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The spatial position of budding yeast chromosomes affects gene expression

Francesca Di Giovanni, Marco Di Stefano, Davide Baù, Lucas B. Carey, Marc A. Marti-Renom, View ORCID ProfileManuel Mendoza
doi: https://doi.org/10.1101/237263
Francesca Di Giovanni
1Cell and Developmental Biology Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
2Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
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Marco Di Stefano
2Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
3Structural Genomics Group, CNAG-CRG, The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
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Davide Baù
2Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
3Structural Genomics Group, CNAG-CRG, The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
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Lucas B. Carey
2Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
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Marc A. Marti-Renom
2Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
3Structural Genomics Group, CNAG-CRG, The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
4Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
5Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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Manuel Mendoza
1Cell and Developmental Biology Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
2Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
6Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch 67400, France.
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  • ORCID record for Manuel Mendoza
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ABSTRACT

The three-dimensional organization of chromosomes can influence transcription. However, the frequency and magnitude of these effects is still controversial. To determine how changes in chromosome positioning affect transcription across thousands of genes with minimal perturbation, we characterized nuclear organization and global gene expression in budding yeast containing growth-rate neutral chromosome fusions. We used computational modelling and single cell imaging to determine chromosome position and integrated these data with genome-wide transcriptional profiles from RNA sequencing. Chromosome displacement relative to the nuclear periphery has mild but widespread and significant effects on transcription. A 10% decrease in the time a gene spends near the nuclear periphery leads to a 10% increase in gene expression. Our study shows that basal transcriptional activity is sensitive to radial changes on chromosomal position, and provides support for the functional relevance of budding yeast chromosome-level three-dimensional organization in gene expression.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted December 20, 2017.
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The spatial position of budding yeast chromosomes affects gene expression
Francesca Di Giovanni, Marco Di Stefano, Davide Baù, Lucas B. Carey, Marc A. Marti-Renom, Manuel Mendoza
bioRxiv 237263; doi: https://doi.org/10.1101/237263
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The spatial position of budding yeast chromosomes affects gene expression
Francesca Di Giovanni, Marco Di Stefano, Davide Baù, Lucas B. Carey, Marc A. Marti-Renom, Manuel Mendoza
bioRxiv 237263; doi: https://doi.org/10.1101/237263

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