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Epigenetics and Functional Genomics Laboratory

Taşkesen, M.*, Collin, G.B.*, Evsikov, A.V.*, Güzel, A., Özgül, R.K., Marshall, J.D., and Naggert, J.K. (2012).  Novel Alu retrotransposon insertion leading to Alström syndrome. Human Genetics 131: 407-413.

Bult, C.J., Drabkin, H., Evsikov, A., Natale, D. Arighi, C., Roberts, N., Ruttenberg, A., D'Eustachio, P., Smith, B., Blake, J.A., and Wu, C. (2011)  The representation of protein complexes in the Protein Ontology (PRO). BMC Bioinformatics 12: 371.

Staier F., Eipel H., Matula P., Evsikov A.V., Kozubek M., Cremer C., Hausmann M. (2011).  Micro Axial Tomography: a miniaturized, versatile stage device to overcome resolution anisotropy in fluorescence light microscopy. Review of Scientific Instruments 82: 093701.

Ratzan, W.J., Evsikov, A.V., Okamura, Y., and Jaffe, L.A. (2011).  Voltage sensitive phosphoinositide phosphatases of Xenopus: their tissue distribution and voltage dependence. Journal of Cellular Physiology 226: 2740–2746.

Natale, D.A., Arighi, C.N., Barker, W.C., Blake, J.A., Bult, C.J., Caudy, M., Drabkin, H.J., D'Eustachio, P., Evsikov, A.V., Huang, H., Nchoutmboube, J., Roberts, N.V., Smith, B., Zhang, J., and Wu, C.H. (2011).  The Protein Ontology (PRO): A Structured Representation of Protein Forms and Complexes. Nucleic Acids Research 39:  D539-D545.

Bui, L.C., Evsikov, A.V., Khan, D.R., Archilla, C., Peynot, N., Henaut, A., Le Bourhis, D., Vignon, X., Renard, J.P., and Duranthon, V. (2009).  Retrotransposon expression as a defining event of genome reprogramming in fertilized and cloned bovine embryos. Reproduction 138: 289-299.

Evsikov, A.V., Dolan, M., Genrich, M., Patek, E., and Bult, C.J. (2009).  MouseCyc: A biochemical pathways database for the laboratory mouse. Genome Biology 10: R84.

Evsikov, A.V., and Marín de Evsikova, C. (2009).  Evolutionary origin and phylogenetic analysis of the novel oocyte-specific eukaryotic translation initiation factor 4E in Tetrapoda. Development, Genes and Evolution 219: 111-118.

11.  Evsikov, A.V., and Marín de Evsikova, C. (2009).  Regulation of gene expression during the oocyte-to-embryo transition in mammals. Molecular Reproduction and Development 76: 805-818.

12.  De Vries, W.N., Evsikov, A.V., Jalbert, L., Anderson, C.P., Graber, J., Knowles, B.B., and Solter, D. (2008).  Reprogramming and differentiation in mammals: motifs and mechanisms. Cold Spring Harbor Symposia on Quantitative Biology: Control & Regulation of Stem Cells 73: 33-38.

13.  Evsikov, A.V., Graber, J.H., Brockman, J.M., Hampl, A., Holbrook, A.E., Singh, P., Eppig, J.J., Solter, D., and Knowles, B.B. (2006).  Cracking the egg: molecular dynamics and evolutionary aspects of the transition from the fully-grown oocyte to embryo. Genes and Development 20: 2713-2727.

14.  Peaston, A.E.*, Evsikov, A.V.*, Graber, J.H., de Vries, W.N., Holbrook, A.E., Solter, D., and Knowles, B.B. (2004).  Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos. Developmental Cell 7: 597-606.

15.  Evsikov, A.V., de Vries, W.N., Peaston, A., Radford, E.E., Fancher, K.S., Chen, F.H., Blake, J.A., Bult, C.J., Latham, K.E., Solter, D., and Knowles, B.B. (2004).  Systems biology of the 2-cell mouse embryo. Cytogenetics and Genome Research 105: 240-250.

16.  Mehlmann, L.M., Saeki, Y., Tanaka, S., Brennan, T.J., Evsikov, A.V., Pendola, F.L., Knowles, B.B., Eppig, J.J., and Jaffe, L.A. (2004).  The Gs-linked receptor GPR3 maintains meiotic arrest in mammalian oocytes. Science 306: 1947-1950.

17.  De Vries, W.N., Evsikov, A.V., Haac, B.E., Fancher, K.S., Holbrook, A.E., Kemler, R., Solter, D., and Knowles, B.B. (2004).  Maternal β-catenin and E-cadherin in mouse development. Development 131: 4435-4445.

18.  Evsikov, A.V., and Solter, D. (2003).  Comment on " 'Stemness': transcriptional profiling of embryonic and adult stem cells" and "A stem cell molecular signature". Science 302: 393.

19.  Solter, D., Hiiragi, T., Evsikov, A.V., Moyer, J., de Vries, W.N., Peaston, A.E., and Knowles, B.B. (2004).  Epigenetic mechanisms in early mammalian development. Cold Spring Harbor Symposia on Quantitative Biology: Epigenetics 69: 11-17.

20.  Knowles, B.B., Evsikov, A.V., de Vries, W.N., Peaston, A.E., and Solter, D. (2003).  Molecular control of the oocyte to embryo transition. Philosophical Transactions of the Royal Society B: Biological Sciences 358: 1381-1387.

22.  Solter, D., deVries, W.N., Peaston, A., Evsikov, A., and Knowles, B.B. (2002).  Fertilization and activation of the embryonic genome. In: Mouse Development: Morphogenesis and Organogenesis, Tamm, P., and Rossant, J., eds. New York: Academic Press. P. 5-19.

23.  Evsikov, A.V. (2000).  Mechanisms of regulation of early embryogenesis. Russian Journal of Developmental Biology 31: 142-153.

24.  Evsikov, A.V., and Solomko, A.P. (1999).  The levels and patterns of translation in preimplantation mouse embryos with repressed cytokinesis. Russian Journal of Developmental Biology 30: 83-88.

25.  Evsikov, A.V., and Solomko, A.P. (1998).  Changes in the cavitation start time in chimeric CB6F1↔BALB/c embryos. Cytology and Genetics 32: 74-77.

26.  Evsikov, A. V. (1997).  Regulatory mechanisms of mouse preimplantation development. Biopolimery i Kletka 13: 93-99. In Russian.

27.  Evsikov, A.V., and Evsikov, S.V. (1995).  Studies of the first and second polar bodies in mouse oogenesis. Russian Journal of Developmental Biology 26: 159-162. In English.

28.  Evsikov, S.V., and Evsikov, A.V. (1994).  Preimplantation development of manipulated mouse zygotes fused with the second polar bodies: a cytogenetic study. International Journal of Developmental Biology 38: 725-730.

Principal Investigators

Graduate Students

Caralina Marin de Evsikova, Ph.D.

Research Interests: The early developmental environment plays a pivotal role in susceptibility to adulthood metabolic disease, such as obesity and diabetes. The long-term goal of this project is to understand how the maternal and embryonic environment alters gene expression, which ultimately leads to disease, via epigenetics. Epigenome of each individual is established during the egg-to-embryo transition, which is sensitive to teratogens, such as alcohol, bisphenol A, or dietary exposures. To identify the role of epigenetics in metabolic disease, I am using a naturally occurring “epigenetic barometer” allele (viable yellow) of the Agouti gene in mice, whose expression is controlled by methylation levels. Nutrigenomics & Healthspan. My long-term goal is to develop new mouse models of adult-onset metabolic diseases by monitoring in vivo physiology coupled with quantitative molecular genetics to detect genes and pathways involved with weight gain. This approach has been successful in identifying changes in eating, activity, and loss of circadian rhythms underlying “normal” weight fluctuations from across the lifespan.

Alexei Evsikov, Ph.D.

Research Interests: The focus of our research program is to understand three seemingly disparate levels of biological organization during gametogenesis and early development: the molecular signatures for totipotency at the beginning of life, their variation among species, and their involvement as mechanisms of evolutionary change. We use comparative genomics and wet-lab approaches to understand how and why speciation primarily affects reproduction and its functions. Our approach provides a conceptual framework for personalized genomic medicine in human reproductive health.

Alexis Killeen

Research Interests: Obesogens are toxic agents that induce excess lipid storage in offspring after an in utero exposure.  The goal of my project is to develop a Caenorhabditis elegans model system to screen putative obesogens and indicate potential causal pathways from resulting shifts in energy balance.  This screen may also function to evaluate in vivo the efficacy of potential therapeutics for obesity at very early stages of the drug development pipeline.  My second project involves identification of  functional C. elegans homologs of mammalian PPARs, which would further validate this organism's utility as a model to study obesity.  PPARγ is especially important, as many obesogens have been shown to operate via a PPARγ-mediated mechanism.  After obtaining my Ph.D., I hope to work for the research division of the Food and Drug Administration or the Consumer Product Safety Commission.

Isaac Raplee

Research Interests: Retroviruses are well known thanks to the awareness spread about HIV. However, not well known about retroviruses is that many are already incorporated into the genome of many animals including humans. Not only are these endogenous retroviruses (ERVs) in our genome, but they are often utilized by the host for beneficial, and sometimes disastrous, outcomes. Within the last two decades ERVs have become well known as markers for advanced stage cancers. However, many ERVs are also expressed during the totipotent and pluripotent stages of embryogenesis. Additionally, new recent findings suggest ERVs are present during early stage cancers. We are interested in determining the roles of these ERVs in driving the pluripotency of early embryogenesis and aberrant cells.