--- module: 091-01 language: en chapter: 91 title: "DNA Replication, Repair, Gene Expression, and Epigenetic Control" module_title: "DNA replication, telomeres, genome surveillance, and repair pathways" source_sha256: 0baed2abd84317dae7541690fdac91b31f63fd32fde7c2be28b253813250f588 --- # DNA replication, telomeres, and repair ## Copying principles ### Antiparallel strands, five-prime-to-three-prime synthesis #### Extension only from a free three-prime hydroxyl ### Semiconservative: old strand templates new ### Pairing, active-site geometry, proofreading #### Residual errors corrected after synthesis ### Genome maintenance is a network ## Origins and the fork ### Thousands of origins across chromosomes ### Licensing in late mitosis and gap one #### Inactive helicases loaded ### Synthesis-phase kinases fire a subset #### Activation blocks relicensing: copied once ### Dormant origins rescue stalled regions ### Helicase unwinds, single-strand binders protect ### Topoisomerases cut and reseal to relieve strain ### Primase makes RNA-DNA primers #### Replicative polymerases cannot start de novo ## Strand synthesis and chromatin restoration ### Leading strand continuous toward fork ### Lagging strand as Okazaki fragments #### Primers removed, gaps filled, ligase seals ### Polymerase epsilon leading, delta lagging ### PCNA sliding clamp gives processivity #### Clamp loaders use ATP ### Histones recycled and new ones deposited ### Epigenetic marks re-established by reader-writers ## Fork stress ### Lesions, bound proteins, transcription, low nucleotides ### Checkpoint kinases stabilise forks #### Restrain origin firing and delay cycle ### Fork reversal protects ends ### Recombination restarts collapsed forks ### Unresolved stress: breaks and rearrangements #### Major source of cancer evolution ## Telomeres ### Repetitive DNA-protein caps ### Incomplete end copying and nucleolytic shortening ### Shelterin stops ends looking like breaks ### Critical dysfunction: checkpoints and fusions #### Breakage-fusion cycles ### Telomerase: reverse transcriptase with RNA template #### Germ cells, stem cells, lymphocytes, most cancers ### Alternative lengthening by recombination ### Shortening limits replication, maintenance immortalises ## Lesions and early correction ### Lesion is chemistry, mutation is fixed sequence ### Repair restores, tolerates, or introduces errors ### Proofreading exonuclease acts immediately ### Mismatch repair after replication #### Excises a stretch of the new strand ### Lynch syndrome #### Microsatellite instability #### Screen tumours, then interpret the cause ## Excision and direct repair ### Base excision for small non-distorting lesions #### Glycosylase leaves an abasic site #### Endonuclease, processing, fill, ligate ### PARP detects single-strand breaks #### Homologous-repair-deficient tumours: synthetic lethality ### Nucleotide excision for bulky distortions #### Global-genome versus transcription-coupled ### Xeroderma pigmentosum: skin and eye cancer ### Cockayne spectrum: growth and neurological disease ### Direct reversal: MGMT suicide reaction #### Silencing raises alkylating-agent sensitivity ## Double-strand breaks and crosslinks ### Homologous recombination uses sister chromatid #### Favoured in synthesis and gap two #### Resection, RAD51 filament, strand invasion ### BRCA variants impair homologous repair #### Genomic scars, secondary mutations restore ### Classical end joining throughout the cycle #### Essential for antigen-receptor rearrangement #### May leave small insertions or deletions ### Alternative end joining uses microhomology ### Crosslinks need nucleases, bypass, recombination #### Fanconi: marrow failure, anomalies, cancer ## Tolerance, signalling, and testing ### Translesion polymerases bypass damage #### Lower fidelity, switch back essential ### ATM responds to double-strand breaks #### Ataxia, telangiectasia, radiosensitivity ### ATR responds to single-stranded DNA ### p53: arrest, senescence, repair, apoptosis ### Repair capacity measured indirectly #### Match the test to the biological question