Time to re-write the textbooks? How DNA is really packed inside the nucleus.

2 meters doesn’t sound like much. However, this is the same length of DNA that is compacted inside the nucleus of each cell. Now, considering that nuclei have a diameter a fraction of a mm and nuclear proteins need to be included as well, this raises the important question, how does DNA fit? This apparent paradox has been meticulously studied by numerous scientists as understanding the way the DNA is packaged gives an insight into gene organisation and regulation. A recent study published in Science (1) by a team at the Salk Institute in collaboration with the University of California, San Diego, provide the latest understanding.
The current model of chromatin compaction
The initial stage of DNA packaging is the formation of chromatin – this is the wrapping of DNA around proteins called histones into units known as nucleosomes. Histones have a net positive charge attracting the negatively charged DNA allowing for tight interactions, 11nm wide. When you have a chain of nucleosomes it is more colloquially known as the ‘beads on a string’ conformation, simply due to its appearance. This 11nm structure is then further folded into a 30nm fibre and subsequent compaction and looping forms 120nm chromonema and finally mitotic chromosomes (Figure 1).

hierachical folding.png
Figure 1: Hierarchical folding of chromatin

The issue with this current understanding of chromatin compaction is that it is based on in vitro experimental results or results from permeabilised cells where important components may have been extracted leading to ‘artificial’ results. Nevertheless, a new method has been developed that overcomes these ambiguities, ChromEMT.

What is ChromEMT?

Quite simply, ChromEMT is the combination of multi-tilt electron microscopy tomography (EMT) and a labelling technique (ChromEM). It is the labelling technique that sets ChromEMT apart from previous techniques; it exploits a DNA binding fluorophore that catalyses the deposition of diaminobenzidine (DAB) polymers when excited that can be visualised when OsO4 is added in EM. Now, if you’re like me, then that last sentence may have sounded a bit mumbo jumbo – to elaborate, when the fluorophore gets excited, this energy can be used to generate reactive oxygen species that turns individual DAB molecules into a polymer that effectively coats DNA. This polymer strongly binds OsO which allows it to be seen under the EM. Using this labelling technique, many images and topographic slices can be taken to visualise the 3D chromatin structure*. Each of the topographic slices were just over 1nm allowing for individual chromatin chains to be resolved.

*If you want to see some of the images check out the video in Ref (2)

Curvilinear chromatin

When ChromEMT was applied to both human interphase and mitotic (dividing) epithelial cells, there was a failure to detect 30- and 120-nm chromatin fibres as suggested in Figure 1, but instead found chromatin to be composed of disordered 5- to 24-nm diameter fibres. These disordered chains can be packed at different concentration densities with more extended curvilinear fibres with less frequent contacts in interphase cells compared to more elaborate bending of chains in mitotic cells. Distinguishing more open (euchromatic) and more compacted (heterochromatic) regions in the nucleus can also be explained through the concentration of the chromatin fibres. This discovery may help understand some previous enigmas such as the rapid condensing of chromatin during mitosis that would presumably take longer to form following the nature of Figure 1.

So, is it time to change the textbooks?

Exciting as the results may be, it is not yet certain if the 5-24nm chromatin fibre is a widespread phenomenon seen in multiple cell types and species. This is hopefully where new research will focus.

Further Reading

(1)  Ou et al. ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells. Science 357, 370 (2017)

(2)  https://www.salk.edu/news-release/salk-scientists-solve-longstanding-biological-mystery-dna-organization/

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