Quo Vadis: Cees Dekker

Speaker: Cees Dekker
Department: Bionanoscience, TU Delft
Location: TU Delft
Date: July 6, 2017
Author: Teun Huijben

As start of the summer Quo Vadis of the Bionanoscience Department, Cees Dekker was invited to give a talk. Literally translated from Latin, Quo Vadis means: ’Where are you going?’. In light of this title Cees decided to give a summarizing talk about covering all the exciting research happening in his lab and what he hopes to achieve in the next years.

Since Cees has the largest lab of the department, of lot of different topics are studied in his group. The different topics can be roughly divided into three categories: developing novel nanotechnologies, studies on chromosomal organization and developing the synthetic cell. Of each of these subject he highlights some interesting ongoing studies and his vision on the future.

The first topic Cees elaborates on are the novel nanotechnological techniques his group is developing. The most important technique is the solid state nanopore, which is a very small hole in a thin membrane. When a voltage is applied over the chip, an ionic current starts running and DNA can be dragged through the pore, because of its overall negative charge. While translocating the pore, the DNA blocks the ionic current partly and the decrease in current can be measured. The nanopore technique can be used in different studies. Firstly, it may enable sequencing of DNA optically, when the pore is used in combination with plasmonic structures. The gold plasmonic structures create a high-energetic field trapping the DNA in the pore. In combination with Raman spectroscopy, chemical structures of the DNA can be deduced from the emitted radiation.

Secondly, nanopores are also useful in studying nuclear pore complexes. By covering the inside of the pore with nuclear pore proteins, the transport of proteins can be mimicked through this artificial pore. The advantage is that it can be done in vitro, instead of in living cells. At last, they are also trying to sequence proteins using biological nanopores.

The second main part of Cees’ talk was about the study of chromosome organization. For multiple years, his group is interested in the higher structures of DNA and how that structure is determined. An important part of chromosome structures are supercoils, in which DNA is coiled up to store it in a compact way and suppress transcription. The main question is whether these supercoils (or plectonemes) are sequence dependent. His group developed a new technique to study the coiling, and indeed the position of the supercoils is dependent on the sequence of the DNA. Modeling of the DNA gave the insight that certain sequences have an intrinsic curvature, and the model predicted which sequence will increase the probability of having a supercoil, since the tip of the supercoils needs Experiments with these sequence indeed showed a higher probability of having a supercoil at that position. This shows that the intrinsic curvature of the DNA determines higher structures of the chromatin, so the DNA sequence not only codes for proteins, but also for its own structure.

The last part of his talk was about making a synthetic cell, the ultimate dream of Cees. The goal is to create a vesicle (liposome) with a working division mechanism inside. One idea is to use the bacterial MinE-MinD oscillating proteins to position a FtsZ-ring in the middle of the cell and actively contract this ring to divide the cell. This idea will need some years to become reality, so right now his group is studying the different components of this idea separately and hopefully the first ’synthetic’ cell will be there is a few years.

What I found particularly nice about this talk was that Cees summarized all the research that is currently done in his large lab. In this way the department got a better idea of all the things happening within this part of Bionanoscience. Besides that, Cees is a very enthusiastic speaker what makes if nice to listen to.

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3D mammalian genome organization and function

Speaker: Wouter de Laat

Department: Bionanoscience

Subject: 3D mammalian genome organization and function          

Location: TU Delft

Date: 11-2-16

Author: Hielke Walinga

Our DNA consists of long strands of bases that appear to have no function at all. Only 3 % of the DNA is actually consisting genes. A long time researchers thought only the genes of the DNA mattered. However, it becomes more and more clear that the junk DNA hides a lot of information related to the expressing of these genes. Not only did they turn out to consist of a large landscape of regulatory elements, they also contain parts which guide to fold the DNA in a specific 3D construction which is also influencing the expressing pattern. Wouter de Laat investigated this 3D construction and talked about methods to reveal this, but also talked about a mechanism explaining the self-organization of this 3D construction.

When taking into account that junk DNA surrounding the genes are important to the expressing of the genes, one can deduce that the position of these genes in the DNA is important for the expressing pattern. A good way to test this is to place genes at random positions in the DNA. The Spitz lab executed these kinds of experiments and indeed showed that the expressing patterns can sometimes change very much.

A way to explain this is given by the hypothesis that when DNA strands are looping, the gene and its enhancer are placed close to each other in space. To test this hypothesis, a technique called Chromosomes Conformation Capture (referred to as 3C) is developed. This technique makes use of formaldehyde proteins which connect to the DNA, creating hairballs of DNA. These hairballs are the loops of DNA. When this is digested, the remaining DNA is all in small parts which used to be the loop. In the next step, it uses PCR with primers linking to the genes and its enhancer. The PCR then reveals if the gene and its enhancer were located in the same loop.

Other more elaborate techniques of the previous mentioned technique are the 4C and the Hi-C method. In the 4C method the topological distance between one locus is measured to all other DNA. The Hi-C method on the other hand measures all loci to all other loci. This method reveals beautifully how DNA is topologically organized.

Next, Wouter de Laat wanted to explain us about the construction of these loops. His hypothesis stated that on the root of the loop there are two CTCF anchors recruiting condensin. This condensin links the strands together creating the loop. To prover this hypothesis, researchers removed one anchor and observed that no loop is formed. (This was then tested with the 3C technique.) Another experiment showed a more surprising result. When one anchor was switched the loop was also not created.

At first, this made sense, but at the end of the presentation somebody made an important note. In a three dimensional world, switching one anchor does not automatically result in a prevention of linking. Especially when the loop is very large, this would make no difference. An important feature Wouter de Laat missed in his presentation was the coiling and super-coiling of the DNA. He missed to mention and elaborate on the physics of DNA. A hole in biology Nanobiology is hoping to fill.

Hi-C
Image 1: A heat map showing the topological distances in chromosome 14. This was created by the Hi-C technique. (Source: Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J,Comprehensive mapping of long-range interactions reveals folding principles of the human genome, Science 326, 289–293, 2009)