Regulation of transcriptional interference by the Swi/Snf complex [TL-seq]

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. Samples were grown as described in Morse et al., 2023. Cells were collected from YPD media that was untreated or treated with 5 mM DTT in mid-log phase. TL-seq libaries were prepared using the methods and pipeline described in Tresenrider et al., 2022. Two biological replicates are included for each genotype. Wild-type samples (SWI3) from untreated and DTT-treated cells that were not treated with Cap-Clip pyrophosphatase are included as controls for inefficient phosphatase activity in the library construction.