The Sen1 Helicase Prevents Genome-Wide Spurious Transcription by Controlling Transcription Termination by RNAPII

It is currently believed that termination by RNAPII occurs differently depending whether a transcript contains or lacks a polyadenylation signal (PAS). By screening for factors deficient for PAS-dependent termination in an in vivo reporter assay, we identified Sen1, a putative helicase mainly known for its role in PAS-independent termination of snoRNAs. We show for the first time that Sen1 regulates transcription termination at protein-encoding genes genome-wide. As well, we show that Sen1 suppresses cryptic transcription genome-wide, besides being required for termination of most snoRNAs. We provide evidence that Sen1 controls termination through its helicase activity and by effectively recruiting to chromatin, factors implicated in PAS-dependent (Rna14 and Rat1) or PAS-independent termination (Nrd1). Importantly, we demonstrate that the effect on transcription termination of Sen1 and Nrd1, although similar, differ quantitatively and qualitatively. Our results suggest that in yeast, termination by RNAPII at protein encoding-genes makes use of redundant pathways. [1] Expression profiling: Genome-wide expression profiling in Sen1 and Nrd1 mutants was performed using Affymetrix tiling microarrays. Termination defects and cryptic transcription were then assessed in pairwise comparisons with wild-type strains that were grown and assayed under the same conditions. [2] Nucleosome profiling: The supplemental CEL files contain the raw hybridization signals from genome-wide nucleosome occupancy experiments in a SEN1tetO7 and a wild type strain. The .BAR files contain the normalized data for each mutant and wild-type compared to the total genomic DNA signal to identify nucleosome occupancy patterns.