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| Status |
Public on Aug 07, 2023 |
| Title |
Regulation of transcriptional interference by the Swi/Snf complex [ChIP-seq] |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Alternative transcription start sites regulate transcript isoform diversity and, in turn, often regulate translation levels for a given gene. Recently, a form of gene regulation was described in which transcriptional and translational interference are coordinated, resulting in transcript isoform-dependent changes in protein expression for affected genes. In this form of gene regulation, a long undecoded transcript isoform (LUTI) is transcribed from a gene-distal promoter, interfering with expression of the gene-proximal promoter. While transcriptional and chromatin features associated with LUTI expression have been described, the mechanism underlying LUTI-based transcriptional interference is not well-understood. Using an unbiased genetic approach followed by integrated genomic analysis, we have found that the Swi/Snf chromatin remodeling complex is required for co-transcriptional nucleosome remodeling that leads to LUTI-mediated repression. We uncovered twelve genes with tandem promoters that rely on Swi/Snf function for transcriptional interference during protein folding stress, including three LUTI-regulated genes. Our results provide evidence that, in addition to its canonical function in gene activation, the Swi/Snf complex directly represses promoters that are subject to transcriptional readthrough.
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| Overall design |
Samples were grown as described in Morse et al. , 2023. Cells were collected and fixed from YPD media that was untreated or treated with 5 mM DTT in late log phase. Chromatin immunoprecipitation was performed on Snf2-3V5 using anti-V5 agarose beads. Two biological replicates are included for each genotype.
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| Contributor(s) |
Morse K, Swerdlow S, Ünal E |
| Citation(s) |
37162931 |
| Submission date |
Apr 15, 2023 |
| Last update date |
Aug 08, 2023 |
| Contact name |
Elçin Ünal |
| E-mail(s) |
elcin@berkeley.edu
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| Organization name |
UC Berkeley
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| Street address |
628 Barker Hall
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| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94706 |
| Country |
USA |
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| Platforms (1) |
| GPL27812 |
Illumina NovaSeq 6000 (Saccharomyces cerevisiae) |
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| Samples (40)
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| This SubSeries is part of SuperSeries: |
| GSE229952 |
Regulation of transcriptional interference by the Swi/Snf complex |
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| Relations |
| BioProject |
PRJNA956070 |
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