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| Status |
Public on Mar 22, 2024 |
| Title |
The yeast genome is globally accessible in living cells [OxfordNanopore] |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Other
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| Summary |
Eukaryotic genomes are packaged into chromatin, which is composed of condensed filaments of regularly spaced nucleosomes, resembling beads on a string. The nucleosome contains ~147 bp of DNA wrapped almost twice around a central core histone octamer. The packaging of DNA into chromatin represents a challenge to transcription factors and other proteins requiring access to their binding sites. Consequently, control of DNA accessibility is thought to play a key role in gene regulation. Here, we measure DNA accessibility genome-wide in living budding yeast cells by inducible expression of DNA methyltransferases. We find that the yeast genome is globally accessible to the methylase in living cells, unlike in nuclei, where DNA accessibility is severely limited. Gene bodies are methylated at only slightly slower rates than promoters, indicating that yeast chromatin is highly dynamic in vivo. In contrast, centromeres are strongly protected in vivo. Global shifts in nucleosome positions occur in cells as they are depleted of RSC, or ISW1 and CHD1, indicating that global nucleosome dynamics are at least partly attributable to ATP-dependent chromatin remodelers. We propose that virtually all yeast chromatin is in a state of continuous flux in living cells, but static in nuclei, suggesting that chromatin packaging is not generally repressive.
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| Overall design |
Time courses of DNA methylation by MSssI methylase in yeast cells; Nanopore long-read sequencing data. Two biological replicates.
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| Contributor(s) |
Coey CT, Kumar-Prajapati H, Clark DJ |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Apr 21, 2023 |
| Last update date |
Mar 23, 2024 |
| Contact name |
David Johannes Clark |
| E-mail(s) |
clarkda@mail.nih.gov
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| Phone |
3014966966
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| Organization name |
NICHD, NIH
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| Department |
DDB
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| Lab |
SCGE
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| Street address |
6 Center Drive Bldg 6A Rm 2A02
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platforms (1) |
| GPL25739 |
MinION (Saccharomyces cerevisiae) |
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| Samples (12)
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| GSM7212151 |
wild type live cells, 0 m SM, replicate 1 |
| GSM7212152 |
wild type live cells, 30 m SM, replicate 1 |
| GSM7212153 |
wild type live cells, 60 m SM, replicate 1 |
| GSM7212154 |
wild type live cells, 120 m SM, replicate 1 |
| GSM7212155 |
wild type live cells, 240 m SM, replicate 1 |
| GSM7212156 |
wild type live cells, 0 m SM, replicate 2 |
| GSM7212157 |
wild type live cells, 30 m SM, replicate 2 |
| GSM7212158 |
wild type live cells, 60 m SM, replicate 2 |
| GSM7212159 |
wild type live cells, 120 m SM, replicate 2 |
| GSM7212160 |
wild type live cells, 240 m SM, replicate 2 |
| GSM7212161 |
wild type live cells, no treatment, replicate 1 |
| GSM7212162 |
wild type live cells, no treatment, replicate 2 |
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| This SubSeries is part of SuperSeries: |
| GSE230309 |
The yeast genome is globally accessible in living cells |
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| Relations |
| BioProject |
PRJNA958224 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE230306_RAW.tar |
11.8 Mb |
(http)(custom) |
TAR (of WIG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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