Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome
| Autor: | Philipp Korber, Mark Heron, Nils Krietenstein, Helmut Blum, Stefan Krebs, Jessica L Ellins, Andrea Schmid, Elisa Oberbeckmann, Michael Roland Wolff, Ulrich Gerland |
|---|---|
| Rok vydání: | 2019 |
| Předmět: |
0303 health sciences
education.field_of_study Population Fungal genetics Computational biology Biology Genome Chromatin 03 medical and health sciences chemistry.chemical_compound 0302 clinical medicine chemistry Genetics biology.protein Nucleosome Chromatin structure remodeling (RSC) complex education Gene 030217 neurology & neurosurgery Genetics (clinical) DNA 030304 developmental biology |
| Zdroj: | Genome Research. 29:1996-2009 |
| ISSN: | 1549-5469 1088-9051 |
| DOI: | 10.1101/gr.253419.119 |
| Popis: | Mapping of nucleosomes, the basic DNA packaging unit in eukaryotes, is fundamental for understanding genome regulation because nucleosomes modulate DNA access by their positioning along the genome. A cell-population nucleosome map requires two observables: nucleosome positions along the DNA (“Where?”) and nucleosome occupancies across the population (“In how many cells?”). All available genome-wide nucleosome mapping techniques are yield methods because they score either nucleosomal (e.g., MNase-seq, chemical cleavage-seq) or nonnucleosomal (e.g., ATAC-seq) DNA but lose track of the total DNA population for each genomic region. Therefore, they only provide nucleosome positions and maybe compare relative occupancies between positions, but cannot measure absolute nucleosome occupancy, which is the fraction of all DNA molecules occupied at a given position and time by a nucleosome. Here, we established two orthogonal and thereby cross-validating approaches to measure absolute nucleosome occupancy across the Saccharomyces cerevisiae genome via restriction enzymes and DNA methyltransferases. The resulting high-resolution (9-bp) map shows uniform absolute occupancies. Most nucleosome positions are occupied in most cells: 97% of all nucleosomes called by chemical cleavage-seq have a mean absolute occupancy of 90 ± 6% (±SD). Depending on nucleosome position calling procedures, there are 57,000 to 60,000 nucleosomes per yeast cell. The few low absolute occupancy nucleosomes do not correlate with highly transcribed gene bodies, but correlate with increased presence of the nucleosome-evicting chromatin structure remodeling (RSC) complex, and are enriched upstream of highly transcribed or regulated genes. Our work provides a quantitative method and reference frame in absolute terms for future chromatin studies. |
| Databáze: | OpenAIRE |
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