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GINS motion reveals replication fork progression is remarkably uniform throughout the yeast genome.

Previous studies have led to a picture wherein the replication of DNA progresses at variable rates over different parts of the budding yeast genome. These prior experiments, focused on production of nascent DNA, have been interpreted to imply that the dynamics of replication fork progression are strongly affected by local chromatin structure/architecture, and by interaction with machineries controlling transcription, repair and epigenetic maintenance. Here, we adopted a complementary approach for assaying replication dynamics using whole genome time-resolved chromatin immunoprecipitation combined with microarray analysis of the GINS complex, an integral member of the replication fork. Surprisingly, our data show that this complex progresses at highly uniform rates regardless of genomic location, revealing that replication fork dynamics in yeast is simpler and more uniform than previously envisaged. In addition, we show how the synergistic use of experiment and modeling leads to novel biological insights. In particular, a parsimonious model allowed us to accurately simulate fork movement throughout the genome and also revealed a subtle phenomenon, which we interpret as arising from low-frequency fork arrest.

Pubmed ID: 20212525 RIS Download

Mesh terms: Chromatin Immunoprecipitation | Chromosomes, Fungal | DNA Replication | Genes, Fungal | Genome, Fungal | Movement | Protein Binding | S Phase | Saccharomyces cerevisiae | Saccharomyces cerevisiae Proteins | Time Factors

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Features Find out about FlowJo features. Don''t forget to check out FlowJo''s special purpose analysis platforms: Compensation, Kinetics, Cell Cycle, Proliferation, Calibration, Derived Parameters and Population Comparison. Version History Mac PC FlowJo uses a standard HTML hypertext format for its documentation, and relies on your web browser to read it. This has several advantages including: it is a flexible linking between related pages; and it allows us to update the content dynamically. However, if you are on a slow network, or overseas, then this access may be too slow. In that case, it is worth the effort to download the entire set of web pages at one time to your hard drive. FlowJo will automatically access those instead. Abstract. Investigating the response of cells to specific agonists may involve the use of cell tracking dyes to assess the extent of stimulated proliferation, frequently reported as the proliferation index (PI). Calculation of PI uses a model for cell division that expects the cell number to double as cells proliferate through each successive generation. It is often useful to compare the PI of a stimulated control population with that of a population in the presence of some agent, whether chemical, pharmacologic, or cellular. For such comparison studies, the nature of the metric being used must be taken into account to accurately assess the extent of inhibition. Specifically, the metric used in ModFit LT (Verity Software House, Topsham, ME) and in FCS Express (De Novo Software, Los Angeles, CA) uses a metric with a lower limit of unity, whereas the metric used in FlowJo (Treestar, Ashland, OR) has a lower limit of zero. For studies involving cell proliferation comparisons using tracking dye dilution, a new equation is proposed as the appropriate calculation to use when determining the percent of relative response based on proliferation index values for a metric whose lower limit is unity.

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