derived from RNA-seq data aligned to a single reference genome
    Kraig R Stevenson
    Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
    BMC Genomics 14:536. 2013
  4. ncbi request reprint Evolutionary genetics: how flies get naked
    Patricia J Wittkopp
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109 1048, USA
    Curr Biol 17:R881-3. 2007
  5. pmc Independent effects of cis- and trans-regulatory variation on gene expression in Drosophila melanogaster
    Patricia J Wittkopp
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Genetics 178:1831-5. 2008
  6. ncbi request reprint Regulatory changes underlying expression differences within and between Drosophila species
    Patricia J Wittkopp
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Nat Genet 40:346-50. 2008
  7. doi request reprint Development and evolution of insect pigmentation: genetic mechanisms and the potential consequences of pleiotropy
    Patricia J Wittkopp
    830 North University Avenue, Department of Ecology and Evolutionary Biology, Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109 1048, USA
    Semin Cell Dev Biol 20:65-71. 2009
  8. doi request reprint Intraspecific polymorphism to interspecific divergence: genetics of pigmentation in Drosophila
    Patricia J Wittkopp
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
    Science 326:540-4. 2009
  9. pmc Variable transcription factor binding: a mechanism of evolutionary change
    Patricia J Wittkopp
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
    PLoS Biol 8:e1000342. 2010
  10. pmc Local adaptation for body color in Drosophila americana
    P J Wittkopp
    Department of Ecology and Evolutionary Biology, Ann Arbor, MI, USA
    Heredity (Edinb) 106:592-602. 2011

Detail Information

Publications27

  1. pmc Contrasting properties of gene-specific regulatory, coding, and copy number mutations in Saccharomyces cerevisiae: frequency, effects, and dominance
    Jonathan D Gruber
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
    PLoS Genet 8:e1002497. 2012
    ..These differences in the frequency, effects, and dominance among functional classes of mutations might help explain why some types of mutations are found to be segregating within or fixed between species more often than others...
  2. pmc Nomadic enhancers: tissue-specific cis-regulatory elements of yellow have divergent genomic positions among Drosophila species
    Gizem Kalay
    Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
    PLoS Genet 6:e1001222. 2010
    ....
  3. pmc Sources of bias in measures of allele-specific expression derived from RNA-seq data aligned to a single reference genome
    Kraig R Stevenson
    Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
    BMC Genomics 14:536. 2013
    ..To improve accuracy of ASE measured using a single reference genome, we identified properties of differentiating sites responsible for biased measures of relative ASE...
  4. ncbi request reprint Evolutionary genetics: how flies get naked
    Patricia J Wittkopp
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109 1048, USA
    Curr Biol 17:R881-3. 2007
    ..Researchers studying evolution of 'naked' (hairless) larval cuticle in Drosophila sechellia have discovered surprising complexity in the pattern of cis-regulatory differences that differentiate this species from its 'hairy' ancestors...
  5. pmc Independent effects of cis- and trans-regulatory variation on gene expression in Drosophila melanogaster
    Patricia J Wittkopp
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Genetics 178:1831-5. 2008
    ..The frequency of such independent interactions on a genomic scale is yet to be determined...
  6. ncbi request reprint Regulatory changes underlying expression differences within and between Drosophila species
    Patricia J Wittkopp
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Nat Genet 40:346-50. 2008
    ..Specifically, cis-regulatory changes seem to accumulate preferentially over time...
  7. doi request reprint Development and evolution of insect pigmentation: genetic mechanisms and the potential consequences of pleiotropy
    Patricia J Wittkopp
    830 North University Avenue, Department of Ecology and Evolutionary Biology, Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109 1048, USA
    Semin Cell Dev Biol 20:65-71. 2009
    ..This review discusses recent work on the development and evolution of insect pigmentation, with a focus on pleiotropy and its effects on color pattern diversification...
  8. doi request reprint Intraspecific polymorphism to interspecific divergence: genetics of pigmentation in Drosophila
    Patricia J Wittkopp
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
    Science 326:540-4. 2009
    ..These alleles appear to predate speciation, which suggests that standing genetic variation present in the common ancestor gave rise to both intraspecific polymorphism and interspecific divergence...
  9. pmc Variable transcription factor binding: a mechanism of evolutionary change
    Patricia J Wittkopp
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
    PLoS Biol 8:e1000342. 2010
    ..This primer discusses a study from Bradley et al. in which changes in transcription factor binding between two Drosophila species are revealed by chromatin immunoprecipitation and high-throughput sequencing...
  10. pmc Local adaptation for body color in Drosophila americana
    P J Wittkopp
    Department of Ecology and Evolutionary Biology, Ann Arbor, MI, USA
    Heredity (Edinb) 106:592-602. 2011
    ..americana. We found no significant effect of pigmentation on desiccation resistance in this experiment, suggesting that pigmentation and desiccation resistance are not unequivocally linked in all Drosophila species...
  11. doi request reprint Using pyrosequencing to measure allele-specific mRNA abundance and infer the effects of cis- and trans-regulatory differences
    Patricia J Wittkopp
    University of Michigan, Ann Arbor, MI, USA
    Methods Mol Biol 772:297-317. 2011
    ..I also describe how such data can be used to infer the relative contribution of cis- and trans-acting changes to expression differences between genotypes...
  12. ncbi request reprint Variable gene expression in eukaryotes: a network perspective
    Patricia J Wittkopp
    Department of Ecology and Evolutionary Biology, Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
    J Exp Biol 210:1567-75. 2007
    ..Here I review the basic structure of eukaryotic regulatory networks and discuss selected case studies that provide insight into how these networks are altered to create expression differences within and between species...
  13. ncbi request reprint Evolution of cis-regulatory sequence and function in Diptera
    P J Wittkopp
    Department of Ecology and Evolutionary Biology, University of Michigan, 1061 Natural Science Building, 830 North University Ave, Ann Arbor, MI 48109 1048, USA
    Heredity (Edinb) 97:139-47. 2006
    ..Biochemical characterization and in vivo assays of cis-regulatory sequences on a genomic-scale will relieve this barrier...
  14. doi request reprint Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence
    Patricia J Wittkopp
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
    Nat Rev Genet 13:59-69. 2012
    ....
  15. pmc Parent-of-origin effects on mRNA expression in Drosophila melanogaster not caused by genomic imprinting
    Patricia J Wittkopp
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Genetics 173:1817-21. 2006
    ..Offspring from reciprocal crosses exhibit differences in total expression without differences in allelic expression, indicating that other types of maternal and/or paternal effects alter expression...
  16. pmc The function and regulation of Ultrabithorax in the legs of Drosophila melanogaster
    Gregory K Davis
    Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
    Dev Biol 308:621-31. 2007
    ..While the enhancer could reside within the small regions we have not surveyed, it is also possible that the enhancer is structurally complex and/or acts only within its native genomic context...
  17. ncbi request reprint Evolutionary changes in cis and trans gene regulation
    Patricia J Wittkopp
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Nature 430:85-8. 2004
    ..These data indicate that interspecific expression differences are not caused by select trans-regulatory changes with widespread effects, but rather by many cis-acting changes spread throughout the genome...
  18. ncbi request reprint A gene necessary for normal male courtship, yellow, acts downstream of fruitless in the Drosophila melanogaster larval brain
    Mark David Drapeau
    Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92697, USA
    J Neurobiol 55:53-72. 2003
    ..Overall, these data suggest that y is a downstream member of the fru branch of the D. melanogaster sex determination hierarchy, where it plays a currently unknown role in the development of adult male wing extension during courtship...
  19. ncbi request reprint Evolution in black and white: genetic control of pigment patterns in Drosophila
    Patricia J Wittkopp
    Molecular Biology and Genetics, 227 Biotechnology Building, Cornell University, Ithaca, NY 14853, USA
    Trends Genet 19:495-504. 2003
  20. ncbi request reprint Genomic sources of regulatory variation in cis and in trans
    P J Wittkopp
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Cell Mol Life Sci 62:1779-83. 2005
    ..I argue that the molecular function of the protein encoded by each gene and how the gene is wired into the genomic regulatory network may influence its propensity for cis and trans regulatory changes...
  21. ncbi request reprint Chance caught on the wing: cis-regulatory evolution and the origin of pigment patterns in Drosophila
    Nicolas Gompel
    Howard Hughes Medical Institute and Laboratory of Molecular Biology, University of Wisconsin, 1525 Linden Drive, Madison, Wisconsin 53706, USA
    Nature 433:481-7. 2005
    ....
  22. pmc Compensatory cis-trans evolution and the dysregulation of gene expression in interspecific hybrids of Drosophila
    Christian R Landry
    Department of Organismic and Evolutionary Biology, The Biological Laboratories, 16 Divinity Avenue, Harvard University, Cambridge, MA 02138, USA
    Genetics 171:1813-22. 2005
    ..Using a mathematical model for the regulation of gene expression, we explored the conditions under which cis-trans compensatory evolution can lead to misexpression in interspecific hybrids...
  23. pmc Drosophila pigmentation evolution: divergent genotypes underlying convergent phenotypes
    Patricia J Wittkopp
    Howard Hughes Medical Institute and Laboratory of Molecular Biology, University of Wisconsin, 1525 Linden Drive, Madison, WI 53706, USA
    Proc Natl Acad Sci U S A 100:1808-13. 2003
    ..These findings bear upon understanding classic models of melanism and mimicry...
  24. ncbi request reprint Evolution of yellow gene regulation and pigmentation in Drosophila
    Patricia J Wittkopp
    Howard Hughes Medical Institute, Laboratory of Molecular Biology, University of Wisconsin, Madison, WI 53706, USA
    Curr Biol 12:1547-56. 2002
    ..Here, we compare the regulation of the yellow gene, which is required for melanization, among distantly related Drosophila species with different pigment patterns and determine the phenotypic effects of divergent Yellow expression...
  25. ncbi request reprint Immunohistochemical colocalization of Yellow and male-specific Fruitless in Drosophila melanogaster neuroblasts
    Anna Radovic
    Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
    Biochem Biophys Res Commun 293:1262-4. 2002
    ..We hypothesize that yellow is downstream of fruitless in a male courtship behavior developmental genetic pathway...
  26. ncbi request reprint Annotating ebony on the fly
    Michael H Kohn
    Mol Ecol 16:2831-3. 2007
    ..In addition, the study raises issues to consider when extrapolating from selection at the molecular level to selection at the phenotypic level...
  27. ncbi request reprint Reciprocal functions of the Drosophila yellow and ebony proteins in the development and evolution of pigment patterns
    Patricia J Wittkopp
    Howard Hughes Medical Institute, Laboratory of Molecular Biology, University of Wisconsin, 1525 Linden Drive, Madison, WI 53706, USA
    Development 129:1849-58. 2002
    ..These findings provide a developmental and genetic framework for understanding the evolution of melanin patterns...

Research Grants1

  1. Evolutionary Genetics: Contribution of Tan to Drosophila Pigmentation Divergence
    Patricia J Wittkopp; Fiscal Year: 2010
    ..This project will identify specific genetic changes underlying divergence in a complex trait as well as reveal how these genetic changes alter development to produce alternative phenotypes. ..