My concern is whether the long LacO arrays can really form a proper chromatin structure with nucleosomes in budding yeast.
It's an interesting question.
As far as I'm aware, nobody has looked into the physical structure of lacO array in budding yeast (using molecular biology techniques), perhaps due to the extensive repeats interferes with many methods.
Many people, including myself, have used lacO arrays to monitor chromosome positions/movements in live budding yeast cells, in combination with LacI-GFP. In this case, typically about 100 copies of lacO is used, which corresponds to ~10 kb.
Assuming that LacI-GFP does not have a strong preference for binding position within the array, you will be able to visualise entire lacO array under microscope.
If a 10-kb DNA segment is totally nucleosome free, you would observe a fibre-like GFP-positive structure under microscope, whose length would be up to ~ 3 µm (longer than the diameter of nucleus), when fully stretched. I have never observed it.
If, on the other hand, the lacO array forms a 30-nm fibre, the 10-kb array will be about 200 nm in length, which is below the resolution of (non-confocal) microscopes. Therefore, what you actually see is "a dot". And in fact we observe lacO/lacI-GFP as a dot.
Therefore, you can perhaps assume that a quite large portion of the lacO array forms (something like) 30-nm fibre.
In the case of lacO-LacI, the lacO array must be bound by some amount of LacI-GFP. Nucleosome could be depleted at such (actual) LacI-GFP associated sites. However, such 'nucleosome depletion' happens within "normal" chromatin.
Here are my thoughts.
I hope somebody else can give better answers.
Thank you very much @Shin-Ichiro Hiraga for your answer. It's a really interesting point of view.
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