Set1-dependent H3K4 methylation is essential for sustained gene expression at newly activated loci

Abstract

Histone H3 lysine 4 trimethylation (H3K4me3) has been associated with active transcription, yet whether it plays a causative role in gene activation remains an open question. In this study, we reveal that the deletion of Paf1 complex subunit Leo1 in Saccharomyces cerevisiae induces robust transcriptional activation at a subset of genes, particularly those involved in sterol transport, without altering global H3K4me3 levels. These induced genes acquire de novo H3K4me3 at promoter-proximal regions, and this transcriptional induction is entirely dependent on Set1, the sole methyltransferase responsible for H3K4me3. Strikingly, loss of Set1 abolishes expression of these genes, even in the presence of previously established H3K4me3, and their expression is fully restored upon Set1 reintroduction. These effects are specific to Leo1 deficiency and not observed in other Paf1C mutants. Furthermore, Set1-dependent gene activation enhances sterol uptake, underscoring its physiological relevance. Our findings provide direct in vivo evidence that Set1-catalyzed H3K4me3 is not merely a transcriptional correlate, but a context-dependent driver of gene expression. DATA AVAILABILITY: The ChIP-seq and RNA-seq data discussed in this study have been deposited in NCBI's Gene Expression Omnibus (Edgar et al., 2002) and are accessible through GEO Series accession number GSE303595 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE303595) and GSE303407 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE303407).

Keywords: H3K4 methylation; Leo1; Set1; gene expression.