Seminar "Genomics-inspired biology: From genes to organisms, and beyond" by Prof. Chris Amemiya

Title: "Genomics-inspired biology: From genes to organisms, and beyond"

Speaker: Prof. Chris Amemiya

Affiliation: University of Washington

Abstract: Charles Darwin was a brilliant naturalist who recognized many biological connections through his observations of the natural world. Darwin would no doubt revel in our ability to draw biological inferences from DNA sequences. Of course, we also know that biological inference and biological content are easily conflated and that genomics can only take us so far without proper authentication via empirical biology. Here, I will discuss some recent efforts in my lab in which unique features of genomes provided insight into problems such as the emergence of adaptive immunity, the vertebrate aquatic-to-terrestrial transition, and noncanonical roles for the glycopolymer, chitin. My thesis is that, while comparisons of the “known” genetic components between species are important and necessary, many salient biological insights will be gleaned only when specifically looking for, and investigating, the differences among lineages. I shall discuss broad implications from our work and how these have led to empirical inquiries at multiple biological levels (genes, cells, tissues, organisms, ecosystems).

Research Interest: I have been interested in the origins of novelty and innovation in organisms (primarily vertebrates) and how changes in the genome can facilitate molecular and organismal adaptation in the long term, and the onset of disease in the short term. My laboratory uses whatever tools are necessary to address fundamental biological questions. This includes large-insert cloning, comparative genomics, computational biology, molecular genetics, imaging, biochemistry, and developmental biology. We often employ "deep branches" in vertebrate phylogeny as they allow us to study the origin of characters germane to higher vertebrates, and they provide very good vantage points for making comparisons with other organisms for deducing the genetic basis of biological innovations, such as limbs, lungs, and adaptive immune systems.
A common thread in my laboratory's research is the use of comparative genomics methods for deducing genomic features that may be important for emergence of novelty. I have been involved in genomics from my early career as a postdoctoral fellow with the Human Genome Project, and have continued to use genome analysis as a tool for biological inquiry. For example, my laboratory has described a novel Hox gene (Hox14) that is ancestral for the vertebrates, and whose cis-regulatory elements have been conserved and used for driving "posterior" HoxA gene expression in the developing placenta (even though tetrapods have lost the Hox14 gene). We have made several similar findings over the years, though the observations of vertebrate chitin (Tang et al., 2015; ref 3) are potentially the most far-reaching, touching on many areas of biology, bioengineering, materials science and regenerative medicine.