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Table of Contents

Table of Contents
DNA Replication in Eukaryotic Cells

Chapters from the Previous Edition

Chapters 1–4
 Figure 1-1. Initiation of DNA replication.
 Figure 1-2. DNA relication forks.
 Figure 2-1. The replicon model.
 Figure 2-2. Functional elements in yeast replicators.
 Figure 2-3. Metazoan replication origins.
 Figure 2-4. Sequence features of metazoan replicators.
 Figure 3-1. Speculative model of pre-RC formation.
 Figure 4-1. Mechanism of helicase activation.
Chapters 5–7
 Figure 5-1. Eukaryotic DNA replication fork.
 Figure 5-2. Subunit interactions in DNA polymerases.
 Figure 5-3. Replicative DNA polymerase model.
 Figure 5-4. Replication stages of the lagging strand.
 Figure 5-5. Nick maintenance by idling or by nick translation.
 Figure 6-1. Conservation of the CAF-1 and HIR histone deposition complexes.
 Figure 6-2. Histone deposition during DNA replication.
 Figure 6-3. Known interaction partners of Asf1.
 Figure 7-1. Maintenance methylation of CpG sites.
Chapters 8–10
 Figure 8-1. Crystal structure of Tus-Ter complex of E. coli.
 Figure 8-2. Repeat units of yeast rDNA.
 Figure 8-3. Nucleotide sequences of Ter1 and Ter2 sites.
 Figure 8-4. 2D gel analyses of replication fork arrest.
 Figure 8-5. Loading of the RENT complex at the rDNA of yeast and of the FEAR pathway.
 Figure 8-6. Mating-type switching locus Mat1 of S. pombe.
 Figure 9-1. Replication foci.
 Figure 9-2. Dual telomere anchoring pathways in yeast.
 Figure 10-1. Regulation of origin initiation time in S. cerevisiae.
 Figure 10-2. Developmentally regulated replication initiation sites.
Chapters 11–14
 Figure 11-1. Changes in origin position related to transcriptional activity.
 Figure 12-1. Structure and protein binding at amplification origins.
 Figure 12-2. Cell biological assays for amplification in Drosophila.
 Figure 13-1. Genetic organization of the four genera of the Geminiviridae family.
 Figure 13-2. Initiation reaction and loading of cellular DNA replication factors.
 Figure 14-1. Sulfolobus origin architecture and recognition by Orc1/Cdc6 homologs.
 Figure 14-2. Mechanisms by which replicative helicases may function.
 Figure 14-3. Archaeal MCM organization.
 Figure 14-4. Uracil-binding pocket.
 Figure 14-5. Human PCNA bound to FEN1.
Chapters 15–17
 Figure 15-2. Chromosome replication cycle.
 Figure 15-3. CDK activity prevents pre-RC assembly.
 Figure 16-1. Regulation of ORC activity in mammal and fly.
 Figure 16-2. Regulation of ORC activity in X. laevis.
 Figure 16-3. Regulation of Cdc6 activity in metazoa.
 Figure 16-4. Regulation of Cdt1 and MCM activity in metazoa.
 Figure 16-5. Structure of a geminin:Cdt1 complex.
 Figure 17-1. Checkpoint pathways in budding and fission yeasts.
 Figure 17-2. Multiple potential configurations of stalled replication forks.
 Figure 17-3. Sister chromatid junctions that resemble hemicatenanes.
 Figure 17-4. Bypassing damage in the template strand.
Chapters 18–22
 Figure 18-1. The different checkpoints operating in S phase.
 Figure 18-2. Signal transduction pathways that regulate S phase.
 Figure 18-3. ATR signaling during S phase.
 Figure 20-1. Putative roles of DNA polymerases in DNA transactions.
 Figure 20-2. Structures of DNA polymerases in five families.
 Figure 21-1. The protein networks that ensure genomic stability on eukaryotic clamps.
 Figure 21-2. Four clamp–clamp loader pathways in eukaryotes.
 Figure 22-1. Active mechanisms of helicase unwinding.
 Figure 22-2. Functional motifs in XPB and XPD helicases.
 Figure 22-3. Alignment of RecQ family helicases.
Chapters 23–26
 Figure 23-1. Disease-associated unstable repeats.
 Figure 23-2. DNA metabolic processes and repeat instability.
 Figure 23-3. Replication and repeat instability.
 Figure 23-4. Replication-mediated TNR instability.
 Figure 23-5. trans-factors and repeat instability.
 Figure 25-3. Dual immunofluorescence staining for Ki67 and other cell cycle markers.
 Figure 26-1. Action of commonly used DNA replication inhibitors.
 Figure 26-2. Action of purine and pyrimidine biosynthesis inhibitors.
 Figure 26-3. Action of DNA polymerase inhibitors.
 Figure 26-4. DNA alkylation by MMS.
 Figure 26-5. DNA alkylating drugs.
 Figure 26-6. Topoisomerase inhibitors.
 Figure 26-7. Common inhibitors of Cdks and checkpoint inhibitors.
Chapters 27–30
 Figure 27-1. Two models of mtDNA replication.
 Figure 27-2. Mouse mtDNA replicative intermediate.
 Figure 27-3. A coherent mode of mtDNA replications.
 Figure 27-4. Aging phenotypes in mtDNA-mutator mice.
 Figure 28-3. Telomere replication and telomerase-mediated extension.
 Figure 29-1. Genome strategies across the Parvovirinae.
 Figure 29-2. Encapsidation strategy for MVM.
 Figure 30-1. Fates of HPV infections of the squamous epithelium.
 Figure 30-2. HPV/host interactions in differentiated keratinocytes.
 Figure 30-3. Clonal selection for an HPV-transformed cell.
 Figure 30-4. How E2 protein might destabilize host chromomes.
Chapters 31–36
 Figure 31-1. Tag structural domains.
 Figure 31-2. Tag interactions with host proteins.
 Figure 32-2. Adenovirus DNA replication.
 Figure 33-1. HSV-1 genome and origins of replication.
 Figure 33-2. UL9-dependent and UL-9-independent HSV DNA replication.
 Figure 34-1. B95-8 laboratory strain of EBV DNA of 165 kbp.
 Figure 34-2. oriP and EBNA1.
 Figure 34-3. oriLyt and its expanded core domain.
 Figure 36-1. The hepatitis B virus genome.
 Figure 36-2. Replication cycle of a hepadnavirus.
 Figure 36-3. Priming of minus-strand DNA.
 Figure 36-4. Priming of plus-strand DNA synthesis.
 Figure 1A-1. Map symbols.
 Figure 1A-2. Examples of MIMs.
 Figure 1A-3. MIM of the signal transduction network that regulates the onset of DNA replication.
 Figure 1B-1. Origins of the components of the pre-RC.

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