A genome-wide comprehensive analysis of nucleosome positioning in yeast.
In eukaryotic cells, the one-dimensional DNA molecules need to be tightly packaged into the spatially constraining nucleus. Folding is achieved on its lowest level by wrapping the DNA around nucleosomes. Their arrangement regulates other nuclear processes, such as transcription and DNA repair. Despi...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2024-01-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011799&type=printable |
| _version_ | 1797319388279341056 |
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| author | Leo Zeitler Kévin André Adriana Alberti Cyril Denby Wilkes Julie Soutourina Arach Goldar |
| author_facet | Leo Zeitler Kévin André Adriana Alberti Cyril Denby Wilkes Julie Soutourina Arach Goldar |
| author_sort | Leo Zeitler |
| collection | DOAJ |
| description | In eukaryotic cells, the one-dimensional DNA molecules need to be tightly packaged into the spatially constraining nucleus. Folding is achieved on its lowest level by wrapping the DNA around nucleosomes. Their arrangement regulates other nuclear processes, such as transcription and DNA repair. Despite strong efforts to study nucleosome positioning using Next Generation Sequencing (NGS) data, the mechanism of their collective arrangement along the gene body remains poorly understood. Here, we classify nucleosome distributions of protein-coding genes in Saccharomyces cerevisiae according to their profile similarity and analyse their differences using functional Principal Component Analysis. By decomposing the NGS signals into their main descriptive functions, we compared wild type and chromatin remodeler-deficient strains, keeping position-specific details preserved whilst considering the nucleosome arrangement as a whole. A correlation analysis with other genomic properties, such as gene size and length of the upstream Nucleosome Depleted Region (NDR), identified key factors that influence the nucleosome distribution. We reveal that the RSC chromatin remodeler-which is responsible for NDR maintenance-is indispensable for decoupling nucleosome arrangement within the gene from positioning outside, which interfere in rsc8-depleted conditions. Moreover, nucleosome profiles in chd1Δ strains displayed a clear correlation with RNA polymerase II presence, whereas wild type cells did not indicate a noticeable interdependence. We propose that RSC is pivotal for global nucleosome organisation, whilst Chd1 plays a key role for maintaining local arrangement. |
| first_indexed | 2024-03-08T04:06:10Z |
| format | Article |
| id | doaj.art-f7ec2bc0d5904c12a5f3d351f9288754 |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2024-03-08T04:06:10Z |
| publishDate | 2024-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj.art-f7ec2bc0d5904c12a5f3d351f92887542024-02-09T05:30:33ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582024-01-01201e101179910.1371/journal.pcbi.1011799A genome-wide comprehensive analysis of nucleosome positioning in yeast.Leo ZeitlerKévin AndréAdriana AlbertiCyril Denby WilkesJulie SoutourinaArach GoldarIn eukaryotic cells, the one-dimensional DNA molecules need to be tightly packaged into the spatially constraining nucleus. Folding is achieved on its lowest level by wrapping the DNA around nucleosomes. Their arrangement regulates other nuclear processes, such as transcription and DNA repair. Despite strong efforts to study nucleosome positioning using Next Generation Sequencing (NGS) data, the mechanism of their collective arrangement along the gene body remains poorly understood. Here, we classify nucleosome distributions of protein-coding genes in Saccharomyces cerevisiae according to their profile similarity and analyse their differences using functional Principal Component Analysis. By decomposing the NGS signals into their main descriptive functions, we compared wild type and chromatin remodeler-deficient strains, keeping position-specific details preserved whilst considering the nucleosome arrangement as a whole. A correlation analysis with other genomic properties, such as gene size and length of the upstream Nucleosome Depleted Region (NDR), identified key factors that influence the nucleosome distribution. We reveal that the RSC chromatin remodeler-which is responsible for NDR maintenance-is indispensable for decoupling nucleosome arrangement within the gene from positioning outside, which interfere in rsc8-depleted conditions. Moreover, nucleosome profiles in chd1Δ strains displayed a clear correlation with RNA polymerase II presence, whereas wild type cells did not indicate a noticeable interdependence. We propose that RSC is pivotal for global nucleosome organisation, whilst Chd1 plays a key role for maintaining local arrangement.https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011799&type=printable |
| spellingShingle | Leo Zeitler Kévin André Adriana Alberti Cyril Denby Wilkes Julie Soutourina Arach Goldar A genome-wide comprehensive analysis of nucleosome positioning in yeast. PLoS Computational Biology |
| title | A genome-wide comprehensive analysis of nucleosome positioning in yeast. |
| title_full | A genome-wide comprehensive analysis of nucleosome positioning in yeast. |
| title_fullStr | A genome-wide comprehensive analysis of nucleosome positioning in yeast. |
| title_full_unstemmed | A genome-wide comprehensive analysis of nucleosome positioning in yeast. |
| title_short | A genome-wide comprehensive analysis of nucleosome positioning in yeast. |
| title_sort | genome wide comprehensive analysis of nucleosome positioning in yeast |
| url | https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011799&type=printable |
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