A typical adult human skeleton is made of 206 bones. Each one of these bones forms at a unique anatomic location and has a unique shape. Skeletal patterning is determined during development, and bone growth, remodelling, maintenance, and injury repair continue throughout adulthood. Key skeletal development genes, for example, Gdf6 and Runx2, regulate these processes, and mutations in them often lead to skeletal disease.

One understudied mechanism of disease is mutations in regulatory switches that turn genes on and off in spatial and temporal manner. There are hundreds of thousands of regulatory switches in the human genome, but the function of only a small fraction of them is known. We aim to uncover the regulatory switches that cause changes in skeletal development. We are taking advantage of the vast diversity of size, shape, and number of bones in vertebrates, including dramatic differences between humans and our closest primate relatives. We combine work in two vertebrate experimental systems (threespine stickleback and mouse), and comparative genomics of humans and other vertebrates to identify candidate enhancers that are linked to skeletal traits. We then test the function of these enhancers using transgenics in sticklebacks and mice. Using the combination of these approaches, we have identified candidate loci that regulate bone size (for example, Figure 1) and may have played an important role in human evolution (for example, Figures 2 and 3).

Evolution of Gene Regulation

Figure 1 – Distinct, but very closely-linked loci regulate different aspects of bony armor plates in sticklebacks. Armor plate height and width were separately fine-mapped using thousands of F2 fish from a genetic cross between a large-plated marine stickleback and an armor-reduced freshwater stickleback. The two QTL intervals (red and green bars) barely overlap.

Evolution of Gene Regulation

Figure 2 – A chimpanzee Gdf6 enhancer missing in humans drives expression of lacZ reporter (blue) in the hindlimbs of developing mouse embryos, but not forelimbs. Humans have reduced the size of their toes, but not fingers, during the transition from arboreal to walking ape. Gdf6 null mice have shorter digits, and loss of this hindlimb enhancer may have played a key role in the evolution of the human foot.

Evolution of Gene Regulation

Figure 3 – A Runx2 enhancer with human-specific mutations drives expression of lacZ reporter (blue) in the face of developing mouse embryos. Evolutionary changes in this enhancer may explain some of the dramatic differences seen between the human and chimpanzee craniofacial bones that occurred during the change in climate, diet, and the expansion of the human brain.

Our ultimate goal is to obtain a blueprint of how to develop a human skeleton. Understanding this process will help us identify novel targets for therapeutic intervention in skeletal disease.

Selected Publications

Indjeian, V.B., Kingman, G.A., Jones, F.C., Guenther, C.A., Grimwood, J., Schmutz, J., Myers, R., and Kingsley, D.M. (2016). Evolving new skeletal traits by cis-regulatory changes in bone morphogenetic proteins. Cell, 164, 45-56.

Hiller, M., Schaar, B. T., Indjeian, V. B., Kingsley, D. M., Hagey, L. R., & Bejerano, G. (2012). A ”forward genomics” approach links genotype to phenotype using independent phenotypic losses among related species. Cell Reports, 2(4), 817–823.

McLean, C. Y., Reno, P. L., Pollen, A. A., Bassan, A. I., Capellini, T. D., Guenther, C., Indjeian, V. B., Lim, X., Menke, D. B., Schaar, B. T., Wenger, A. M., Bejerano, G., & Kingsley, D. M. (2011). Human-specific loss of regulatory DNA and the evolution of human-specific traits. Nature, 471(7337), 216–219.

Indjeian, V. B., & Murray, A. W. (2007). Budding yeast mitotic chromosomes have an intrinsic bias to biorient on the spindle. Current Biology, 17(21), 1837–1846.

Indjeian, V. B., Stern, B. M., & Murray, A. W. (2005). The centromeric protein sgo1 is required to sense lack of tension on mitotic chromosomes. Science, 307(5706), 130–133.

View All Publications For This Group