A Top2 and Hmo1-mediated genome architectural pathway preventing chromosome fragility.

Specialized topoisomerases solve the topological constraints arising when replication forks encounter transcription. We have investigated Top2 contribution in S phase transcription. Specifically in S phase, Top2 binds intergenic regions close to transcribed genes without influencing their transcription. The Top2-bound loci exhibit low nucleosome density and accumulate yH2A when Top2 is defective. These intergenic loci associate with the HMG-protein Hmo1 throughout the cell cycle and are refractory to the histone variant Htz1. In top2 mutants, Hmo1 is deleterious and accumulates at pericentromeric regions in G2/M. Our data indicate that Top2 is dispensable for transcription and that Hmo1 and Top2 bind in the proximity of genes transcribed in S phase suppressing chromosome fragility at the M-G1 transition. We propose that an Hmo1-dependent epigenetic signature together with Top2 mediate a S-phasen architectural pathway controlling replicon dynamics when forks encounter transcriptionto preserve genome integrity. Signal tracks in BED format suitable for visualization on the UCSC genome browser can be found at http://bio.ifom-ieo-campus.it/supplementary/Bermejo_et_al_CELL_2009 The Chip on chip analysis was carried out as described (Bermejo et al., 2007; Katou et al., 2006; Katou et al., 2003), employing anti-Flag monoclonal antibody M2 (Sigma-Aldrich) anti-PK SV5-Pk1 antibody (AbD Serotec) and anti-γH2A antibodies (a gift from Alain Verreault). Labelled probes were hybridized to Affymetrix S.cerevisiae whole genome tiling R arrays and processed with TAS software Rev 1.1.