Evidence for nucleosome depletion at active regulatory regions genome-wide
Abstract
The identification of nuclease-hypersensitive sites in an active globin gene and in the 5' regions of fruit fly heat shock genes first suggested that chromatin changes accompany gene regulation in vivo. Here we present evidence that the basic repeating units of eukaryotic chromatin, nucleosomes, are depleted from active regulatory elements throughout the Saccharomyces cerevisiae genome in vivo. We found that during rapid mitotic growth, the level of nucleosome occupancy is inversely proportional to the transcriptional initiation rate at the promoter. We also observed a partial loss of histone H3 and H4 tetramers from the coding regions of the most heavily transcribed genes. Alterations in the global transcriptional program caused by heat shock or a change in carbon source resulted in an increased nucleosome occupancy at repressed promoters, and a decreased nucleosome occupancy at promoters that became active. Nuclease-hypersensitive sites occur in species from yeast to humans and result from chromatin perturbation. Given the conservation of sequence and function among components of both chromatin and the transcriptional machinery, nucleosome depletion at promoters may be a fundamental feature of eukaryotic transcriptional regulation.
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Genomic sequences with high chromatin accessibility are typically bound by one or more TFs, although the identity of the TF is not directly measured by the experiment.
“DNA is typically accessible in a highly local and cell-type-specific manner, and in particular, genomic sequences with high accessibility are typically bound by one or more TFs, although the identity of the TF is not directly measured by the experiment (Lee et al., 2004).”
From WILDS: A Benchmark of in-the-Wild Distribution Shifts (2020) · cites this paper as Lee et al., 2004
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- Authors
- Lee, C.-K., Shibata, Y., Rao, B., Strahl, B. D., & Lieb, J. D.
- Affiliations
- University of North Carolina at Chapel Hill (US)
- Corresponding author
- Lieb, Jason D
- Venue
- Nature Genetics
- Published
- 2004-07-11
- Volume
- 36
- Issue
- 8
- Pages
- 900-905
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- OpenAlex
- W1996270170
- Cited by
- 738
- References
- 2
- Citations by year
- 2026: 7 · 2025: 11 · 2024: 17 · 2023: 16 · 2022: 17 · 2021: 22 · 2020: 12 · 2019: 20 · 2018: 22 · 2017: 13 · 2016: 27 · 2015: 20 · 2014: 36 · 2013: 31 · 2012: 34
- FWCI
- 21.42
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- nucleosome depletion, nucleosome occupancy, nuclease hypersensitive sites, chromatin structure, transcriptional regulation, promoter activity, heat shock response, carbon source shift, Saccharomyces cerevisiae, mitotic growth, gene expression regulation
- MeSH terms
- Genes, Fungal, Histones, Nucleosomes, Regulatory Sequences, Nucleic Acid, Saccharomyces cerevisiae, Transcription, Genetic
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