Two projects in molecular evolution through data mining and experiments
Studying the evolutionary role of the "language gene" FoxP2 in mouse populations
In the past years we have performed several screens in our lab to identify genes that show signatures of positive selection in wild populations of the house mouse (e.g. Staubach et al. PLoS Genetics 2012: e1002891). This provides us now with a lot of information about loci that may have been adaptively relevant in these populations. One of these is the FoxP2 gene that shows an interesting sweep signature, accompanied by a sweep signature in its target gene CNTNAP2. This may have influenced differentiation in ultrasonic communication between house mouse populations (see von Merten et al. PLoS ONE 2014: e97244). The project would start with an in depth population genetic analysis based on data analysis from genome re-sequencing projects and additional PCR screens. It would then go on with functional validations, using transcription factor/promotor interaction assays (CHiP-Seq) and eventually CRISPR/Cas based genome editing in mice. The project would be associated to other projects studying ultrasonic vocalization in mice at a phenotypic and behavioural level.
Identification and functional analysis of de novo evolved secondary reading frames in genes
The emergence of new genes has been usually attributed to gene duplications or similar events. Over the last decade it has become clear that de novo gene birth is more than a theoretical possibility, and with the development of comparative genomics it has been possible to study this phenomenon in detail (reviewed in Tautz and Domazet-Lošo, Nat Rev Genet (2011), 12: 692-702). One aspect of de novo evolution is the possibility of "overprinting", i.e. the use of a second reading frame within an existing gene. We have identified a few such candidate loci (Neme and Tautz, BMC Genomics (2013) 14:117. doi: 10.1186/1471-2164-14-117), but an in depth study is bound to find more. The project would be on the one hand a bio-informatic data-mining project, but should go on with collecting experimental evidence for the function of the double reading frames. This would entail antibody production and proteomic analysis, and eventually CRISPR/Cas based genome editing in cell cultures and possibly in mice.