Professor Director, Developmental Biology Alliance Ph.D. (2002) Massachusetts Institute of Technology Member, Anolis Gene Nomenclature Committee Grant Support - "Developmental Context and the Control of Appendage cis-Regulatory Networks", NIH/NICHD "EDGE: Establishment of genome-editing and transgenic tools in Anolis lizards", NSF "Collaborative Research: Enhancers and the Convergent Evolution of Limb Reduction in Squamates", NSF "Dimensions US-South Africa: Convergent evolution across time and space: Evolutionary diversity and contemporary adaptation in New and Old World lizards", NSF "Does Evolution Repeat Itself? Genome Evolution and Phenotypic Convergence in Island Lizards", Human Frontiers Science Program Research Interests - How is vertebrate morphology encoded in the genome, and how does vertebrate morphology evolve? Vertebrate limbs are ideal structures in which to study these questions because they are both highly patterned and show remarkable changes in size and form in animals adapted to running, swimming, hopping, digging, or flying. Although many of the genes that control limb growth and patterning have been identified, we know relatively little about how the expression of these genes is regulated and to what degree changes in the regulation of these limb genes has contributed to the evolution of divergent limb morphologies. My lab uses a combination of comparative genomics and functional assays in mice and lizards to identify key cis-regulatory elements that control the expression of developmentally important genes. We recently established CRISPR-based gene-editing in Anolis lizards. This is the first reptilian model system where targeted gene knockouts can be generated, and our current work is focused on applying this method to investigate the gene function in reptile development and evolution. Research Research Areas: Molecular Genetics Developmental Biology Evolutionary Genetics Genomics and Bioinformatics Selected Publications Selected Publications: Rasys, A.M., Park, S., Ball, R.E., Alcala, A.J., Lauderdale, J.D., Menke, D.B. 2019. CRISPR-Cas9 Gene Editing in Lizards through Microinjection of Unfertilized Oocytes. Cell Rep. Aug 27;28(9):2288-2292.e3. Thompson, A.C., Capellini, T.D., Guenther, C.A., Chan, Y.F., Infante, C.R., Menke, D.B., Kingsley, D.M. 2018. A novel enhancer near the Pitx1 gene influences development and evolution of pelvic appendages in vertebrates. eLife. 7. pii: e38555. VanLeuven, A.J., Park, S., Menke, D.B., Lauderdale JD. 2018. A PAGE screening approach for identifying CRISPR-Cas9-induced mutations in zebrafish. Biotechniques. 64(6):275-278. Tollis, M., Hutchins, E.D., Stapley, J., Rupp, S.M., Eckalbar, W.L., Maayan, I., Lasku, E., Infante, C.R., Dennis, S.R., Robertson, J.A., May, C.M., Crusoe, M.R., Bermingham, E., DeNardo, D.F., Hsieh, S.T., Kulathinal, R.J., McMillan, W.O., Menke, D.B., Pratt, S.C., Rawls, J.A., Sanjur, O., Wilson-Rawls, J., Wilson Sayres, M.A., Fisher, R.E., Kusumi, K. 2018. Comparative Genomics Reveals Accelerated Evolution in Conserved Pathways during the Diversification of Anole Lizards. Genome Biol Evol. 10(2):489-506. Wang, J.S., Infante, C.R., Park, S., Menke, D.B. 2018. PITX1 promotes chondrogenesis and myogenesis in mouse hindlimbs through conserved regulatory targets. Dev Biol. 434(1):186-195. Ching, S.T., Infante, C.R., Du, W., Sharir, A., Park, S., Menke, D.B., Klein, O.D. 2018. Isl1 mediates mesenchymal expansion in the developing external genitalia via regulation of Bmp4, Fgf10 and Wnt5a. Hum Mol Genet. 27(1):107-119. Infante, C.R., Rasys, A.M., Menke, D.B. 2018. Appendages and gene regulatory networks: Lessons from the limbless. Genesis. 56(1). doi: 10.1002/dvg.23078. Domyan, E.T, Z. Kronenberg, C. R. Infante, A.I. Vickrey, S.A. Stringham, R. Bruders, M.W. Guernsey, S. Park, J. Payne, R.B. Beckstead, G. Kardon, D.B. Menke, M. Yandell, M.D. Shapiro. 2016. Molecular shifts in limb identity underlie development of feathered feet in two domestic avian species. eLife. 5: e12115. Infante, C.R., A.G. Mihala, S. Park, J.S. Wang, K.K. Johnson, J.D. Lauderdale, and D.B. Menke. 2015. Shared enhancer activity in the limbs and phallus and functional divergence of a limb-genital cis-regulatory element in snakes. Dev Cell. 35(1):107-19. Kumar, M.E., P.E.Bogard, F.H. Espinoza, D.B. Menke, D.M. Kingsley, and M.A. Krasnow. 2014. Defining a mesenchymal progenitor niche at single-cell resolution. Science. 346(6211): 1258810. Park, S., C.R. Infante, L.C. Rivera-Davila and D.B. Menke. 2014. Conserved regulation of hoxc11 by pitx1 in Anolis lizards. Journal of Experimental Zoology B. 322: 156-165. D.B. Menke. 2013. Engineering subtle targeted mutations into the mouse genome. Genesis. 51: 605-618. Infante, C.R., S. Park, A. Mihala, D.M. Kingsley and D.B. Menke. 2013. Pitx1 Broadly Associates with Limb Enhancers and is Enriched on Hindlimb cis-Regulatory Elements. Developmental Biology. 374: 234-244. Kusumi, K., R.J. Kulanthinal, A. Abzhanov, S. Boissinot, N.G. Crawford, B.C. Faircloth, T.C. Glenn, D.E. Janes, J.B. Losos, D.B. Menke, S. Poe, T.J. Sanger, C.J. Schneider, J. Stapley, J. Wade and J. Wilson-Rawls. 2011. Developing a community-based genetic nomenclature for anole lizards. BMC Genomics. 12: 554. McLean, C.Y., P.L. Reno, A.A. Pollen, A.I. Bassan, T.D. Capellini, C. Guenther, V.B. Indjeian, X. Lim, D.B. Menke, B.T. Schaar, A.M. Wenger, G. Bejerano and D.M. Kingsley. Human-specific loss of regulatory DNA and the evolution of human-specific traits. Nature. 471: 216-219. Menke, D.B., C. Guenther and D.M. Kingsley. 2008. Dual hindlimb control elements in the Tbx4 gene and region-specific control of bone size in vertebrate limbs. Development. 135: 2543-2553.
