Constitutive turnover of histone H2A.Z at yeast promoters requires the preinitiation complex
- Stony Brook University, United States
- Cold Spring Harbor Laboratory, United States
Abstract
The assembly of the preinitiation complex (PIC) occurs upstream of the +1 nucleosome which, in yeast, obstructs the transcription start site and is frequently assembled with the histone variant H2A.Z. To understand the contribution of the transcription machinery in the disassembly of the +1 H2A.Z nucleosome, conditional mutants were used to block PIC assembly. A quantitative ChIP-seq approach, which allows detection of global occupancy change, was employed to measure H2A.Z occupancy. Blocking PIC assembly resulted in promoter-specific H2A.Z accumulation, indicating that the PIC is required to evict H2A.Z. By contrast, H2A.Z eviction was unaffected upon depletion of INO80, a remodeler previously reported to displace nucleosomal H2A.Z. Robust PIC-dependent H2A.Z eviction was observed at active and infrequently transcribed genes, indicating that constitutive H2A.Z turnover is a general phenomenon. Finally, sites with strong H2A.Z turnover precisely mark transcript starts, providing a new metric for identifying cryptic and alternative sites of initiation.
Data availability
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Constitutive H2A.Z turnover at yeast promoters requires the preinitiation complexPublicly available at the NCBI Short Read Archive (accession no: SRP051897).
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The transcription preinitiation complex regulates the eviction of the histone variant H2A.Z at yeast promotersPublicly available at the NCBI BioProject database (accession no: PRJNA271808).
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Subnucleosomal Structures and Nucleosome Asymmetry across a GenomePublicly available at the NCBI Short Read Archive (accession no: SRA059355).
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Nucleosome Stability Distinguishes Two Different Promoter Types at All Protein-Coding Genes in YeastPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE73337).
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Quantification of the yeast transcriptome by single-molecule sequencingPublicly available at the NCBI Short Read Archive (accession no: SRA008810).
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Genome-wide structure and organization of eukaryotic pre-initiation complexesPublicly available at the NCBI Short Read Archive (accession no: SRA046523).
Article and author information
Author details
Funding
National Institute of General Medical Sciences (RO1 GM104111)
- Ed Luk
National Institute of General Medical Sciences (T32 GM008468)
- Michael Tramantano
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2016, Tramantano et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Constitutive turnover of histone H2A.Z at yeast promoters requires the preinitiation complex
eLife 5:e14243.
https://doi.org/10.7554/eLife.14243
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