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DNA-loop-extrusion-by-condensin

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The basis of all living organisms—the individual cell—is a very small and fascinating structure. Our understanding of cells has improved enormously over the last decades, but there are still a lot of mysteries.

One big question, debated amongst scientists for decades, is about how a cell compacts and evenly divides its DNA when dividing.

Scientist from Delft University now got  the answer: Loop Extrusion

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A human cell carries over two meters of DNA in its nucleus in a big jumble of strands. Before cell division, the cell needs to package it into very small chromosomes so that DNA can be evenly distributed over two daughter cells.

This process itself was already observed under a microscope in 1882.

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For decades, however, the question of how exactly a cell manages to compact DNA has puzzled scientists.

That question is now firmly answered by new experiments by scientists from the Kavli Institute of Delft University and EMBL Heidelberg: the key is ‘loop extrusion’, a process that condenses DNA by pulling it in many tiny loops.

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It was already clear that a protein complex called ‘condensin’ plays a key role in compacting chromosomes, but until now biologists were divided on exactly how that protein works.

There were two theories: one states that condensin works like a hook that can grasp somewhere in the jumble of DNA, thus tying it together. An alternative proposal suggests that the ring-shaped condensin pulls the DNA inwards to create a loop.

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For many years, the grappling-hook approach was the dominant theory, although questions remained. A strong objection against loop extrusion was ‘fuel consumption’: the mechanism would require far more energy than observed in cells.

However, in 2017, the tide shifted...

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In September 2017, researchers from Delft University, EMBL Heidelberg, and Columbia University showed that condensin has a motor function.

By attaching a fluorescent molecule (starting at the red arrow in this movie) to condensin, the researchers could observe how it actually moved over DNA. The protein did so making rather large steps over the DNA molecule, which made the energy consumption of the process much more in-line with observations. That was a big clue, but…

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.... as Prof. Kim Nasmyth from Oxford University—one of the leading scientists that has studied DNA organization for many years—noted in the accompanying perspective in Science:

 “the discovery that condensin is a DNA translocase is certainly consistent with the idea that it functions as a loop extruder, but by no means proves it. The challenge will be to observe extrusion as well as translocation, to establish whether it is a property of individual or multimeric complexes, and to elucidate the molecular mechanism.”


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In November 2017, the group of Prof. Cees Dekker in Delft made a breakthrough discovery. Postdoc Dr. Mahipal Ganji fixed a DNA molecule on a glass surface at both ends in a microfluidic channel, so that he could monitor the molecule under a microscope.

In collaboration with scientists of the Christian Haering group from EMBL Heidelberg who established the purification and fluorescence labeling of the protein, they managed to make actual movies that caught the action of the condensin complex in the act.

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Ganji and Dekker went one step further: they applied a fluid flow from the side, so  the DNA molecule assumed a U-shape.

To his surprise, Ganji could see (and even film) a condensin protein attach itself to the DNA, where it started extruding a very long loop of DNA...


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This is a major finding, as it provides compelling evidence that DNA organizes its chromosomes by loop extrusion induced by condensin.

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The approach also allows measurement of all types of interesting details of the process, such as the speed of the loop formation. It showed that condensin pulls in up to 1500 base pairs per second while consuming only a modest amount of ATP – the ‘fuel’ of the condensin motor.

Surprisingly, the loop extrusion is asymmetric: condensin is found to fix itself rigidly to DNA and starts reeling in DNA from one side only, like a sailor on a boat reels in a hawser. Another interesting result: when the DNA is under tension, the looping process slows down. Apparently, with tension, condensin seems to struggle more to create a loop.

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Not only does this settle a long-standing debate in biology, it also opens a window on further research.

It is not pure academic interest, as it can also be important for medicine: almost all major diseases originate from defects on the molecular level within cells. Problems with the protein family to which condensin belongs, the SMC proteins, are related to hereditary conditions such as Cornelia de Lange Syndrome.

Condensin is also crucial in the organisation of the chromosomes during cell division, and errors in the process can result in cancer. A better understanding of these processes is vital for tracking down the molecular origins of serious illnesses.

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This result is reported in Science (First Release, Febr. 22 2018)

Real-time imaging of DNA loop extrusion by condensin

Authors: Mahipal Ganji,1 Indra A. Shaltiel,2* Shveta Bisht,2* Eugene Kim,1 Ana Kalichava,1 Christian H. Haering,2† Cees Dekker1†

Affiliations:
1 Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands.
2 Cell Biology and Biophysics Unit, Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.


DOI






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More information can be found on

ceesdekkerlab.nl

All materials used are available for reuse for news purposes, except cover image Science (see below). 

Credit: Cees Dekker lab, Kavli Institute of Nanoscience, Delft University of Technology.

Page 1,4,6,9,11: Artwork from the 3 November 2017 cover of Science. Illustration: C. Bickel/Science; coordinates Cees Dekker/Delft University of Technology and Christian Haering/European Molecular Biology Laboratory. Used with permission from AAAS. Further distribution of this material is not permitted without prior permission from AAAS

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