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| Status |
Public on Dec 15, 2016 |
| Title |
MNase-sensitive complexes in yeast: nucleosomes and non-histone barriers |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Micrococcal nuclease (MNase) is commonly used to map nucleosomes genome-wide, but nucleosome maps are affected by the degree of digestion. It has been proposed that many yeast promoters are not nucleosome-free but occupied by easily digested, unstable, “fragile” nucleosomes. We analyzed the histone content of all MNase-sensitive complexes by MNase-ChIP-seq and Sonication-ChIP-seq. We find that yeast promoters are predominantly bound by non-histone protein complexes, with little evidence for fragile nucleosomes. We do detect MNase-sensitive nucleosomes elsewhere in the genome, including transcription termination sites. However, they have high A/T-content, suggesting that MNase sensitivity does not indicate instability, but the preference of MNase for A/T-rich DNA, such that A/T-rich nucleosomes are digested faster than G/C-rich nucleosomes. We confirm our observations by analyzing ChIP-exo, chemical mapping and ATAC-seq data from other laboratories. Thus, histone ChIP-seq experiments are essential to distinguish nucleosomes from other DNA-binding proteins that protect against MNase.
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| Overall design |
We mapped MNase-sensitive complexes in budding yeast by comparing protected DNA fragments at different levels of digestion (MNase titration). We used MNase-ChIP-seq and Sonication-ChIP-seq to detect histones H4 and H2B in order to distinguish between MNase-sensitive nucleosomes and non-histone complexes.
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| Contributor(s) |
Chereji RV, Ocampo J, Clark DJ |
| Citation missing |
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| Submission date |
Jun 08, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Razvan V. Chereji |
| E-mail(s) |
razvan.chereji@nih.gov
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| Phone |
301-435-8670
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| Organization name |
National Institutes of Health
|
| Department |
NICHD
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| Lab |
David J. Clark Lab
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| Street address |
6 Center Drive, Room 2A14
|
| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platforms (1) |
| GPL13821 |
Illumina HiSeq 2000 (Saccharomyces cerevisiae) |
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| Samples (26)
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| Relations |
| BioProject |
PRJNA324842 |
| SRA |
SRP076296 |
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