Abstract
The budding yeast Saccharomyces cerevisiae is a long-standing model for the three-dimensional organization of eukaryotic genomes. However, even in this well-studied model, it is unclear how homolog pairing in diploids or environmental conditions influence overall genome organization. Here, we performed high-throughput chromosome conformation capture on diverged Saccharomyces hybrid diploids to obtain the first global view of chromosome conformation in diploid yeasts. After controlling for the Rabl-like orientation using a polymer model, we observe significant homolog proximity that increases in saturated culture conditions. Surprisingly, we observe a localized increase in homologous interactions between the HAS1-TDA1 alleles specifically under galactose induction and saturated growth. This pairing is accompanied by relocalization to the nuclear periphery and requires Nup2, suggesting a role for nuclear pore complexes. Together, these results reveal that the diploid yeast genome has a dynamic and complex 3D organization.
Highlights
The genome is actively organized in the nucleus in both space and time, and this organization impacts fundamental biological processes like transcription, DNA repair, and recombination (Taddei et al, 2010)
Multiple studies have argued that a simple volume-exclusion polymer model of chromosomes in a Rabl-like orientation is sufficient to explain microscopy and Hi-C data of the budding yeast genome (Tjong et al, 2012; Wong et al, 2012), at least in haploids grown under standard lab conditions
We find that nocodazole arrest does not substantially reduce homolog proximity in the diverged hybrid S. cerevisiae x S. uvarum (Figure 2E)
Summary
The genome is actively organized in the nucleus in both space and time, and this organization impacts fundamental biological processes like transcription, DNA repair, and recombination (Taddei et al, 2010). Multiple studies have argued that a simple volume-exclusion polymer model of chromosomes in a Rabl-like orientation is sufficient to explain microscopy and Hi-C data of the budding yeast genome (Tjong et al, 2012; Wong et al, 2012), at least in haploids grown under standard lab conditions. These studies have argued that even the functional clustering that is observed may be a consequence of
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