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Articles by John F.X. Diffley
Light-years of DNA
Mission notes by John Diffley Questions When you’re thinking about science, it’s a good idea to have a 30-year question, a five-year question and a one‑year question. You have to start with stuff that you can actually do. Then you have to be more expansive, and then you have to have some end point that you’re really trying to get to. Imagination Science Fiction is quite an interesting thing.
Biochemical reconstitution of sister chromatid cohesion establishment during DNA replication
Keywords chromosome replication chromosome segregation sister chromatid cohesion cohesin biochemical reconstitution S. cerevisiae Introduction Concurrently with genome replication during the S phase of the eukaryotic cell cycle, the chromosomal cohesin complex establishes physical links between the two replication products.1,2,3,4 These links are known as sister chromatid cohesion.
The DNA replication checkpoint prevents PCNA/RFC depletion to protect forks from HLTF-induced collapse in human cells
Keywords PCNA RFC Okazaki fragments polymerase α DNA damage DNA replication checkpoint DNA replication fork collapse DNA replication fork stabilization RPA exhaustion HLTF Introduction DNA replication fork stalling in response to nucleotide depletion, inhibition of DNA polymerases, or DNA damage activates the checkpoint protein kinases ATR and its downstream effector Chk1.1,2,3 In humans, mice, and budding yeast, these damage checkpoint kinases are essential for cell...
The DNA replication checkpoint limits Okazaki fragment accumulation to protect and restart stalled forks
Keywords DNA replication fork stabilization DNA replication checkpoint DNA polymerase α Okazaki fragments replication fork collapse RPA exhaustion PCNA RFC DNA polymerase δ DNA polymerase ε Introduction Accurate and efficient DNA replication is crucial for genome maintenance.
Cell Cycle Regulation has Shaped Budding Yeast Replication Origin Structure and Function
Abstract Eukaryotic DNA replication initiates from multiple genomic loci known as origins. At budding yeast origins like ARS1, a double hexamer (DH) of the MCM replicative helicase is assembled by Origin Recognition Complex (ORC), Cdc6 and Cdt1 via sequential hexamer loading from two opposed ORC binding sites. Cyclin Dependent Kinase (CDK) inhibits DH assembly, which prevents re-replication by restricting helicase loading to G1 phase.
Cyclin E-induced replicative stress drives p53-dependent whole-genome duplication
Aphidicolin-induced RPE1 EC-G1 cells did not reload MCM or proliferate after release from aphidicolin (Figures 6A and S7A ), in contrast to U2OS (Figures 3F–3H) or RPE1 cells expressing cyclin E (Figure 4B). RPE1 EC-G1 cells generated by aphidicolin treatment were positive for β-galactosidase activity (Figure 7B), suggesting that they have become senescent. Previous work has shown that transient activation of p53 in G2 can cause mitotic bypass and promote entry into senescence.
The Initiation of Eukaryotic DNA Replication
1. INTRODUCTION The emergence of complex, multicellular life on Earth was enabled by the evolution of molecular machines and regulatory pathways that bring about the accurate and rapid duplication of large genomes. In bacteria, like Escherichia coli, the entire genome is contained on a single circular chromosome and is replicated by two DNA replication machines (replisomes) traveling in opposite directions from a single initiation site (oriC) known as a replication origin (1).
Tackling SARS-CoV-2 biochemistry
Tackling SARS-CoV-2 biochemistry The beginning of the COVID-19 pandemic launched a race to produce effective vaccines, several of which have now been rolled out with remarkable speed. Frequent emergence of SARS-CoV-2 variants, however, serves as an important warning that this will be an ongoing battle. New generations of vaccines will be required, and effective antiviral compounds will be crucial tools in the armory against newly emerging virus variants.
Unchecked nick ligation can promote localized genome re-replication
Summary Single-stranded DNA breaks, or nicks, are amongst the most common forms of DNA damage in cells. They can be repaired by ligation; however, if a nick occurs just ahead of an approaching replisome, the outcome is a collapsed replication fork comprising a single-ended double-strand break and a ‘hybrid nick’ with parental DNA on one side and nascent DNA on the other (Figure 1A).
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