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Yeast Has Defined Origins

Yeast Has Defined Origins. ARS directs autonomous replication of plasmid DNA. S. cerevisiae ARS contains a conserved 11 bp ARS consensus sequence and multiple B elements. The ORC complex binds to the ARS during most of the cell cycle. The S. pombe origin is larger and

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Yeast Has Defined Origins

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  1. Yeast Has Defined Origins ARS directs autonomous replication of plasmid DNA S. cerevisiae ARS contains a conserved 11 bp ARS consensus sequence and multiple B elements The ORC complex binds to the ARS during most of the cell cycle The S. pombe origin is larger and binds ORC by a distinct mechanism from Bell, Genes Dev. 16, 659 (2002)

  2. Some Features of Metazoan Origins No strong consensus sequences for origins exist Several sequence motifs can be present at origins, but are not present at all origins Replication domains often correlate with TADs Local chromatin structure influences origin choice from Aladjem and Redon, Nature Rev.Genet. 18, 101 (2017)

  3. Different Classes of Replication Origins in Metazoans Only a small subset of origins are active during a given cell cycle Constitutive origins are used all the time and are relatively rare Flexible origins are used to a different extent in different cells and follow the Jesuit Model “Many are called but few are chosen” Inactive or dormant origins are only used during replication stress or during certain cellular programs from Méchali, Nature Rev.Mol.Cell.Biol. 11, 728 (2010)

  4. Origins Are Activated at Different Times preRCs are formed during G1 on origins Heterochromatic regions replicate later than euchromatic regions from Méchali, Nature Rev.Mol.Cell.Biol. 11, 728 (2010)

  5. The Replicative Helicase Mcm2-7, Cdc45, and GINS (CMG complex) form the replicative helicase from Moyer et al., Proc.Nat.Acad.Sci.USA 103, 10236 (2006)

  6. The Formation of the preRC Mcm2-7 is loaded as a double hexamer by ORC, Cdc6 and Cdt1 Sld3 and Cdc45 bind weakly to Mcm2-7 Mcm2-7 helicase is inactive until S phase from Labib, Genes Dev. 24, 1208 (2010)

  7. Initiation of Chromosome Replication DDK phosphorylates Mcm proteins CDK phosphorylates Sld2 and Sld3 to interact with Dpb11 GINS and Pol e are recruited to form the RPC (replisome progression complex) Activation of the helicase allows priming by Pol a Pol e extends the leading strand and Pol d extends each Okazaki fragment from Labib, Genes Dev. 24, 1208 (2010)

  8. Helicase Loading and Activation in DNA Replication DnaA and ORC are structural homologs Replication competence is conferred by Mcm2-7 loading and is prevented by inhibition of pre-RC proteins CDKs prevent Mcm2-7 loading and are required for helicase activation from Remus and Diffley, Curr.Opin.Cell Biol. 21, 771 (2009)

  9. Division of Labor at the Replication Fork from Jinks-Robertson and Klein, Nature Rev.Struct.Mol.Biol. 22, 176 (2015)

  10. The Eukaryotic Replication Fork CMG unwinds parental DNA CMG recruits Pole PCNA recruits Pold Ribonucleotides are incorporated every 1,000 – 10,000 nucleotides from Kunkel and Burgers, Nature Struct.Mol.Biol. 21, 649 (2014)

  11. Chromatin Dynamics During DNA Replication from Ransom et al., Cell140, 183 (2010) Nucleosome assembly is coupled to DNA replication Half of histones on newly replicated DNA are recycled from parental histones Parental and newly synthesized H2A/H2B dimers and H3/H4 heterotetramers associate with histone chaperones

  12. Consequences of Stalled Replication Forks SAMHD1 binds to and activates MRE11 at stalled forks and resects DNA and prevents the release of ssDNA In the absence of SAMHD1, other enzymes process the nascent DNA and ssDNA is exported to the cytoplasm Cytoplasmic ssDNA triggers pro-inflammatory responses from Crossley and Cimprich, Nature557, 34 (2018)

  13. Replication Fork Reversal from Neelsen and Lopes, Nature Rev.Mol.Cell Biol. 16, 207 (2015) Replication fork reversal is induced at stalled or uncoupled forks Fork reversal promotes DNA damage tolerance and repair Failure of fork reversal leads to replication uncoupling The regressed arm resembles dsb

  14. Mechanisms of Replication Fork Reversal from Quinnet et al., Molecular Cell68, 830 (2017) ssDNA at uncoupled forks recruits a ubiquitin ligase which ubiquitylates PCNA ZRANB3 translocase binds to PCNA-Ub to promote fork reversal BRCA2 promotes Rad51 binding and its stabilization to avoid gap formation Presistent ssDNA gaps are remodeled into a reversed fork by SMARCAL1

  15. Stabilization of Reversed Forks BRCA2 stabilizes the RAD51 filament on the regressed arm and inhibits its degradation from Quinnet et al., Molecular Cell68, 830 (2017)

  16. PARP1 Maintains Replication Fork Stability PARP1 is recruited to stalled forks and prevents restart by inhibiting RECQ1 After lesion repair, RECQ1 is activated to promote branch migration and restart The replication fork can also restart by RAD51-assisted invasion of the parental DNA by the regressed arm from Chaudhuri and Nussenzweig, Nature Rev.Mol.Cell Biol. 18, 610 (2017)

  17. Replication Origins are Licensed in Late M and G1 Origins are licensed by Mcm2-7 binding to form part of the pre-RC Mcm2-7 is displaced as DNA replication is initiated Licensing is turned off at late G1 by CDKs and/or geminin from Blow and Dutta, Nature Rev.Mol.Cell Biol.6, 476 (2005)

  18. Control of Licensing Differs in Yeasts and Metazoans CDK activity prevents licensing in yeast Geminin activation downregulates Cdt1 in metazoans from Blow and Dutta, Nature Rev.Mol.Cell Biol.6, 476 (2005)

  19. The End Replication Problem Leading strand is synthesized to the end of the chromosome Lagging strand utilizes RNA primers which are removed The lagging strand is shortened at each cell division from Lodish et al., Molecular Cell Biology, 6th ed. Fig 6-49

  20. Solutions to the End Replication Problem 3’-terminus is extended using the reverse transcriptase activity of telomerase Dipteran insects use retrotransposition with the 3’-end of the chromosome as a primer Kluyveromyces lactis uses a rolling circle mechanism in which the 3’-end is extended on an extrachromosomal template Telomerase-deficient yeast use a recombination- dependent replication pathway in which one telomere uses another telomere as a template Formation of T-loops using terminal repeats allow extension of invaded 3’-ends from de Lange, Nature Rev.Mol.Cell Biol. 5, 323 (2004)

  21. Telomerase Solves the Replication Problem Telomerase-associated RNA base pairs to the G overhang Telomerase catalyzes reverse transcription to a specific site Telomerase dissociates and base pairs to a more 3’-region of the G overhang Successive reverse transcription, dissociation, and reannealing extends the G overhang The C-strand is filled in using the extended template from Alberts et al., Molecular Biology of the Cell, 4th ed. Fig 5-43

  22. Structure of Human Telomerase Telomerase contains RNA and protein A portion of the RNA component is a template for telomeric repeats The catalytic core contains a reverse transcriptase The H/ADA lobe facilitates telomerase assembly and controls trafficking from Stone Nature 557, 174 (2018)

  23. Telomerase Action is Restricted to a Subset of Ends Telomere length is regulated by shelterin Increased levels of shelterin inhibits telomerase action from Bertuch and Lundblad, Curr.Opin.Cell Biol. 18, 247 (2006)

  24. Telomeres are Specialized Structures at the Ends of Chromosomes Telomeres contain multiple copies of short repeated sequences and contain a 3’-G-rich overhang Telomeres are bound by proteins which protect the telomeric ends initiate heterochromatin formation and facilitate progression of the replication fork from Gilson and Geli, Nature Rev.Mol.Cell Biol. 8, 825 (2007)

  25. Functions of Telomeres from Nandakumar and Cech, Nature Rev.Mol.Cell Biol. 14, 69 (2013) Deprotected telomeres induce checkpoint activation, the DNA damage response and DNA repair Telomerase is recruited by telomeric proteins and counteracts telomere shortening during DNA replication

  26. Structure of Human Telomeres Telomeres consist of numerous short dsDNA repeats and a 3’-ssDNA overhang The G-tail is sequestered in the T-loop Shelterin is a protein complex that binds to telomeres TRF1 and TRF2 binds duplex repeat and recruits other shelterin components Shelterin inhibits the DNA damage response and blocks telomerase activity TRF2 inhibits RNF168 to inhibit NHEJ TERRA accumulates at short telomeres, promotes ALT and delays senescence from O’Sullivan and Karlseder, Nature Rev.Mol.Cell Biol. 11, 171 (2010)

  27. Maintenance of Chromosome Ends TPP1 and POT1 recruits telomerase which extends G-strands The CST complex binds to the extended G-strand and suppresses telomerase access and activity CST promotes C-strand fill-in by Pol a-Primase from Martinez and Blasco, Trends Biochem.Sci. 40, 504 (2015)

  28. Heterochromatin at Telomeres Chromosome ends are enriched in H3K9me3, H4K20me3 and HP1 Subtelomeric DNA is heavily methylated Telomeric heterochromatin restricts telomerase access and suppresses recombination from Martinez and Blasco, Trends Biochem.Sci. 40, 504 (2015)

  29. G Overhang Generation at Telomeres TRF2 recruits Apollo at leading telomeres and initiations overhang generation POT1 binds to inhibit hyperresection Exo1 generates elongated overhangs CST is recruited by POT1 and recruits Pola-primase to fill in C-strand from Martinez and Blasco, Trends Biochem.Sci. 40, 504 (2015)

  30. Endogenous DNA Damage from Marnett and Plastaras, Trends Genet. 17, 214 (2001)

  31. Biological Molecules are Labile RNA is susceptible to hydrolysis Reduction of ribose to deoxyribose gives DNA greater stability N-glycosyl bond of DNA is more labile DNA damage occurs from normal cellular operations and random interactions with the environment

  32. Spontaneous Changes that Alter DNA Structure deamination oxidation depurination from Alberts et al., Molecular Biology of the Cell,4th ed., Fig 5-46

  33. Hydrolysis of the N-glycosyl Bond of DNA from Alberts et al., Molecular Biology of the Cell,4th ed., Fig 5-47 Spontaneous depurination results in loss of 10,000 bases/cell/day Causes formation of an AP site – not mutagenic

  34. Deamination of Cytosine to Uracil from Alberts et al., Molecular Biology of the Cell,4th ed., Fig 5-47 Cytosine is deaminated to uracil at a rate of 100-500/cell/day Uracil is excised by uracil-DNA-glycosylase to form AP site

  35. 5-Methyl Cytosine Deamination is Highly Mutagenic Deamination of 5-methyl cytosine to T occurs rapidly - base pairs with A 5-me-C is a target for spontaneous mutations from Alberts et al., Molecular Biology of the Cell,4th ed., Fig 5-52

  36. Deamination of A and G Occur Less Frequently A is deaminated to HX – base pairs with C G is deaminated to X – base pairs with C from Alberts et al., Molecular Biology of the Cell,4th ed., Fig 5-52

  37. Ribonucleotide Excision Repair rNTP incorporation is the most common DNA lesion (1/103) RNase H2 cleaves 5’ to the incorporated ribonucleotide The nascent strand is extended and flap is cleaved by Fen1 Cleavage by Top1 leads to small deletions from Ganai and Johansson, Molecular Cell 62, 745 (2016)

  38. RNA Editing Discovered when there is a discrepancy between genomic and mRNA sequences Adenosine deaminase converts adenosine to inosine Inosine is interpreted as guanosine during translation 108 sites are edited RNA editing expands the functional output of expressed genes RNA editing is essential for neuronal function and is turned on during neuronal differentiation Mediators of synaptic transmission are targets of RNA editing RNA editing influences splice site choice and miRNA targeting capacity

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