title: Developmental control of gene copy number by repression of replication initiation and fork progression.
abstract: Precise DNA replication is crucial for genome maintenance, yet this process has been inherently difficult to study on a genome-wide level in untransformed differentiated metazoan cells. To determine how metazoan DNA replication can be repressed, we examined regions selectively under-replicated in Drosophila polytene salivary glands, and found they are transcriptionally silent and enriched for the repressive H3K27me3 mark. In the first genome-wide analysis of binding of the origin recognition complex (ORC) in a differentiated metazoan tissue, we find that ORC binding is dramatically reduced within these large domains, suggesting reduced initiation as one mechanism leading to under-replication. Inhibition of replication fork progression by the chromatin protein SUUR is an additional repression mechanism to reduce copy number. Although repressive histone marks are removed when SUUR is mutated and copy number restored, neither transcription nor ORC binding is reinstated. Tethering of the SUUR protein to a specific site is insufficient to block replication, however. These results establish that developmental control of DNA replication, at both the initiation and elongation stages, is a mechanism to change gene copy number during differentiation.
authors.affiliation: Whitehead Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA.
authors.forename: Noa
authors.initials: N
authors.lastname: Sher
authors.forename: George W
authors.initials: GW
authors.lastname: Bell
authors.forename: Sharon
authors.initials: S
authors.lastname: Li
authors.forename: Jared
authors.initials: J
authors.lastname: Nordman
authors.forename: Thomas
authors.initials: T
authors.lastname: Eng
authors.forename: Matthew L
authors.initials: ML
authors.lastname: Eaton
authors.forename: David M
authors.initials: DM
authors.lastname: Macalpine
authors.forename: Terry L
authors.initials: TL
authors.lastname: Orr-Weaver
mesh_terms: D000818:Animals; D002454:Cell Differentiation / Q000502:physiology; D004261:DNA Replication / Q000502:physiology*; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D029721:Drosophila Proteins / Q000235:genetics / Q000378:metabolism*; D004331:Drosophila melanogaster; D018628:Gene Dosage / Q000502:physiology*; D018507:Gene Expression Regulation, Developmental / Q000502:physiology*; D006657:Histones / Q000235:genetics / Q000378:metabolism*; D059007:Polytene Chromosomes / Q000235:genetics / Q000378:metabolism*
chemical_list: D004268:DNA-Binding Proteins; D029721:Drosophila Proteins; D006657:Histones; C464850:SuUR protein, Drosophila
references.citation: Genes Dev. 1999 Oct 15;13(20):2639-49
references.pmid: 10541550
references.citation: Genes Dev. 2011 Jul 1;25(13):1384-98
references.pmid: 21724831
references.citation: Proc Natl Acad Sci U S A. 1997 Apr 15;94(8):3888-92
references.pmid: 9108074
references.citation: J Cell Sci. 2007 Jul 15;120(Pt 14):2344-51
references.pmid: 17606990
references.citation: Genes Dev. 2009 Mar 1;23(5):589-601
references.pmid: 19270159
references.citation: Genome Res. 2011 Mar;21(3):377-89
references.pmid: 21173031
references.citation: Cell. 2001 May 4;105(3):297-306
references.pmid: 11348589
references.citation: Nature. 2004 Jul 15;430(6997):372-6
references.pmid: 15254542
references.citation: Proc Natl Acad Sci U S A. 2008 Aug 26;105(34):12343-8
references.pmid: 18711130
references.citation: Nat Struct Mol Biol. 2010 Jul;17(7):894-900
references.pmid: 20562853
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D876-82
references.pmid: 20959295
references.citation: Genes Dev. 2004 Dec 15;18(24):3094-105
references.pmid: 15601823
references.citation: Proc Natl Acad Sci U S A. 2007 Oct 23;104(43):16739-46
references.pmid: 17940024
references.citation: Cell Cycle. 2009 May 15;8(10):1501-9
references.pmid: 19372757
references.citation: Annu Rev Genet. 1987;21:373-403
references.pmid: 3327470
references.citation: Genes Dev. 2009 Nov 1;23(21):2461-77
references.pmid: 19884253
references.citation: PLoS Biol. 2008 Oct 7;6(10):e245
references.pmid: 18842067
references.citation: Proc Natl Acad Sci U S A. 2008 Oct 14;105(41):15837-42
references.pmid: 18838675
references.citation: Genome Res. 2011 Sep;21(9):1438-49
references.pmid: 21750104
references.citation: Nat Genet. 2002 Nov;32(3):438-42
references.pmid: 12355067
references.citation: BMC Bioinformatics. 2007 Jun 26;8:221
references.pmid: 17594472
references.citation: Mol Cell Biol. 2008 Oct;28(19):5977-85
references.pmid: 18662996
references.citation: Nat Biotechnol. 2008 Dec;26(12):1351-9
references.pmid: 19029915
references.citation: Nat Biotechnol. 2009 Jan;27(1):66-75
references.pmid: 19122651
references.citation: Nucleic Acids Res. 2010 Jan;38(Database issue):D613-9
references.pmid: 19906737
references.citation: Nat Rev Genet. 2007 Jan;8(1):9-22
references.pmid: 17173055
references.citation: Mol Biol Cell. 2010 Feb 1;21(3):393-404
references.pmid: 19955211
references.citation: PLoS Genet. 2009 Apr;5(4):e1000446
references.pmid: 19360092
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D555-9
references.pmid: 18948289
references.citation: Nat Rev Genet. 2010 Oct;11(10):673-84
references.pmid: 20811343
references.citation: Dokl Biochem Biophys. 2009 Jul-Aug;427:175-8
references.pmid: 19817130
references.citation: Genome Res. 2010 Feb;20(2):155-69
references.pmid: 19952138
references.citation: Dev Cell. 2004 Jan;6(1):145-55
references.pmid: 14723854
references.citation: Proc Natl Acad Sci U S A. 1998 Jun 23;95(13):7532-7
references.pmid: 9636184
references.citation: Genome Res. 2011 Feb;21(2):164-74
references.pmid: 21177973
references.citation: Genome Res. 2008 Nov;18(11):1851-8
references.pmid: 18714091
references.citation: Proc Natl Acad Sci U S A. 2005 Jun 7;102(23):8269-74
references.pmid: 15928082
references.citation: Chromosoma. 2003 Mar;111(6):377-98
references.pmid: 12644953
references.citation: Genome Res. 2011 Feb;21(2):175-81
references.pmid: 21177957
references.citation: Genome Biol. 2007;8(8):R178
references.pmid: 17727723
references.citation: Nat Protoc. 2006;1(2):729-48
references.pmid: 17406303
references.citation: Proc Natl Acad Sci U S A. 2008 Jul 15;105(28):9651-6
references.pmid: 18621687
references.citation: J Cell Biol. 2002 Oct 28;159(2):225-36
references.pmid: 12403810
references.citation: EMBO Rep. 2007 Aug;8(8):770-7
references.pmid: 17668008
references.citation: Cell. 2010 Oct 15;143(2):212-24
references.pmid: 20888037
references.citation: Curr Opin Biotechnol. 2008 Feb;19(1):36-40
references.pmid: 18162393
references.citation: Chromosoma. 2008 Oct;117(5):411-8
references.pmid: 18491121
references.citation: Genetics. 2002 Mar;160(3):1023-34
references.pmid: 11901119
references.citation: Genome Res. 2010 Feb;20(2):201-11
references.pmid: 19996087
references.citation: Nat Rev Mol Cell Biol. 2010 Oct;11(10):728-38
references.pmid: 20861881