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Chromatin Determinants of Origin Selection and Activation

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The Initiation of DNA Replication in Eukaryotes

Abstract

DNA replication is an essential cell cycle-regulated process necessary for the accurate duplication of the genome. DNA replication begins at cis-acting replicator loci (replication origins) that are distributed throughout each of the eukaryotic chromosomes. The first factor to bind to the replicator is the origin recognition complex (ORC). ORC directs the recruitment of the Mcm2-7 helicase complex to form the pre-replication complex (pre-RC), licensing the origin for activation. Origin selection and activation are dependent on both DNA sequence and epigenetic features. The cis-acting sequence elements that function as replicators are well defined in Saccharomyces cerevisiae; in contrast, metazoan replicators are not defined by primary sequence, but rather by secondary structural features like G-quadruplexes. In both yeast and higher eukaryotes, however, cis-acting sequences or G-quadruplexes are not sufficient for origin function, implying the necessity for epigenetic mechanisms in regulating the selection and activation of DNA replication origins. In higher eukaryotes, the chromatin landscape surrounding origins of replication is important for the plasticity of the DNA replication program, allowing it to adapt and respond to developmental and environmental signals. Here we describe the role of chromatin structure and histone modifications in specifying and regulating eukaryotic DNA replication origins.

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References

  1. Leonard AC, Méchali M. DNA replication origins. Cold Spring Harb Perspect Biol. 2013;5(10):a010116.

    Google Scholar 

  2. Green BM, Finn KJ, Li JJ. Loss of DNA replication control is a potent inducer of gene amplification. Science. 2010;329(5994):943–6.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  3. Jacob F, Brenner S, Cuzin F. On the regulation of DNA replication in bacteria. Cold Spring Harb Symp Quant Biol. 1963;28:329–48.

    Article  CAS  Google Scholar 

  4. O’Donnell M, Langston L, Stillman B. Principles and concepts of DNA replication in bacteria, archaea, and eukarya. Cold Spring Harb Perspect Biol. 2013;5(7):a010108.

    Google Scholar 

  5. Blumenthal AB, Kriegstein HJ, Hogness DS. The units of DNA replication in Drosophila melanogaster chromosomes. Cold Spring Harb Symp Quant Biol. 1974;38:205–23.

    Article  PubMed  CAS  Google Scholar 

  6. Hyrien O, Maric C, Méchali M. Transition in specification of embryonic metazoan DNA replication origins. Science. 1995;270(5238):994–7.

    Article  PubMed  CAS  Google Scholar 

  7. Mantiero D, Mackenzie A, Donaldson A, Zegerman P. Limiting replication initiation factors execute the temporal programme of origin firing in budding yeast. EMBO J. 2011;30(23):4805–14.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  8. Tanaka S, Nakato R, Katou Y, Shirahige K, Araki H. Origin association of Sld3, Sld7, and Cdc45 proteins is a key step for determination of origin-firing timing. Curr Biol. 2011;21(24):2055–63.

    Article  PubMed  CAS  Google Scholar 

  9. Vogelauer M, Rubbi L, Lucas I, Brewer BJ, Grunstein M. Histone acetylation regulates the time of replication origin firing. Mol Cell. 2002;10(5):1223–33.

    Article  PubMed  CAS  Google Scholar 

  10. Aggarwal BD, Calvi BR. Chromatin regulates origin activity in Drosophila follicle cells. Nature. 2004;430(6997):372–6.

    Article  PubMed  CAS  Google Scholar 

  11. Goren A, Tabib A, Hecht M, Cedar H. DNA replication timing of the human beta-globin domain is controlled by histone modification at the origin. Genes Dev. 2008;22(10):1319–24.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  12. Bell SP, Stillman B. ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex. Nature. 1992;357(6374):128–34.

    Article  PubMed  CAS  Google Scholar 

  13. Bleichert F, Botchan MR, Berger JM. Crystal structure of the eukaryotic origin recognition complex. Nature. 2015;519(7543):321–6.

    Google Scholar 

  14. Bell SP, Kaguni JM. Helicase loading at chromosomal origins of replication. Cold Spring Harb Perspect Biol. 2013;5(6):a010124.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  15. Blow JJ, Laskey RA. A role for the nuclear envelope in controlling DNA replication within the cell cycle. Nature. 1988;332(6164):546–8.

    Article  PubMed  CAS  Google Scholar 

  16. Tanaka S, Araki H. Helicase activation and establishment of replication forks at chromosomal origins of replication. Cold Spring Harb Perspect Biol. 2013;5(12):a010371.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  17. Yabuuchi H, Yamada Y, Uchida T, Sunathvanichkul T, Nakagawa T, Masukata H. Ordered assembly of Sld3, GINS and Cdc45 is distinctly regulated by DDK and CDK for activation of replication origins. EMBO J. 2006;25(19):4663–74.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  18. Heller RC, Kang S, Lam WM, Chen S, Chan CS, Bell SP. Eukaryotic origin-dependent DNA replication in vitro reveals sequential action of DDK and S-CDK kinases. Cell. 2011;146(1):80–91.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  19. Muramatsu S, Hirai K, Tak YS, Kamimura Y, Araki H. CDK-dependent complex formation between replication proteins Dpb11, Sld2, Pol, and GINS in budding yeast. Genes Dev. 2010;24(6):602–12.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  20. Zegerman P, Diffley JFX. Phosphorylation of Sld2 and Sld3 by cyclin-dependent kinases promotes DNA replication in budding yeast. Nature. 2007;445(7125):281–5.

    Article  PubMed  CAS  Google Scholar 

  21. Ilves I, Petojevic T, Pesavento JJ, Botchan MR. Activation of the MCM2-7 helicase by association with Cdc45 and GINS proteins. Mol Cell. 2010;37(2):247–258.

    Article  PubMed  CAS  Google Scholar 

  22. Moyer SE, Lewis PW, Botchan MR. Isolation of the Cdc45/Mcm2-7/GINS (CMG) complex, a candidate for the eukaryotic DNA replication fork helicase. Proc Natl Acad Sci U S A. 2006;103(27):10236–41.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  23. Aparicio OM, Weinstein DM, Bell SP. Components and dynamics of DNA replication complexes in S. cerevisiae: redistribution of MCM proteins and Cdc45p during S phase. Cell. 1997;91(1):59–69.

    Article  PubMed  CAS  Google Scholar 

  24. Celniker SE, Campbell JL. Yeast DNA replication in vitro: initiation and elongation events mimic in vivo processes. Cell. 1982;31(1):201–13.

    Article  PubMed  CAS  Google Scholar 

  25. Vashee S, Cvetic C, Lu W, Simancek P, Kelly TJ, Walter JC. Sequence-independent DNA binding and replication initiation by the human origin recognition complex. Genes Dev. 2003;17(15):1894–908.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  26. Valton AL, Hassan-Zadeh V, Lema I, Boggetto N, Alberti P, Saintomé C, et al. G4 motifs affect origin positioning and efficiency in two vertebrate replicators. EMBO J. 2014;33(7):732–46.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  27. Stinchcomb DT, Struhl K, Davis RW. Isolation and characterisation of a yeast chromosomal replicator. Nature. 1979;282(5734):39–43.

    Article  PubMed  CAS  Google Scholar 

  28. Marahrens Y, Stillman B. A yeast chromosomal origin of DNA replication defined by multiple functional elements. Science. 1992;255(5046):817–23.

    Article  PubMed  CAS  Google Scholar 

  29. Wilmes GM, Bell SP. The B2 element of the Saccharomyces cerevisiae ARS1 origin of replication requires specific sequences to facilitate pre-RC formation. Proc Natl Acad Sci U S A. 2002;99(1):101–6.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  30. Huang RY, Kowalski D. A DNA unwinding element and an ARS consensus comprise a replication origin within a yeast chromosome. EMBO J. 1993;12(12):4521–31.

    PubMed Central  PubMed  CAS  Google Scholar 

  31. Liachko I, Youngblood RA, Keich U, Dunham MJ. High-resolution mapping, characterization, and optimization of autonomously replicating sequences in yeast. Genome Res. 2013;23(4):698–704.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  32. Breier AM, Chatterji S, Cozzarelli NR. Prediction of Saccharomyces cerevisiae replication origins. Genome Biol. 2004;5(4):R22.

    Article  PubMed Central  PubMed  Google Scholar 

  33. Nieduszynski CA, Knox Y, Donaldson AD. Genome-wide identification of replication origins in yeast by comparative genomics. Genes Dev. 2006;20(14):1874–79.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  34. Dershowitz A, Newlon CS. The effect on chromosome stability of deleting replication origins. Mol Cell Biol. 1993;13(1):391–98.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  35. Bogenschutz NL, Rodriguez J, Tsukiyama T. Initiation of DNA replication from non-canonical sites on an origin-depleted chromosome. PLoS One. 2014;9(12):e114545.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  36. Gros J, Devbhandari S, Remus D. Origin plasticity during budding yeast DNA replication in vitro. EMBO J. 2014;33(6):621–36.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  37. Heinzel SS, Krysan PJ, Tran CT, Calos MP. Autonomous DNA replication in human cells is affected by the size and the source of the DNA. Mol Cell Biol. 1991;11(4):2263–72.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  38. Remus D, Beall EL, Botchan MR. DNA topology, not DNA sequence, is a critical determinant for Drosophila ORC–DNA binding. EMBO J. 2004;23(4):897–907.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  39. Ariga H, Imamura Y, Iguchi-Ariga SM. DNA replication origin and transcriptional enhancer in c-myc gene share the c-myc protein binding sequences. EMBO J. 1989;8(13):4273–9.

    PubMed Central  PubMed  CAS  Google Scholar 

  40. Delidakis C, Kafatos FC. Amplification enhancers and replication origins in the autosomal chorion gene cluster of Drosophila. EMBO J. 1989;8(3):891–901.

    PubMed Central  PubMed  CAS  Google Scholar 

  41. Kitsberg D, Selig S, Keshet I, Cedar H. Replication structure of the human beta-globin gene domain. Nature. 1993;366(6455):588–90.

    Article  PubMed  CAS  Google Scholar 

  42. MacAlpine HK, Gordan R, Powell SK, Hartemink AJ, MacAlpine DM. Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading. Genome Res. 2010;20(2):201–11.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  43. Dellino GI, Cittaro D, Piccioni R, Luzi L, Banfi S, Segalla S, et al. Genome-wide mapping of human DNA-replication origins: levels of transcription at ORC1 sites regulate origin selection and replication timing. Genome Res. 2013;23(1):1–11.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  44. Cayrou C, Coulombe P, Vigneron A, Stanojcic S, Ganier O, Peiffer I, et al. Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features. Genome Res. 2011;21(9):1438–49.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  45. Cadoret JC, Meisch F, Hassan-Zadeh V, Luyten I, Guillet C, Duret L, et al. Genome-wide studies highlight indirect links between human replication origins and gene regulation. Proc Natl Acad Sci U S A. 2008;105(41):15837–42.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  46. Martin MM, Ryan M, Kim R, Zakas AL, Fu H, Lin CM, et al. Genome-wide depletion of replication initiation events in highly transcribed regions. Genome Res. 2011;21(11):1822–32.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  47. Cayrou C, Coulombe P, Puy A, Rialle S, Kaplan N, Segal E, et al. New insights into replication origin characteristics in metazoans. Cell Cycle. 2012;11(4):658–67.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  48. Besnard E, Babled A, Lapasset L, Milhavet O, Parrinello H, Dantec C, et al. Unraveling cell type-specific and reprogrammable human replication origin signatures associated with G-quadruplex consensus motifs. Nat Struct Mol Biol. 2012;19(8):837–44.

    Article  PubMed  CAS  Google Scholar 

  49. Bochman ML, Paeschke K, Zakian VA. DNA secondary structures: stability and function of G-quadruplex structures. Nat Rev Genet. 2012;13(11):770–80.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  50. Lam EY, Beraldi D, Tannahill D, Balasubramanian S. G-quadruplex structures are stable and detectable in human genomic DNA. Nat Commun. 2013;4:1796.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  51. Hoshina S, Yura K, Teranishi H, Kiyasu N, Tominaga A, Kadoma H, et al. Human origin recognition complex binds preferentially to G-quadruplex-preferable RNA and single-stranded DNA. J Biol Chem. 2013;288(42):30161–71.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  52. Epner E, Forrester WC, Groudine M. Asynchronous DNA replication within the human beta-globin gene locus. Proc Natl Acad Sci U S A. 1988;85(21):8081–5.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  53. Luger K, Mäder AW, Richmond RK, Sargent DF, Richmond TJ. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature. 1997;389(6648):251–60.

    Article  PubMed  CAS  Google Scholar 

  54. Thoma F, Bergman LW, Simpson RT. Nuclease digestion of circular TRP1ARS1 chromatin reveals positioned nucleosomes separated by nuclease-sensitive regions. J Mol Biol. 1984;177(4):715–33.

    Article  PubMed  CAS  Google Scholar 

  55. Simpson RT. Nucleosome positioning can affect the function of a cis-acting DNA element in vivo. Nature. 1990;343(6256):387–9.

    Article  PubMed  CAS  Google Scholar 

  56. Mavrich TN, Jiang C, Ioshikhes IP, Li X, Venters BJ, Zanton SJ, et al. Nucleosome organization in the Drosophila genome. Nature. 2008;453(7193):358–62.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  57. Jiang C, Pugh BF. A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome. Genome Biol. 2009;10(10):R109.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  58. Gaffney DJ, McVicker G, Pai AA, Fondufe-Mittendorf YN, Lewellen N, Michelini K, et al. Controls of nucleosome positioning in the human genome. PLoS Genet. 2012;8(11):e1003036.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  59. Mavrich TN, Ioshikhes IP, Venters BJ, Jiang C, Tomsho LP, Qi J, et al. A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res. 2008;18(7):1073–83.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  60. Shivaswamy S, Bhinge A, Zhao Y, Jones S, Hirst M, Iyer VR. Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation. PLoS Biol. 2008;6(3):e65.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  61. Berbenetz NM, Nislow C, Brown GW. Diversity of eukaryotic DNA replication origins revealed by genome-wide analysis of chromatin structure. PLoS Genet. 2010;6(9):e1001092.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  62. Eaton ML, Galani K, Kang S, Bell SP, MacAlpine DM. Conserved nucleosome positioning defines replication origins. Genes Dev. 2010;24(8):748–53.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  63. Lubelsky Y, Sasaki T, Kuipers MA, Lucas I, Le Beau MM, Carignon S, et al. Pre-replication complex proteins assemble at regions of low nucleosome occupancy within the Chinese hamster dihydrofolate reductase initiation zone. Nucleic Acids Res. 2011;39(8):3141–55.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  64. Xu J, Yanagisawa Y, Tsankov AM, Hart C, Aoki K, Kommajosyula N, et al. Genome-wide identification and characterization of replication origins by deep sequencing. Genome Biol. 2012;13(4):R27.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  65. Lipford JR, Bell SP. Nucleosomes positioned by ORC facilitate the initiation of DNA replication. Mol Cell. 2001;7(1):21–30.

    Article  PubMed  CAS  Google Scholar 

  66. Belsky JA, MacAlpine HK, Lubelsky Y, Hartemink AJ, MacAlpine DM. Genome-wide chromatin footprinting reveals changes in replication origin architecture induced by pre-RC assembly. Genes Dev. 2015;29(2):212–24.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  67. Groth A, Corpet A, Cook AJL, Roche D, Bartek J, Lukas J, et al. Regulation of replication fork progression through histone supply and demand. Science. 2007;318(5858):1928–31.

    Article  PubMed  CAS  Google Scholar 

  68. Müller P, Park S, Shor E, Huebert DJ, Warren CL, Ansari AZ, et al. The conserved bromo-adjacent homology domain of yeast Orc1 functions in the selection of DNA replication origins within chromatin. Genes Dev. 2010;24(13):1418–33.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  69. Deal RB, Henikoff JG, Henikoff S. Genome-wide kinetics of nucleosome turnover determined by metabolic labeling of histones. Science. 2010;328(5982):1161–4.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  70. Ahmad K, Henikoff S. The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly. Mol Cell. 2002;9(6):1191–200.

    Article  PubMed  CAS  Google Scholar 

  71. Eaton ML, Prinz JA, MacAlpine HK, Tretyakov G, Kharchenko PV, MacAlpine DM. Chromatin signatures of the Drosophila replication program. Genome Res. 2011;21(2):164–74.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  72. Euskirchen GM, Auerbach RK, Davidov E, Gianoulis TA, Zhong G, Rozowsky J, et al. Diverse roles and interactions of the SWI/SNF chromatin remodeling complex revealed using global approaches. PLoS Genet. 2011;7(3):e1002008.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  73. Sugimoto N, Yugawa T, Iizuka M, Kiyono T, Fujita M. Chromatin remodeler sucrose nonfermenting 2 homolog (SNF2H) is recruited onto DNA replication origins through interaction with Cdc10 protein-dependent transcript 1 (Cdt1) and promotes pre-replication complex formation. J Biol Chem. 2011;286(45):39200–10.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  74. Kouzarides T. Chromatin modifications and their function. Cell. 2007;128(4):693–705.

    Article  PubMed  CAS  Google Scholar 

  75. Jenuwein T, Allis CD. Translating the histone code. Science. 2001;293(5532):1074–80.

    Article  PubMed  CAS  Google Scholar 

  76. Hsu TC, Schmid W, Stubblefield E. DNA replication sequences in higher animals. In: Locke M, editor. The role of chromosomes in development. New York: Academic; 1964. p. 83–112.

    Chapter  Google Scholar 

  77. Lyon MF. Chromosomal and subchromosomal inactivation. Annu Rev Genet. 1968;2(1):31–52.

    Article  Google Scholar 

  78. Stambrook PJ, Flickinger RA. Changes i chromosomal DNA replication tterns in developing frog embryos. J Exp Zool. 1970;174(1):101–13.

    Article  PubMed  CAS  Google Scholar 

  79. ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, et al. Identification and analysis of functional elements in 1 % of the human genome by the ENCODE pilot project. Nature. 2007;447(7146):799–816.

    Article  CAS  Google Scholar 

  80. The modENCODE Consortium, Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science. 2010;330(6012):1787–97.

    Google Scholar 

  81. Kuo AJ, Song J, Cheung P, Ishibe-Murakami S, Yamazoe S, Chen JK, et al. The BAH domain of ORC1 links H4K20me2 to DNA replication licensing and Meier-Gorlin syndrome. Nature. 2012;484(7392):115–9.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  82. Schotta G, Sengupta R, Kubicek S, Malin S, Kauer M, Callén E, et al. A chromatin-wide transition to H4K20 monomethylation impairs genome integrity and programmed DNA rearrangements in the mouse. Genes Dev. 2008;22(15):2048–61.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  83. Bicknell LS, Bongers EMHF, Leitch A, Brown S, Schoots J, Harley ME, et al. Mutations in the pre-replication complex cause Meier-Gorlin syndrome. Nat Genet. 2011;43(4):356–59.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  84. Bicknell LS, Walker S, Klingseisen A, Stiff T, Leitch A, Kerzendorfer C, et al. Mutations in ORC1, encoding the largest subunit of the origin recognition complex, cause microcephalic primordial dwarfism resembling Meier-Gorlin syndrome. Nat Genet. 2011;43(4):350–55.

    Article  PubMed  CAS  Google Scholar 

  85. Fang J, Feng Q, Ketel CS, Wang H, Cao R, Xia L, et al. Purification and functional characterization of SET8, a nucleosomal histone H4-lysine 20-specific methyltransferase. Curr Biol. 2002;12(13):1086–99.

    Article  PubMed  CAS  Google Scholar 

  86. Nishioka K, Rice JC, Sarma K, Erdjument-Bromage H, Werner J, Wang Y, et al. PR-Set7 is a nucleosome-specific methyltransferase that modifies lysine 20 of histone H4 and is associated with silent chromatin. Mol Cell. 2002;9(6):1201–13.

    Article  PubMed  CAS  Google Scholar 

  87. Abbas T, Shibata E, Park J, Jha S, Karnani N, Dutta A. CRL4(Cdt2) regulates cell proliferation and histone gene expression by targeting PR-Set7/Set8 for degradation. Mol Cell. 2010;40(1):9–21.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  88. Centore RC, Havens CG, Manning AL, Li JM, Flynn RL, Tse A, et al. CRL4(Cdt2)-mediated destruction of the histone methyltransferase Set8 prevents premature chromatin compaction in S phase. Mol Cell. 2010;40(1):22–33.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  89. Oda H, Hübner MR, Beck DB, Vermeulen M, Hurwitz J, Spector DL, et al. Regulation of the histone H4 monomethylase PR-Set7 by CRL4(Cdt2)-mediated PCNA-dependent degradation during DNA damage. Mol Cell. 2010;40(3):364–76.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  90. Jørgensen S, Elvers I, Trelle MB, Menzel T, Eskildsen M, Jensen ON, et al. The histone methyltransferase SET8 is required for S-phase progression. J Cell Biol. 2007;179(7):1337–45.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  91. Houston SI, McManus KJ, Adams MM, Sims JK, Carpenter PB, Hendzel MJ, et al. Catalytic function of the PR-Set7 histone H4 lysine 20 monomethyltransferase is essential for mitotic entry and genomic stability. J Biol Chem. 2008;283(28):19478–88.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  92. Oda H, Okamoto I, Murphy N, Chu J, Price SM, Shen MM, et al. Monomethylation of histone H4-Lysine 20 is involved in chromosome structure and stability and is essential for mouse development. Mol Cell Biol. 2009;29(8):2278–95.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  93. Tardat M, Brustel J, Kirsh O, Lefevbre C, Callanan M, Sardet C, et al. The histone H4 Lys 20 methyltransferase PR-Set7 regulates replication origins in mammalian cells. Nat Cell Biol. 2010;12(11):1086–93.

    Article  PubMed  CAS  Google Scholar 

  94. Beck DB, Burton A, Oda H, Ziegler-Birling C, Torres-Padilla ME, Reinberg D. The role of PR-Set7 in replication licensing depends on Suv4-20h. Genes Dev. 2012;26(23):2580–89.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  95. Sakaguchi A, Karachentsev D, Seth-Pasricha M, Druzhinina M, Steward R. Functional characterization of the Drosophila Hmt4-20/Suv4-20 histone methyltransferase. Genetics. 2008;179(1):317–22.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  96. Doyon Y, Cayrou C, Ullah M, Landry AJ, Côté V, Selleck W, et al. ING tumor suppressor proteins are critical regulators of chromatin acetylation required for genome expression and perpetuation. Mol Cell. 2006;21(1):51–64.

    Article  PubMed  CAS  Google Scholar 

  97. Iizuka M, Stillman B. Histone acetyltransferase HBO1 interacts with the ORC1 subunit of the human initiator protein. J Biol Chem. 1999;274(33):23027–34.

    Article  PubMed  CAS  Google Scholar 

  98. Burke TW, Cook JG, Asano M, Nevins JR. Replication factors MCM2 and ORC1 interact with the histone acetyltransferase HBO1. J Biol Chem. 2001;276(18):15397–408.

    Article  PubMed  CAS  Google Scholar 

  99. Iizuka M, Matsui T, Takisawa H, Smith MM. Regulation of replication licensing by Acetyltransferase Hbo1. Mol Cell Biol. 2006;26(3):1098–108.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  100. Miotto B, Struhl K. HBO1 histone acetylase is a coactivator of the replication licensing factor Cdt1. Genes Dev. 2008;22(19):2633–38.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  101. Chen X, Liu G, Leffak M. Activation of a human chromosomal replication origin by protein tethering. Nucleic Acids Res. 2013;41(13):6460–74.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  102. Pryde F, Jain D, Kerr A, Curley R, Mariotti FR, Vogelauer M. H3 k36 methylation helps determine the timing of cdc45 association with replication origins. PLoS One. 2009;4(6):e5882.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  103. Rizzardi LF, Dorn ES, Strahl BD, Cook JG. DNA replication origin function is promoted by H3K4 di-methylation in Saccharomyces cerevisiae. Genetics. 2012;192(2):371–84.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  104. Trujillo KM, Osley MA. A role for H2B ubiquitylation in DNA replication. Mol Cell. 2012;48(5):734–46.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  105. Fu H, Maunakea AK, Martin MM, Huang L, Zhang Y, Ryan M, et al. Methylation of histone H3 on lysine 79 associates with a group of replication origins and helps limit DNA replication once per cell cycle. PLoS Genet. 2013;9(6):e1003542.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  106. Jacob Y, Stroud H, Leblanc C, Feng S, Zhuo L, Caro E, et al. Regulation of heterochromatic DNA replication by histone H3 lysine 27 methyltransferases. Nature. 2010;466(7309):987–91.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  107. Straub T, Becker PB. Dosage compensation: the beginning and end of generalization. Nat Rev Genet. 2007;8(1):47–57.

    Article  PubMed  CAS  Google Scholar 

  108. Berendes HD. Differential replication of male and female X-chromosomes in Drosophila. Chromosoma. 1966;20(1):32–43. doi:10.1007/BF00331896

    Article  Google Scholar 

  109. Schwaiger M, Stadler MB, Bell O, Kohler H, Oakeley EJ, Schübeler D. Chromatin state marks cell-type- and gender-specific replication of the Drosophila genome. Genes Dev. 2009;23(5):589–601.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  110. Lubelsky Y, Prinz JA, DeNapoli L, Li Y, Belsky JA, MacAlpine DM. DNA replication and transcription programs respond to the same chromatin cues. Genome Res. 2014;24(7):1102–14.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  111. Aparicio JG, Viggiani CJ, Gibson DG, Aparicio OM. The Rpd3-Sin3 histone deacetylase regulates replication timing and enables intra-S origin control in Saccharomyces cerevisiae. Mol Cell Biol. 2004;24(11):4769–80.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  112. Knott SRV, Viggiani CJ, Tavaré S, Aparicio OM. Genome-wide replication profiles indicate an expansive role for Rpd3L in regulating replication initiation timing or efficiency, and reveal genomic loci of Rpd3 function in Saccharomyces cerevisiae. Genes Dev. 2009;23(9):1077–90.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  113. Crampton A, Chang F, Pappas J Donald L, Frisch RL, Weinreich M. An ARS element inhibits DNA replication through a SIR2-dependent mechanism. Mol Cell. 2008;30(2):156–66.

    Article  PubMed  CAS  Google Scholar 

  114. Yoshida K, Bacal J, Desmarais D, Padioleau I, Tsaponina O, Chabes A, et al. The histone deacetylases sir2 and rpd3 act on ribosomal DNA to control the replication program in budding yeast. Mol Cell. 2014;54(4):691–97.

    Article  PubMed  CAS  Google Scholar 

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Acknowledgements

We thank members of the MacAlpine laboratory for critical comments and suggestions. This work is supported by the National Institute Of General Medical Sciences of the National Institutes of Health under Award Number R01-GM104079 to D.M.M and F31-GM115158 to M.P.G.

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Authors and Affiliations

  1. University Program in Genetics and Genomics, Duke University Medical Center, Durham, NC, USA

    Mónica P. Gutiérrez

  2. Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA

    David M. MacAlpine

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  1. Mónica P. Gutiérrez
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  2. David M. MacAlpine
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Correspondence to David M. MacAlpine .

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  1. Florida State Univ. College of Medi, TALLAHASSEE, Florida, USA

    Daniel L. Kaplan

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Gutiérrez, M.P., MacAlpine, D.M. (2016). Chromatin Determinants of Origin Selection and Activation. In: Kaplan, D. (eds) The Initiation of DNA Replication in Eukaryotes. Springer, Cham. https://doi.org/10.1007/978-3-319-24696-3_5

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