Nucleosomes containing histone variant H2A.Z (Htz1) serve to poise quiescent genes for activation and transcriptional initiation. However, little is known about their role in transcription elongation. Here we show that dominant mutations in the elongation genes SPT5 and SPT16 suppress the hypersensitivity of htz1Δ strains to drugs that inhibit elongation, indicating that Htz1 functions at the level of transcription elongation. Direct kinetic measurements of RNA polymerase II (Pol II) movement across the 9.5-kb GAL10p-VPS13 gene revealed that the elongation rate of polymerase is 24% slower in the absence of Htz1. We provide evidence for two nonexclusive mechanisms. First, we observed that both the phospho-Ser2 levels in the elongating isoform of Pol II and the loading of Spt5 and Elongator over the GAL1 open reading frame (ORF) depend on Htz1. Second, in the absence of Htz1, the density of nucleosome occupancy is increased over the GAL10p-VPS13 ORF and the chromatin is refractory to remodeling during active transcription. These results establish a mechanistic role for Htz1 in transcription elongation and suggest that Htz1-containing nucleosomes facilitate Pol II passage by affecting the correct assembly and modification status of Pol II elongation complexes and by favoring efficient nucleosome remodeling over the gene.
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| Gene/Complex | Qualifier | Gene Ontology Term | Annotation Extension | Evidence | Source | Assigned On |
|---|---|---|---|---|---|---|
| HTZ1 | involved in | transcription elongation by RNA polymerase II | IMP | SGD | 2024-03-22 | |
| HTZ1 | involved in | chromatin remodeling | part of transcription elongation by RNA polymerase II | IMP | SGD | 2014-07-10 |
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| Gene | Phenotype | Experiment Type | Mutant Information | Strain Background | Chemical | Details |
|---|---|---|---|---|---|---|
| SPT5 | cold sensitivity: increased | classical genetics | reduction of function Allele: spt5-28 | W303 | Temperature: reduced temperature, 17 °C | |
| SWR1 | resistance to chemicals: decreased | classical genetics | null Allele: swr1-Δ | W303 | mycophenolic acid | |
| SWR1 | resistance to chemicals: decreased | classical genetics | null Allele: swr1-Δ | W303 | 50 ug/ml 6-azauracil | |
| HTZ1 | resistance to chemicals: decreased | classical genetics | null Allele: htz1-Δ | W303 | mycophenolic acid | |
| HTZ1 | resistance to chemicals: decreased | classical genetics | null Allele: htz1-Δ | W303 | 50 ug/ml 6-azauracil | |
| SPT4 | resistance to chemicals: decreased | classical genetics | null Allele: spt4-Δ | W303 | 50 ug/ml 6-azauracil | |
| DST1 | resistance to chemicals: decreased | classical genetics | null Allele: dst1-Δ | W303 | 50 ug/ml 6-azauracil |
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| Evidence ID | Analyze ID | Interactor | Interactor Systematic Name | Interactor | Interactor Systematic Name | Allele | Assay | Annotation | Action | Phenotype | SGA score | P-value | Source | Reference | Note |
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Increase the total number of rows showing on this page by using the pull-down located below the table, or use the page scroll at the table's top right to browse through the table's pages; use the arrows to the right of a column header to sort by that column; filter the table using the "Filter" box at the top of the table; click on the small "i" buttons located within a cell for an annotation to view further details about experiment type and any other genes involved in the interaction.