title: Genome-wide localization of Rrm3 and Pif1 DNA helicases at stalled active and inactive DNA replication forks of Saccharomyces cerevisiae.
abstract: The genome of the budding yeast Saccharomyces cerevisiae is sequenced and the location and dynamic of activation of DNA replication origins are known. G1 synchronized yeast cells can be released into S-phase in the presence of hydroxyurea (HU) (1), which slows down DNA replication and retains replication forks in proximity of DNA replication origins. In this condition, the Chromatin Immuno-Precipitation on chip (ChIP on chip) (2-4) of replisome components allows the precise localization of all active DNA replication forks. This analysis can be coupled with the ssDNA-BromodeoxyUridine (ssDNA-BrdU) Immuno-Precipitation on chip (ssDNA-BrdU IP on chip) technique (5-7), which detects the location of newly synthesized DNA. Comparison of binding and BrdU incorporation profiles allows to locate a factor of interest at DNA replication forks genome wide. We present datasets deposited in the gene expression omnibus (GEO) database under accession number GSE68214, which show how the DNA helicases Rrm3 and Pif1 (8) associate to active and inactive DNA replication forks.
authors.affiliation: IFOM (Fondazione Istituto FIRC di Oncologia Molecolare) via Adamello 16, 20139 Milan, Italy; Università degli Studi di Milano, Dipartimento di Bioscienze, Via Celoria 26, 20133 Milan, Italy.
authors.forename: Silvia Emma
authors.initials: SE
authors.lastname: Rossi
authors.affiliation: IFOM (Fondazione Istituto FIRC di Oncologia Molecolare) via Adamello 16, 20139 Milan, Italy.
authors.forename: Walter
authors.initials: W
authors.lastname: Carotenuto
authors.affiliation: IFOM (Fondazione Istituto FIRC di Oncologia Molecolare) via Adamello 16, 20139 Milan, Italy; Università degli Studi di Milano, Dipartimento di Bioscienze, Via Celoria 26, 20133 Milan, Italy.
authors.forename: Michele
authors.initials: M
authors.lastname: Giannattasio
keywords: ChIP on chip and ssDNA-BrdU IP on chip; DNA replication fork; DNA replication stress; Rad53 and hydroxyurea; Rrm3 and Pif1