Alternative transcription start sites can affect transcript isoform diversity and translation levels. In a recently described form of gene regulation, coordinated transcriptional and translational interference results in transcript isoform-dependent changes in protein expression. Specifically, a long undecoded transcript isoform (LUTI) is transcribed from a gene-distal promoter, interfering with expression of the gene-proximal promoter. Though it contains the coding sequence of the downstream gene, translation of the LUTI is restricted by uORFs present in its 5′ leader sequence. 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 uncovered that the Swi/Snf chromatin remodeling complex is required for co-transcriptional nucleosome remodeling that leads to LUTI-based repression. We identified 12 genes with tandem promoters that rely on Swi/Snf function for transcriptional interference during protein folding stress, including LUTI-regulated genes.

We further explored Swi/Snf repressive activity by performing kinetic and molecular assays for the LUTI-regulated gene histidine triad nucleotide-binding 1 (HNT1), revealing that Swi/Snf recruitment and repressive function at the HNT1 locus depends on transcription initiation and elongation of HNT1LUTI. This prompted our further investigation into a role for Swi/Snf in transcription elongation, leading to the finding that Swi/Snf performs co-transcriptional nucleosome remodeling at its target loci independently of its canonical role in transcriptional activation. We conclude this co-transcriptional remodeling function by Swi/Snf may function to promote transcription elongation at canonical gene targets but serves a repressive function at target genes with tandem promoters and transcriptional readthrough. To our knowledge, this is the first evidence of Swi/Snf's direct involvement in gene repression via a cis transcriptional interference mechanism.