Overview
We use both experimental genetics and computational genomics to study the intersection of evolution, developmental biology, and gene regulation.
Our systems
Germ cells are an ideal biological system to study the complex relationships between epigenetics, development, and evolution. Germ cells are direct targets of natural selection: an organism without functional germ cells cannot reproduce and has an adaptive fitness of zero. Male germ cells, especially, are subject to extreme selection pressure, and sperm-specific proteins often exhibit evidence of rapid sequence evolution. We are exploring how these strong selection pressures impact chromatin and epigenetic regulation in developing sperm, and how selection on germ cells can in turn affect the regulatory biology of the genome more generally.
Embryonic stem cells (ESCs) represent a tractable in vitro model that shares many (but not all!) epigenetic features with germ cells. We use ESCs to develop tools, explore ideas, and test hypotheses that can be followed up in germ cells in vivo.
Epigenetic poising
Much of our work focuses on an epigenetic state called 'poising' or bivalency. Poising is defined by the simultaneous presence of two histone modifications: H3K4me3, usually associated with transcriptional activation, and H3K27me3, usually associated with transcriptional repression. When many genetic loci are poised, the cell often has broad developmental potential (pluripotency). This is true in germ cells and ESCs. In addition, we found that poising is strongly conserved at developmental genes in the mammalian germ line, and that it also evolves at specific loci in conjunction with evolution of developmental function. This finding provides strong evidence for the biological importance of poising, but leaves many questions unanswered. For example, how is poising first set up in the germ line, and how is it regulated and maintained? And, critically, what is its biological function?
Current projects
Molecular features of the poised state
One of our major interests is uncovering exactly what poising is at the molecular level. We recently found that unimodal H3K4me1 is found at poised loci along with H3K4me3 and H3K27me3 (reference here), potentially facilitating memory of poising across cell divisions. We are leveraging integrated molecular, developmental, and evolutionary information to better define and classify poised sites in germ cells and ESCs. We are developing tools for locus-specific manipulation of poising, and we are searching for new regulatory factors controlling the poised state.
Evolutionary divergence in poising
We have defined two types of poised genes in mammalian male germ cells: those at which poising has been conserved since before the time of the mammalian common ancestor, and those where it is more rapidly evolving (reference here). Starting from this point, we are working to systematically characterize the evolutionary dynamics of the poised state in the mammalian germline. In addition, we are performing functional experiments in vitro and in vivo to understand the molecular drivers and biological consequences of lineage-specific divergence in poising.
Cross-generation consequences of disrupted chromatin
As a natural extension of our studies of germ cell chromatin, we are investigating how transmission of altered chromatin states through sperm may affect somatic development in the next generation. We found that deletion of the H3K27me3 demethylase Utx (Kdm6a) in the mouse male germ line increases cancer frequency and reduces lifespan in the next generation, even in the absence of an inherited mutation (reference here). We are characterizing the molecular information that is passed across generations in the Utx model, as well as the developmental consequences of Utx germline deletion.
Using spermatogenesis to discover new aspects of chromatin regulation
During spermatogenesis, cells endure extreme chromatin states as the nucleus undergoes complete repackaging and extensive compaction. Discovering how spermatogenic cells navigate these extreme nuclear conditions can reveal new aspects of general chromatin regulation. New insights into the biology of spermatogenesis may also reveal novel targets for treating male infertility. In addition to studying the poised state, we are also examining the molecular and biological roles of other chromatin marks and putative chromatin regulators in ESCs and spermatogenic cells.