Integrative analysis of gene amplification in drosophila follicle cells: Parameters of origin activation and repression

Genes and Development

Volumn 25, Issue 13, 2011, Pages 1384-1398

  Kim, Jane C ^a,b   Nordman, Jared ^a   Xie, Fang ^a,b   Kashevsky, Helena ^a   Eng, Thomas ^a   Li, Sharon ^a   MacAlpine, David M ^c   Orr Weaver, Terry L ^a,b  

^a WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^c DUKE UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

Chorion; DNA replication; H4 acetylation; Oogenesis; ORC; Transcription

Indexed keywords

ORIGIN RECOGNITION COMPLEX;

AMPLICON; ARTICLE; CELL; COMPARATIVE GENOMIC HYBRIDIZATION; DNA REPLICATION ORIGIN; DROSOPHILA AMPLICON FOLLICLE CELL; GENE ACTIVATION; GENE AMPLIFICATION; GENE EXPRESSION; GENE LOCATION; GENE REPRESSION; GENETIC TRANSCRIPTION; HISTONE ACETYLATION; IN VIVO CULTURE; NONHUMAN; PRIORITY JOURNAL;

ACETYLATION; ANIMALS; DROSOPHILA MELANOGASTER; GENE AMPLIFICATION; GENE EXPRESSION REGULATION; HISTONES; ORIGIN RECOGNITION COMPLEX; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY;

METAZOA;

EID: 79959936930     PISSN: 08909369     EISSN: 15495477     Source Type: Journal    
DOI: 10.1101/gad.2043111     Document Type: Article

References (44)

1. Aggarwal BD, Calvi BR. 2004. Chromatin regulates origin activity in Drosophila follicle cells. Nature 430: 372-376.
2. Aladjem MI. 2007. Replication in context: dynamic regulation of DNA replication patterns in metazoans. Nat Rev Genet 8: 588-600.
3. Austin RJ, Orr-Weaver TL, Bell SP. 1999. Drosophila ORC specifically binds to ACE3, an origin of DNA replication control element. Genes Dev 13: 2639-2649.
4. Bryant Z, Subrahmanyan L, Tworoger M, LaTray L, Liu CR, Li MJ, van den Engh G, Ruohola-Baker H. 1999. Characterization of differentially expressed genes in purified Drosophila follicle cells: toward a general strategy for cell type-specific developmental analysis. Proc Natl Acad Sci 96: 5559-5564.
5. 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.
6. Cayirlioglu P, Ward WO, Silver Key SC, Duronio RJ. 2003. Transcriptional repressor functions of Drosophila E2F1 and E2F2 cooperate to inhibit genomic DNA synthesis in ovarian follicle cells. Mol Cell Biol 23: 2123-2134.
7. Chintapalli VR, Wang J, Dow JA. 2007. Using FlyAtlas to identify better Drosophila models of human disease. Nat Genet 39: 715-720.
8. Claycomb JM, Orr-Weaver TL. 2005. Developmental gene amplification: insights into DNA replication and gene expression. Trends Genet 21: 149-162.
9. Claycomb JM, Benasutti M, Bosco G, Fenger DD, Orr-Weaver TL. 2004. Gene amplification as a developmental strategy: isolation of two developmental amplicons in Drosophila. Dev Cell 6: 145-155.
10. Cvetic C, Walter JC. 2005. Eukaryotic origins of DNA replication: could you please be more specific? Semin Cell Dev Biol 16: 343-353.
11. 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.
12. Eaton ML, Galani K, Kang S, Bell SP, MacAlpine DM. 2010. Conserved nucleosome positioning defines replication origins. Genes Dev 24: 748-753.
13. Gilbert DM. 2004. In search of the holy replicator. Nat Rev Mol Cell Biol 5: 848-855.
14. Gilbert DM. 2010. Evaluating genome-scale approaches to eukaryotic DNA replication. Nat Rev Genet 11: 673-684.
15. Griffin-Shea R, Thireos G, Kafatos FC. 1982. Organization of a cluster of four chorion genes in Drosophila and its relationship to developmental expression and amplification. Dev Biol 91: 325-336.
16. Hamlin JL, Mesner LD, Dijkwel PA. 2010. A winding road to origin discovery. Chromosome Res 18: 45-61.
17. Hansen RS, Thomas S, Sandstrom R, Canfield TK, Thurman RE, Weaver M, Dorschner MO, Gartler SM, Stamatoyannopoulos JA. 2010. Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc Natl Acad Sci 107: 139-144.
18. Hartl T, Boswell C, Orr-Weaver TL, Bosco G. 2007. Developmentally regulated histone modifications in Drosophila follicle cells: initiation of gene amplification is associated with histone H3 and H4 hyperacetylation and H1 phosphorylation. Chromosoma 116: 197-214.
19. 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.
20. Karnani N, Taylor CM, Malhotra A, Dutta A. 2010. Genomic study of replication initiation in human chromosomes reveals the influence of transcription regulation and chromatin structure on origin selection. Mol Biol Cell 21: 393-404.
21. Landis G, Tower J. 1999. The Drosophila chiffon gene is required for chorion gene amplification, and is related to the yeast Dbf4 regulator of DNA replication and cell cycle. Development 126: 4281-4293.
22. Landis G, Kelley R, Spradling AC, Tower J. 1997. The k43 gene, required for chorion gene amplification and diploid cell chromosome replication, encodes the Drosophila homolog of yeast origin recognition complex subunit 2. Proc Natl Acad Sci 94: 3888-3892.
23. Lilly MA, Spradling AC. 1996. The Drosophila endocycle is controlled by Cyclin E and lacks a checkpoint ensuring S-phase completion. Genes Dev 10: 2514-2526.
24. Lu L, Tower J. 1997. A transcriptional insulator element, the su(Hw) binding site, protects a chromosomal DNA replication origin from position effects. Mol Cell Biol 17: 2202-2206.
25. Lu L, Zhang H, Tower J. 2001. Functionally distinct, sequencespecific replicator and origin elements are required for Drosophila chorion gene amplification. Genes Dev 15: 134-146.
26. MacAlpine DM, Rodriguez HK, Bell SP. 2004. Coordination of replication and transcription along a Drosophila chromosome. Genes Dev 18: 3094-3105.
27. MacAlpine HK, Gordan R, Powell SK, Hartemink AJ, MacAlpine DM. 2010. Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading. Genome Res 20: 201-211.
28. Mechali M. 2010. Eukaryotic DNA replication origins: many choices for appropriate answers. Nat Rev Mol Cell Biol 11: 728-738.
29. Mesner LD, Hamlin JL. 2005. Specific signals at the 39 end of the DHFR gene define one boundary of the downstream origin of replication. Genes Dev 19: 1053-1066.
30. Mesner LD, Valsakumar V, Karnani N, Dutta A, Hamlin JL, Bekiranov S. 2011. Bubble-chip analysis of human origin distributions demonstrates on a genomic scale significant clustering into zones and significant association with transcription. Genome Res 21: 377-389.
31. Meyerson M, Gabriel S, Getz G. 2010. Advances in understanding cancer genomes through second-generation sequencing. Nat Rev Genet 11: 685-696.
32. Mindrinos MN, Scherer LJ, Garcini FJ, Kwan H, Jacobs KA, Petri WH. 1985. Isolation and chromosomal location of putative vitelline membrane genes in Drosophila melanogaster. EMBO J 4: 147-153.
33. Nordman J, Li S, Eng T, MacAlpine DM, Orr-Weaver TL. 2011. Developmental control of the DNA replication and transcription programs. Genome Res 21: 175-181.
34. Pak DT, Pflumm M, Chesnoov I, Huang DW, 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.
35. Park EA, Macalpine DM, Orr-Weaver TL. 2007. Drosophila follicle cell amplicons as models for metazoan DNA replication: a cyclinE mutant exhibits increased replication fork elongation. Proc Natl Acad Sci 104: 16739-16746.
36. Parks S, Spradling A. 1987. Spatially regulated expression of chorion genes during Drosophila oogenesis. Genes Dev 1: 497-509.
37. Parks S, Wakimoto B, Spradling A. 1986. Replication and expression of an X-linked cluster of Drosophila chorion genes. Dev Biol 117: 294-305.
38. Schwed G, May N, Pechersky Y, Calvi BR. 2002. Drosophila minichromosome maintenance 6 is required for chorion gene amplification and genomic replication. Mol Biol Cell 13: 607-620.
39. 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.
40. Song JS, Johnson WE, Zhu X, Zhang X, Li W, 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.
41. Spradling AC. 1981. The organization and amplification of two chromosomal domains containing Drosophila chorion genes. Cell 27: 193-201.
42. 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.
43. Toedling J, Skylar O, Krueger T, Fischer JJ, Sperling S, Huber W. 2007. Ringo-an R/Bioconductor package for analyzing ChIP- chip readouts. BMC Bioinformatics 8: 221. doi: 10.1186/1471-2105-8-221.
44. Xie F, Orr-Weaver TL. 2008. Isolation of a Drosophila amplification origin developmentally activated by transcription. Proc Natl Acad Sci 105: 9651-9656.