Ellenberg Group

Figure 1: Embryonic pre-implantation development: Tracking of all cells throughout the first mitotic divisions, from zygote to blastocyst stage, using an inverted light-sheet microscope. Nuclei detected by their H2B signal are shown. Colour-coded spheres indicate cells of different fate: trophoectoderm (TE; blue) or inner cell mass (ICM; red) (Strnad P et al. 2016).

The Ellenberg group studies cell division and nuclear organisation, focusing on chromosome organisation, the formation and segregation of mitotic chromosomes, as well as nuclear pore complex structure and assembly.

Previous and current research

Our overall goal is to elucidate the molecular and physical principles underlying cell division and nuclear organisation. We are developing a broad range of advanced fluorescence-based imaging technologies to assay the functions of the involved molecular machinery non-invasively, automate imaging to address all its molecular components, and computationally process image data to extract biochemical and biophysical parameters. Our research focuses on three areas: systems biology of somatic mitosis, nuclear structure, and molecular mechanisms of early embryonic mitosis.

We have previously identified hundreds of new cell division genes by RNAi-based screening of the entire human genome and we are now studying – in live cells and with high-throughput – protein function, interactions and networks. For a  systems-level understanding of all crucial protein interactions during cell division, we are combining automated single molecule calibrated imaging and computational  data analysis with advanced machine learning and modelling approaches to  build an integrated protein atlas of the human dividing cell.

We also determined the positions of various nuclear pore complex (NPC) components and directly resolved the ring-like structure of the NPC, combining stochastic super-resolution microscopy with single particle averaging. Currently, we elucidate the assembly mechanism of the NPC and chromatin dynamics over the cell cycle.

By complete kinetochore tracking we demonstrated that meiotic chromosome biorientation is highly error-prone. We have now developed a gentle light-sheet- based microscope for high-throughput imaging of mouse oocytes and embryos to enable systematic molecular analysis of meiosis and early embryonic mitosis (figure 1).

Ellenberg Group

Figure 2: Condensin subunit SMC4 tagged with mEGFP and nanobody-stained in a prometaphase HeLa cell visualised by an astigmatic 3D STORM microscope. Color encodes z level of single molecule localisations. Scale bar, 500 nm.

Future projects and goals

We want to gain comprehensive mechanistic insight into the division of human mitotic cells, provide a biophysical basis to understand nuclear organisation, and establish methods for systems analysis of the first mitotic divisions of mammalian embryos.

To come to a structural understanding of nuclear organisation, we will explore and further improve correlative imaging approaches, combining live cell confocal microscopy, super-resolution and electron tomography to unravel the  structure and mechanisms of NPC assembly and disassembly.

In order to understand the function of the human genome, knowing the genome  sequence alone is not sufficient. We are studying chromatin organisation and  compaction, as well as the 4D human genome architecture by correlative imaging  approaches, including live cell imaging and various super-resolution techniques  (figure 2).

To be able to apply systems biology tools to early embryonic mitosis, we will push light-sheet-based imaging technology development further to improve its light efficiency and resolution in order to establish a physiological molecular model for early mammalian development and infertility.