Speaker: Christof Gebhardt
Department: Institute of Biophysics, Universität Ulm
Subject: Quantitative single molecule imaging in living cells and animals
Location: Bionanoscience Department, TU Delft
Author: Mirte Golverdingen
Life is an interplay of inanimate biomolecules, Christof Gebhardt tries to understand how these biomolecules function in isolation, interaction and what happens with them when we are ill. To understand this the research to reaction kinetics, their spatial distribution, stoichiometry and forces can help. Moreover, biomolecules can be better understood if we manipulate single biomolecules in vitro and in vivo.
Super resolution methods in combination with fluorescent proteins as markers can help us to understand biomolecules better. Gebhardt uses super resolution in combination with GFP. Next to green colours, other colours of the fluorescent protein are developed. However, single GFP expression for single molecule detection is hard to visualize using fluorescent microscopy because of the fluorescent background.
HILO illumination is an imaging method that only measures a small part of the cell, in this way the background can be reduced. By adding a mirror to the HILO set-up, the side of the object can be imaged and in this way, you have more space to alter the cell at the top (See Figure 1). Moreover, imaging from the side reduces the contrast. The 3D image of the cell can be imaged by moving the objective up and down. By using other tags than GFP, Gebhardt was able to use HILO for in vitro, in cellula, in vivo and in silico studies.
Figure 1: Scheme of the reflected light-sheet principle (not drawn to scale). A laser beam is focused by an objective to form a vertical light sheet that is reflected by 90° off an AFM cantilever next to a cell in a Petri dish. Fluorescence is detected by a second high-NA objective. Three-dimensional optical sectioning is achieved through vertical displacement of the sample. Adapted from: Gebhardt, J. C. M., et. al (2013). Single-molecule imaging of transcription factor binding to DNA in live mammalian cells. Nature methods, 10(5), 421-426.
Gebhardt for instance, studied the transcription factor and DNA (TF-DNA) interaction times in chromatin organisation and transcription regulation. The transcriptional repressor CTCF interacts with the chromatin, however, it is not known how CtCF interacts with the chromatin during the cell cycle. Moreover, the influence of the regulator role of TF-DNA interaction time on transcription repression is a research topic of the research group of Gebhardt.
Kinetic information from the data can be obtained by researching video images of with an HoloAR labelled nuclear receptors the diffusion coefficient, the DNA bound tag and the DNA residence time of molecules can be obtained. To overcome the problem of photobleaching that occurs after continuous illumination, dark times were used. By measuring the DNA residence time of different TFs, Gebhardt showed that every transcription factor has another DNA residence time. There can be made a differentiation between specific (1/10/100 s) and unspecific (<1) DNA binding residence times.
CtCF chromatin interaction kinetics
The 3D organization of chromatin exists of nucleosomes, looped gene loci and chromosome territories. The chromatin architecture influences gene expression, differentiation, development, DNA replication and DNA repair. However, the control of the DNA loops is still unclear.
Chromatin topology is mediated by architectural proteins. Gebhardt was able to calculate the topologically associating domain, this shows how likely it is in a loop if chromatins interact with each other. There are certain TFs that is able to interact with the architectural proteins. CtCF is one of these transcription factors, therefore, it is seen as a potential ‘master weaver’. However, it is not clear if CtCF is activating, repressing or insulating the architectural proteins. CtCF contains 11 zinc finger motives that are able to dimerize the DNA. It has more than 100000 target sites on the DNA and it recruites cohesion. Gebhardt his study focusses on the kinetics of the CtCF TF, how long does it bind to the chromatin? And is the TF stable or mobile?
He was able to design a method by using fluorescent proteins that shows a wide spread binding kinetics. By developing a method based on the measured fluorescence, Gebhardt showed that CtCF shows three dissociation states. The residence times of these states are: <1s, <10s and ~1000s. The last two are specific, while the first one is specific and occurring in G1 and G2 phase of the cell cycle.
CtCF has low- and high-affinity sites on the DNA and its dynamic interactions (~4s) are changing the loops within topological associating domains (TADs) or initiate abortive loop formation. CtCF chromatin interaction depends on the current phase of the cell-cycle. In the S-phase, much less high (stable) resistance times are measures, so in the S-phase an overexpression of CtCF blocks cells. It could be that replication dissolves CTCF-chromatin interactions during S-phase. In the M-phase: CtCF is excluded from chromatin, this may be caused by phosphorylation.
By studying the interaction of CtCF with the DNA, Gebhardt et al. showed that CtCF-chromatin interaction is cell-cycle dependent. Kinetic information on the interaction of biomolecules with DNA can help us understand the complex interactions in the cell better. I liked that he was able to adapt the traditional way of imaging with HILO to a more advanced and better adapted method. Moreover, the discovery of the tree dissociation states of CtCF with their corresponding residence times invites us to research the dissociation states of other transcription factors, giving more insight to the complex cell dynamics.