Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading

Genome Research

Volumn 20, Issue 2, 2010, Pages 201-211

  MacAlpine, Heather K ^a   Gordân, Raluca ^b   Powell, Sara K ^a   Hartemink, Alexander J ^b   MacAlpine, David M ^a  

^a DUKE UNIVERSITY MEDICAL CENTER   (United States)

^b Duke University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COHESIN; HISTONE H3; ORIGIN RECOGNITION COMPLEX;

ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; BINDING SITE; CHROMATIN; CHROMOSOMAL LOCALIZATION; CHROMOSOME; COMPLEX FORMATION; CONTROLLED STUDY; DNA REPLICATION; DROSOPHILA; MACHINE LEARNING; NONHUMAN; NUCLEOSOME; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN LOCALIZATION; PROTEIN MOTIF; SEQUENCE ANALYSIS; TRANSCRIPTION INITIATION SITE;

ANIMALS; CELL CYCLE PROTEINS; CELL LINE; CHROMATIN; CHROMOSOMAL PROTEINS, NON-HISTONE; DROSOPHILA MELANOGASTER; DROSOPHILA PROTEINS; ORIGIN RECOGNITION COMPLEX; PROMOTER REGIONS, GENETIC; SEQUENCE ANALYSIS, DNA;

EUKARYOTA; SACCHAROMYCES CEREVISIAE;

EID: 75649109712     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.097873.109     Document Type: Article

References (69)

1. Aggarwal BD, Calvi BR. 2004. Chromatin regulates origin activity in Drosophila follicle cells. Nature 430: 372-376.
2. Ahmad K, Henikoff S. 2002. The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly. Mol Cell 9: 1191-1200.
3. Aladjem MI, Fanning E. 2004. The replicon revisited: An old model learns new tricks in metazoan chromosomes. EMBO Rep 5: 686-691.
4. Austin R, Orr-Weaver T, Bell S. 1999. Drosophila ORC specifically binds to ACE3, an origin of DNA replication control element. Genes & Dev 13: 2639-2649.
5. Balasov M, Huijbregts RP, Chesnokov I. 2007. Role of the Orc6 protein in origin recognition complex-dependent DNA binding and replication in Drosophila melanogaster. Mol Cell Biol 27: 3143-3153.
6. Bartkuhn M, Straub T, Herold M, Herrmann M, Rathke C, Saumweber H, Gilfillan GD, Becker PB, Renkawitz R. 2009. Active promoters and insulators are marked by the centrosomal protein 190. EMBO J 28: 877-888.
7. Beall E, Manak J, Zhou S, Bell M, Lipsick J, Botchan M. 2002. Role for a Drosophila Myb-containing protein complex in site-specific DNA replication. Nature 420: 833-837.
8. Bell S, Dutta A. 2002. DNA replication in eukaryotic cells. Annu Rev Biochem 71: 333-374.
9. Bell S, Kobayashi R, Stillman B. 1993. Yeast origin recognition complex functions in transcription silencing and DNA replication. Science 262: 1844-1849.
10. Bosco G, Du W, Orr-Weaver T. 2001. DNA replication control through interaction of E2F-RB and the origin recognition complex. Nat Cell Biol 3: 289-295.
11. Cadoret JC, Meisch F, Hassan-Zadeh V, Luyten I, Guillet C, Duret L, Quesneville H, Prioleau MN. 2008. Genome-wide studies highlight indirect links between human replication origins and gene regulation. Proc Natl Acad Sci 105: 15837-15842.
12. Celniker SE, Dillon LA, Gerstein MB, Gunsalus KC, Henikoff S, Karpen GH, Kellis M, Lai EC, Lieb JD, MacAlpine DM, et al. 2009. Unlocking the secrets of the genome. Nature 459: 927-930.
13. Core LJ, Waterfall JJ, Lis JT. 2008. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322: 1845-1848.
14. Cvetic C,Walter JC. 2005. Eukaryotic origins of DNA replication: Could you please be more specific? Semin Cell Dev Biol 16: 343-353.
15. Danis E, Brodolin K, Menut S, Maiorano D, Girard-Reydet C, Mechali M. 2004. Specification of a DNA replication origin by a transcription complex. Nat Cell Biol 6: 721-730.
16. Dillin A, Rine J. 1998. Roles for ORC in M phase and S phase. Science 279: 1733-1737.
17. Dion MF, Kaplan T, Kim M, Buratowski S, Friedman N, Rando OJ. 2007. Dynamics of replication-independent histone turnover in budding yeast. Science 315: 1405-1408.
18. Dominguez-Sola D, Ying CY, Grandori C, Ruggiero L, Chen B, Li M, Galloway DA, Gu W, Gautier J, Dalla-Favera R, et al. 2007. Nontranscriptional control of DNA replication by c-Myc. Nature 448: 445-451.
19. Foss M, McNally F, Laurenson P, Rine J. 1993. Origin recognition complex (ORC) in transcriptional silencing and DNA replication in S. cerevisiae. Science 262: 1838-1844.
20. Gillespie PJ, Hirano T. 2004. Scc2 couples replication licensing to sister chromatid cohesion in Xenopus egg extracts. Curr Biol 14: 1598-1603.
21. Glynn EF, Megee PC, Yu HG, Mistrot C, Unal E, Koshland DE, DeRisi JL, Gerton JL. 2004. Genome-wide mapping of the cohesin complex in the yeast Saccharomyces cerevisiae. PLoS Biol 2: e259. doi: 10.1371/ journal.pbio.0020259.
22. Goren A, Tabib A, Hecht M, Cedar H. 2008. DNA replication timing of the human beta-globin domain is controlled by histone modification at the origin. Genes & Dev 22: 1319-1324.
23. Henikoff S, Henikoff JG, Sakai A, Loeb GB, Ahmad K. 2009. Genomewide profiling of salt fractions maps physical properties of chromatin. Genome Res 19: 460-469.
24. Hiratani I, Ryba T, Itoh M, Yokochi T, Schwaiger M, Chang CW, Lyou Y, Townes TM, Schubeler D, Gilbert DM, et al. 2008. Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol 6: e245. doi: 10.1371/journal.pbio.0060245.
25. Huang DW, Fanti L, Pak DT, Botchan MR, Pimpinelli S, Kellum R. 1998. Distinct cytoplasmic and nuclear fractions of Drosophila heterochromatin protein 1: Their phosphorylation levels and associations with origin recognition complex proteins. J Cell Biol 142: 307-318.
26. Hyrien O, Maric C, Mechali M. 1995. Transition in specification of embryonic metazoan DNA replication origins. Science 270: 994-997.
27. Iyer V, Struhl K. 1995. Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure. EMBO J 14: 2570-2579.
28. Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, Field Y, LeProust EM, Hughes TR, Lieb JD, Widom J, et al. 2009. The DNA-encoded nucleosome organization of a eukaryotic genome. Nature 458: 362-366.
29. Karnani N, Taylor C, Malhotra A, Dutta A. 2007. Pan-S replication patterns and chromosomal domains defined by genome-tiling arrays of ENCODE genomic areas. Genome Res 17: 865-876.
30. Knott SR, Viggiani CJ, Tavare S, Aparicio OM. 2009. 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 23: 1077-1090.
31. Kriegstein H, Hogness D. 1974. Mechanism of DNA replication in Drosophila chromosomes: Structure of replication forks and evidence for bidirectionality. Proc Natl Acad Sci 71: 135-139.
32. Kunst F, Ogasawara N, Moszer I, Albertini AM, Alloni G, Azevedo V, Bertero MG, Bessieres P, Bolotin A, Borchert S, et al. 1997. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 390: 249-256.
33. Lengronne A, Katou Y, Mori S, Yokobayashi S, Kelly GP, Itoh T,Watanabe Y, Shirahige K, Uhlmann F. 2004. Cohesin relocation from sites of chromosomal loading to places of convergent transcription. Nature 430: 573-578.
34. Lucas I, Palakodeti A, Jiang Y, Young DJ, Jiang N, Fernald AA, Le Beau MM. 2007. High-throughput mapping of origins of replication in human cells. EMBO Rep 8: 770-777.
35. MacAlpine D, Rodriguez H, Bell S. 2004. Coordination of replication and transcription along a Drosophila chromosome. Genes&Dev 18: 3094-3105.
36. Maiorano D, Moreau J, Mechali M. 2000. XCDT1 is required for the assembly of pre-replicative complexes in Xenopus laevis. Nature 404: 622-625.
37. Misulovin Z, Schwartz YB, Li XY, Kahn TG, Gause M, MacArthur S, Fay JC, Eisen MB, Pirrotta V, Biggin MD, et al. 2008. Association of cohesin and Nipped-B with transcriptionally active regions of the Drosophila melanogaster genome. Chromosoma 117: 89-102.
38. Mito Y, Henikoff JG, Henikoff S. 2007. Histone replacement marks the boundaries of cis-regulatory domains. Science 315: 1408-1411.
39. Narlikar L, Gordan R, Hartemink A. 2007. A nucleosome-guided map of a transcription factor binding sites in yeast. PLoS Comput Biol 3: e215. doi: 10.1371/journal.pcbi.0030215.
40. Nasmyth K. 2002. Segregating sister genomes: The molecular biology of chromosome separation. Science 297: 559-565.
41. Norio P, Kosiyatrakul S, Yang Q, Guan Z, Brown NM, Thomas S, Riblet R, Schildkraut CL. 2005. Progressive activation of DNA replication initiation in large domains of the immunoglobulin heavy chain locus during B cell development. Mol Cell 20: 575-587.
42. Ozsolak F, Song J, Liu X, Fisher D. 2007. High-throughput mapping of the chromatin structure of human promoters. Nat Biotechnol 25: 244-248.
43. Pak DT, PflummM, Chesnokov I, HuangDW, Kellum R, Marr J, Romanowski P, Botchan MR. 1997. Association of the origin recognition complex with heterochromatin and HP1 in higher eukaryotes. Cell 91: 311-323.
44. Parelho V, Hadjur S, Spivakov M, Leleu M, Sauer S, Gregson HC, Jarmuz A, Canzonetta C,Webster Z, Nesterova T, et al. 2008. Cohesins functionally associate with CTCF on mammalian chromosome arms. Cell 132: 422-433.
45. Rando OJ, Chang HY. 2009. Genome-wide views of chromatin structure. Annu Rev Biochem 78: 245-271.
46. Remus D, Beall E, Botchan M. 2004. DNA topology, not DNA sequence, is a critical determinant for Drosophila ORC-DNA binding. EMBO J 23: 897-907.
47. Royzman I, Austin R, Bosco G, Bell S, Orr-Weaver T. 1999. ORC localization in Drosophila follicle cells and the effects of mutations in dE2F and dDP. Genes & Dev 13: 827-840.
48. Rusche LN, Kirchmaier AL, Rine J. 2003. The establishment, inheritance, and function of silenced chromatin in Saccharomyces cerevisiae. Annu Rev Biochem 72: 481-516.
49. Saha S, Shan Y, Mesner L, Hamlin J. 2004. The promoter of the Chinese hamster ovary dihydrofolate reductase gene regulates the activity of the local origin and helps define its boundaries. Genes & Dev 18: 397-410.
50. Santocanale C, Diffley JF. 1998. A Mec1- and Rad53-dependent checkpoint controls late-firing origins of DNA replication. Nature 395: 615-618.
51. Schübeler D, Scalzo D, Kooperberg C, van Steensel B, Delrow J, Groudine M. 2002. Genome-wide DNA replication profile for Drosophila melanogaster: A link between transcription and replication timing. Nat Genet 32: 438-442.
52. Schwaiger M, Stadler MB, Bell O, Kohler H, Oakeley EJ, Schubeler D. 2009. Chromatin state marks cell-type- and gender-specific replication of the Drosophila genome. Genes & Dev 23: 589-601.
53. Seila AC, Calabrese JM, Levine SS, Yeo GW, Rahl PB, Flynn RA, Young RA, Sharp PA. 2008. Divergent transcription from active promoters. Science 322: 1849-1851.
54. Sequeira-Mendes J, Diaz-Uriarte R, Apedaile A, Huntley D, Brockdorff N, Gomez M. 2009. Transcription initiation activity sets replication origin efficiency in mammalian cells. PLoS Genet 5: e1000446. doi: 10.1371/ journal.pgen.1000446.
55. Shimada K, Gasser SM. 2007. The origin recognition complex functions in sister-chromatid cohesion in Saccharomyces cerevisiae. Cell 128: 85-99.
56. Shirahige K, Hori Y, Shiraishi K, Yamashita M, Takahashi K, Obuse C, Tsurimoto T, Yoshikawa H. 1998. Regulation of DNA-replication origins during cell-cycle progression. Nature 395: 618-621.
57. Song JS, Johnson WE, Zhu X, Zhang X, LiW, Manrai AK, Liu JS, Chen R, Liu XS. 2007. Model-based analysis of two-color arrays (MA2C). Genome Biol 8: R178. doi: 10.1186/gb-2007-8-8-r178.
58. Stamatoyannopoulos JA, Adzhubei I, Thurman RE, Kryukov GV, Mirkin SM, Sunyaev SR. 2009. Human mutation rate associated with DNA replication timing. Nat Genet 41: 393-395.
59. Suter B, Schnappauf G, Thoma F. 2000. Poly(dA·dT) sequences exist as rigid DNA structures in nucleosome-free yeast promoters in vivo. Nucleic Acids Res 28: 4083-4089.
60. Takahashi TS, Yiu P, Chou MF, Gygi S, Walter JC. 2004. Recruitment of Xenopus Scc2 and cohesin to chromatin requires the pre-replication complex. Nat Cell Biol 6: 991-996.
61. Takahashi TS, Basu A, Bermudez V, Hurwitz J, Walter JC. 2008. Cdc7/Drf1 kinase links chromosome cohesion to the initiation of DNA replication in Xenopus egg extracts. Genes & Dev 22: 1894-1905.
62. Tower J. 2004. Developmental gene amplification and origin regulation. Annu Rev Genet 38: 273-304.
63. Uhlmann F, Nasmyth K. 1998. Cohesion between sister chromatids must be established during DNA replication. Curr Biol 8: 1095-1101.
64. van Daal A, Elgin SC. 1992. A histone variant, H2AvD, is essential in Drosophila melanogaster. Mol Biol Cell 3: 593-602.
65. Vashee S, Cvetic C, Lu W, Simancek P, Kelly T, Walter J. 2003. Sequence independent DNA binding and replication initiation by the human origin recognition complex. Genes & Dev 17: 1894-1908.
66. Vogelauer M, Rubbi L, Lucas I, Brewer B, Grunstein M. 2002. Histone acetylation regulates the time of replication origin firing. Mol Cell 10: 1223-1233.
67. Wendt KS, Yoshida K, Itoh T, Bando M, Koch B, Schirghuber E, Tsutsumi S, Nagae G, Ishihara K, Mishiro T, et al. 2008. Cohesin mediates transcriptional insulation by CCCTC-binding factor. Nature 451: 796-801.
68. Wohlschlegel JA, Dwyer BT, Dhar SK, Cvetic C, Walter JC, Dutta A. 2000. Inhibition of eukaryotic DNA replication by geminin binding to Cdt1. Science 290: 2309-2312.
69. Wysocka J, Reilly PT, Herr W. 2001. Loss of HCF-1-chromatin association precedes temperature-induced growth arrest of tsBN67 cells. Mol Cell Biol 21: 3820-3829.