Estimated wild-type DNA replication fork velocity

Value 2.3 kb/min Range: previous estimates 1.6-3kb/min kb/min
Organism Budding yeast Saccharomyces cerevisiae
Reference Gispan A, Carmi M, Barkai N. Model-based analysis of DNA replication profiles: Predicting replication fork velocity and initiation rate by profiling free-cycling cells. Genome Res. 2016 Dec 27. pii: gr.205849.116. doi: 10.1101/gr.205849.116 p.5 top paragraph link PubMed ID28028072
Primary Source Sekedat MD, Fenyo D, Rogers RS, Tackett AJ, Aitchison JD, Chait BT. 2010. GINS motion reveals replication fork progression is remarkably uniform throughout the yeast genome. Mol Syst Biol 6: 353. link DOI: 10.1038/msb.2010.8 AND Yang SC, Rhind N, Bechhoefer J. 2010. Modeling genome-wide replication kinetics reveals a mechanism for regulation of replication timing. Mol Syst Biol 6: 404. link DOI: 10.1038/msb.2010.61 AND Hyrien O, Goldar A. 2010. Mathematical modelling of eukaryotic DNA replication. Chromosom Res 18: 147–161. link doi: 10.1007/s10577-009-9092-4 AND Yabuki N, Terashima H, Kitada K. 2002. Mapping of early firing origins on a replication profile of budding yeast. Genes Cells 7: 781–789. link AND Raghuraman MK et al., 2001. Replication dynamics of the yeast genome. Science (80- ) 294: 115–121. link DOI: 10.1126/science.294.5540.115 PubMed ID20212525, 20739926, 20205354, 12167157, 11588253
Method P.5 top paragraph: "Validating predicted changes in fork velocity and initiation capacity using time-resolved profiling: [Investigators] next wished to verify predicted changes in fork velocity or initiation capacity. This required an independent means for measuring these parameters. To this end, [they] profiled cells that progress synchronously through S phase. Cells were arrested at the end of G1 using α-factor, and were followed for sixty minutes upon release, with samples taken every three minutes for DNA sequencing. Synchronized progression was verified by DNA staining (Fig. 4A). Plotting DNA content as a function of chromosomal coordinates at different times showed the expected v-shape increase in DNA content around replication origins, capturing the symmetric progression of the replication fork (Fig. 4B)."
Comments P.5 top paragraph: "Based on this pattern around well-characterized origins [see Measurement Method], [investigators] estimated wild-type fork velocity to be 2.3 kb/min, consistent with previous estimates (1.6-3 kb/min)(primary sources)."
Entered by Uri M
ID 113067