Physical proximity of chromatin to nuclear pores prevents harmful R loop accumulation contributing to maintain genome stability.

Abstract

During transcription, the mRNA may hybridize with DNA, forming an R loop, which can be physiological or pathological, constituting in this case a source of genomic instability. To understand the mechanism by which eukaryotic cells prevent harmful R loops, we used human activation-induced cytidine deaminase (AID) to identify genes preventing R loops. A screening of 400 <i>Saccharomyces cerevisiae</i> selected strains deleted in nuclear genes revealed that cells lacking the Mlp1/2 nuclear basket proteins show AID-dependent genomic instability and replication defects that were suppressed by RNase H1 overexpression. Importantly, DNA-RNA hybrids accumulated at transcribed genes in <i>mlp1/2</i> mutants, indicating that Mlp1/2 prevents R loops. Consistent with the Mlp1/2 role in gene gating to nuclear pores, artificial tethering to the nuclear periphery of a transcribed locus suppressed R loops in <i>mlp1</i>∆ cells. The same occurred in THO-deficient <i>hpr1</i>∆ cells. We conclude that proximity of transcribed chromatin to the nuclear pore helps restrain pathological R loops.