The Ellenberg group studies cell division and nuclear organisation, focusing on chromatin structure, formation and segregation of 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 and quantitatively, automate imaging to address all its molecular components, and computationally process image data to extract biochemical and biophysical parameters.

We have previously applied systems biology approaches to identify 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 – crucial protein functions, interactions and networks during cell division. We are combining automated single molecule-calibrated imaging and computational  data analysis with advanced machine learning and modelling approaches to extend the first integrated protein atlas of the human dividing cell (video 1) [Cai et al., Nature 2018].

Video1: The mitotic cell atlas. Five different proteins are tracked during cell division (from metaphase to telophase): AURKB (red), NUP107 (green), CENPA (purple), CEP192 (yellow), and TUBB4B (cyan). The video represents what users could create by themselves when using the mitotic cell atlas homepage [movie by Rybina & Hossain].

We also determined the positions of various nuclear pore complex (NPC) components and directly resolved the ring-like structure of the NPC by single molecule localisation  microscopy [Szymborska et al., Science 2013]. Currently, we elucidate the assembly mechanisms of the NPC and the structure of its dynamic components. We further study chromatin dynamics throughout the cell cycle and unravel the 3D architecture of the human genome in situ.

By complete kinetochore tracking we demonstrated that meiotic chromosome biorientation is highly error-prone [Kitajima et al., Cell 2011]. We have now developed a gentle light-sheet-based microscope for high-throughput imaging of mouse embryos to enable systematic molecular analysis of early embryonic mitosis [Strnad et al. Nat Methods 2016]. This allowed us to demonstrate that parental genome are kept apart by a dual-spindle in mouse zygotes [Reichmann et al., Science 2018].

Ellenberg Group

Figure 1: Super-resolution microscopy of chromatin organisers. Condensin subunit SMC4 tagged with mEGFP and nanobody-stained in a rometaphase HeLa cell visualised by an astigmatic 3D STORM microscope. Color encodes z level of single molecule localisations. Scale bar, 500 nm. [Walther et al., JCB 2018].

Future projects and goals

We want to gain further comprehensive mechanistic insight into the division of human mitotic cells, provide a biophysical basis to understand nuclear organisation, and establish methods for systematic analysis of the surprisingly error-prone 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 several super-resolution techniques (Figure 1).

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.

ERC ADVANCED INVESTIGATOR