In recent years, liquid-liquid phase separation (LLPS) has proven to be a widely occurring and important mechanism of subcellular organization. Nevertheless, many questions remain regarding LLPS function and regulation. Germ cells represent a great model system to study LLPS, which, in the form of so-called germ granules (or germ plasm), is known to be important for their function or even their specification. Germ granules are known to be highly dynamic, to occur in different variants and to contain germ cell-relevant factors, thus making them great models for studying biologically relevant aspects of LLPS. In particular, small RNA pathways are present in these granules. Our past work has generated many tools to study small RNA pathways in light of LLPS mechanisms and function. For instance, we have recently identified a disordered protein, PID-2, that plays a role in the homeostasis of a germ granule in C. elegans, known as Z granule. Interestingly, PID-2 interacts stably (as identified by mass spectrometry) with two proteins that are found in another germ granule: the P granule (Placentino et al., EMBO J 2020), suggesting communication between P and Z granules. We also recently identified a novel male-specific germ granule that plays a role in epigenetic inheritance of small RNAs via sperm (Schreier et al., in revision). Finally, in zebrafish we have identified a germ granule-regulatory mechanism, which is important for the proper specification of germ cells (Roovers et al., Dev Cell 2018).
Our studies have thus far been mainly built on genetics and microscopy in model organisms (C. elegans, zebrafish and cell culture), and only limited biochemistry. We want to extend our research to include biochemical approaches to understand the LLPS characteristics, and thereby the functions of the proteins, in isolation or in combination, that we and others identified, or will identify. This is an important new direction for us, as in in vivo studies it remains difficult to resolve the molecular mechanisms that underlie the results we obtain in detail. Thus, we are looking for an experienced biochemist, with an interest to study LLPS in an interactive setting where results are bounced between recombinant protein work and in vivo germ cell models (worked upon by current lab members), with the aim to understand how LLPS functions and/or is regulated.
We are looking for a collaborative, curious and creative personality with experience in recombinant protein studies. Experience with biophysical assays to assess LLPS would be beneficial, but is not a requirement (available expertise on campus). Interests to work with C. elegans or zebrafish can be accommodated.
Publications Relevant to the Project
Ketting RF and Cochella L (2020) Concepts and functions of small RNA pathways in C. elegans. Curr. Top. Dev. Biol., doi: 10.1016/bs.ctdb.2020.08.002
Placentino M, de Jesus Domingues AM, Schreier J, Dietz S, Hellmann S, de Albuquerque BFM, Butter F, Ketting RF (2020). Intrinsically disordered protein PID-2 modulates Z granules and is required for heritable piRNA-induced silencing in the C. elegans embryo. EMBO J. in press (Early version available at BioRxiv: DOI: doi.org/10.1101/2020.04.14.040584)
Roovers EF, Kaaij LJT, Redl S, Bronkhorst AW, Wiebrands K, de Jesus Domingues AM, Huang HY, Han CT, Riemer S, Dosch R, Salvenmoser W, Grün D, Butter F, van Oudenaarden A, Ketting RF (2018) Tdrd6a Regulates the Aggregation of Buc into Functional Subcellular Compartments that Drive Germ Cell Specification. Dev Cell. 46(3):285-301