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Series GSE16258 Query DataSets for GSE16258
Status Public on Sep 05, 2009
Title A Top2 and Hmo1-mediated genome architectural pathway preventing chromosome fragility.
Organism Saccharomyces cerevisiae
Experiment type Genome binding/occupancy profiling by genome tiling array
Summary 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
Overall design 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.
Contributor(s) Bermejo R, Capra T, Gonzalez-Huici V, Fachinetti D, Cocito A, Natoli G, Katou Y, Mori H, Kurokawa K, Shirahige K, Foiani M
Citation(s) 19737516
Submission date May 27, 2009
Last update date Jan 09, 2016
Contact name Andrea Cocito
Phone +3902574303853
Fax +3902574303231
Organization name IFOM Institute FIRC of Molecular Oncology
Department Molecular Medicine Program
Lab Cocito
Street address Via Adamello 16
City Milano
State/province MI
ZIP/Postal code 20139
Country Italy
Platforms (1)
GPL7250 [Sc03b_MR] Affymetrix GeneChip S. cerevisiae Tiling 1.0R Array
Samples (22)
GSM409325 Top2
GSM409326 Rpb3
GSM409327 Top2-GAL
BioProject PRJNA115093

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE16258_RAW.tar 1.9 Gb (http)(custom) TAR (of BAR, CEL, TXT)
Processed data provided as supplementary file

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