The dynamic three-dimensional organization of the diploid yeast genome
- University of Washington, United States
- Northwestern University, United States
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.
Data availability
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Data from The dynamic three-dimensional organization of the diploid yeast genomePublicly available at the NCBI Gene Expression Omnibus (accession no: GSE88952).
Article and author information
Author details
Funding
National Institutes of Health (GM080484 to JHB P41GM103533 to MJD U54 DK107979 to JS and WSN)
- William S Noble
- Jason H Brickner
- Jay Shendure
- Maitreya J Dunham
National Science Foundation (graduate research fellowship DGE-1256082 to SK 1516330 to MJD)
- Seungsoo Kim
Howard Hughes Medical Institute (JS is an investigator of HHMI MJD was supported in part by a Faculty Scholar grant from HHMI)
- Jay Shendure
- Maitreya J Dunham
Canadian Institute for Advanced Research (MJD is a senior fellow in the Genetic Networks Program)
- Maitreya J Dunham
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2017, Kim et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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