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Chromosomes occupy discrete regions of the nucleus, referred to as 'Chromosome Territories'. This spatial organization is emerging as a crucial aspect of gene regulation and genome stability in health and disease.

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But how is this the case when:

Most eukaryotes seem to have Chromosome Territories, but yeast S. cerevisiae is an exception to this.

So if some eukaryotes do, and some do not, what information do Chromosome Territories provide? Some literature uses the phrase 'non-random chromosome territory arrangements'. Thus, I am confused.

Chromosome territories are randomly arranged in some eukaryotes.

How are chromosome territories crucial for gene regulation and genome stability in health and disease in some eukaryotes, but random in other eukaryotes?

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First, this idea was discredited or ignored during several decades, some studies suggest that CT is random in some eukaryotes that isn't necessary the truth. It is not easy at all to determine is CT are random or not

Second, not all eukaryotic organism are the same. Plants and Fungi have cell walls, animals do not. Fungi can have a dikaryotic cell or even undergo somatic hybridisation.

Third, "chromosomes are more unfolded in lower eukaryotes such as yeast."Chromosome Territories: The Arrangement of Chromosomes in the Nucleus

This article does not mention that S. cerevisiae is an exception, on the contrary "and may even hold for single-cell eukaryotes, such as budding and fission yeast".

Thank you for the question, I learnt a lot while searching for an answer

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