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.

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)




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