The ATP-dependent chromatin remodelling enzyme Uls1 prevents Topoisomerase II poisoning

Abstract

Topoisomerase II (Top2) is an essential enzyme that decatenates DNA via a transient Top2-DNA covalent intermediate. This intermediate can be stabilised by a class of drugs termed Top2 poisons, resulting in massive DNA damage. Thus, Top2 activity is a double-edged sword that needs to be carefully controlled to maintain genome stability. We show that Uls1, an ATP-dependent chromatin remodelling (Snf2) enzyme, can alter Top2 chromatin binding and prevent Top2 poisoning in yeast. Deletion mutants of ULS1 are hypersensitive to the Top2 poison acriflavine (ACF), activating the DNA damage checkpoint. We map Uls1’s Top2 interaction domain and show that this, together with its ATPase activity, is essential for Uls1 function. By performing ChIP-seq, we show that ACF leads to a general increase in Top2 binding across the genome. We map Uls1 binding sites and identify tRNA genes as key regions where Uls1 associates after ACF treatment. Importantly, the presence of Uls1 at these sites prevents ACF-dependent Top2 accumulation. Our data reveal the effect of Top2 poisons on the global Top2 binding landscape and highlights the role of Uls1 in antagonising Top2 function. Remodelling Top2 binding is thus an important new means by which Snf2 enzymes promote genome stability.

The impediment to replication at tRNA genes inS. cerevisiaedoes not require tRNA transcription, and is facilitated by topoisomerases and Rad18-dependent repair pathways

“…The role of topoisomerases at these loci is likely to be complex. Topoisomerase I has been shown to promote fork progression by removing R loops in mammalian cells (Tuduri et al 2009) and tDNAs were sites of increased Top2 binding in a defective chromatin remodeling background in S. cerevisiae (Swanston et al 2019). Top2 was required for the transcription of long (>3kb) transcripts by RNAPII (Joshi et al 2012) in yeast, but not required for transcription of short transcripts like U4 snRNA or RNAPIII-transcribed genes (Fig.S3B).…”