Evaluating genome-scale approaches to eukaryotic DNA replication.
Mechanisms regulating where and when eukaryotic DNA replication initiates remain a mystery. Recently, genome-scale methods have been brought to bear on this problem. The identification of replication origins and their associated proteins in yeasts is a well-integrated investigative tool, but corresponding data sets from multicellular organisms are scarce. By contrast, standardized protocols for evaluating replication timing have generated informative data sets for most eukaryotic systems. Here, I summarize the genome-scale methods that are most frequently used to analyse replication in eukaryotes, the kinds of questions each method can address and the technical hurdles that must be overcome to gain a complete understanding of the nature of eukaryotic replication origins.
Gilbert
David M
DM
Department of Biological Science, Florida State University, Tallahassee, 32306, USA. gilbert@bio.fsu.edu
D000818:Animals; D004261:DNA Replication / Q000235:genetics*; D005057:Eukaryotic Cells / Q000378:metabolism*; D016678:Genome / Q000235:genetics; D023281:Genomics / Q000379:methods*; D006801:Humans; D008957:Models, Genetic; D018741:Replication Origin / Q000235:genetics*; D015203:Reproducibility of Results
Genetics. 2008 Dec;180(4):1833-47
18832352
Proc Natl Acad Sci U S A. 1999 Mar 16;96(6):2656-61
10077566
Proc Natl Acad Sci U S A. 2008 Jul 1;105(26):8956-61
18579778
EMBO J. 2006 Nov 1;25(21):5171-9
17053780
EMBO J. 2007 Mar 7;26(5):1327-39
17304213
Cell. 1987 Jul 3;50(1):59-68
3036365
BMC Mol Biol. 2007 Dec 19;8:112
18093330
Genome Res. 2009 Dec;19(12):2288-99
19767418
Trends Genet. 2009 Dec;25(12):523-7
19853958
Chromosome Res. 2010 Jan;18(1):63-77
19904620
Cell Cycle. 2005 Jan;4(1):172-6
15611667
Chromosome Res. 2010 Jan;18(1):91-102
20039120
J Cell Biol. 2006 Jun 5;173(5):673-83
16754955
Cell. 2009 Sep 4;138(5):870-84
19737516
Nat Struct Mol Biol. 2010 Feb;17(2):251-7
20118936
EMBO J. 2004 Feb 25;23(4):897-907
14765124
Exp Cell Res. 2001 Dec 10;271(2):263-8
11716538
Curr Opin Genet Dev. 2009 Apr;19(2):142-9
19345088
Genome Res. 2010 Jun;20(6):781-90
20219942
Methods Mol Biol. 2009;556:191-203
19488880
PLoS Genet. 2010 Jun 10;6(6):e1000982
20548960
Cold Spring Harb Protoc. 2010 Feb;2010(2):pdb.prot5385
20150148
Genes Dev. 2004 Dec 15;18(24):3094-105
15601823
J Cell Biochem. 2008 Oct 1;105(2):321-9
18680119
Nat Cell Biol. 2009 Mar;11(3):357-62
19182789
Science. 2001 Dec 14;294(5550):2357-60
11743203
Nature. 2003 Aug 28;424(6952):1078-83
12944972
J Cell Biol. 2006 Jul 17;174(2):185-94
16831888
Mol Cell. 2009 Jun 26;34(6):767-74
19560427
Small. 2008 Oct;4(10):1785-93
18814174
Nat Struct Mol Biol. 2008 Jul;15(7):722-9
18536724
Mol Biol Evol. 2010 May;27(5):1077-86
20026481
Nat Rev Mol Cell Biol. 2004 Oct;5(10):848-55
15459665
Nat Rev Genet. 2007 Aug;8(8):588-600
17621316
Mol Cell Biol. 2007 Sep;27(18):6396-406
17636020
Chromosome Res. 2005;13(3):309-26
15868424
PLoS Biol. 2008 Oct 7;6(10):e245
18842067
Exp Cell Res. 2005 Aug 1;308(1):53-64
15904920
Proc Natl Acad Sci U S A. 2008 Oct 14;105(41):15837-42
18838675
Nat Genet. 2002 Nov;32(3):438-42
12355067
Methods. 1997 Nov;13(3):271-80
9441853
Nature. 2010 May 20;465(7296):363-7
20436457
Genes Dev. 2009 Mar 1;23(5):589-601
19270159
J Cell Biol. 2010 Jun 14;189(6):967-80
20530209
Proc Natl Acad Sci U S A. 2009 Nov 17;106(46):19363-8
19889976
PLoS Genet. 2010 May 13;6(5):e1000946
20485513
Genes Dev. 2009 Mar 1;23(5):643-54
19270162
Genome Res. 2010 Apr;20(4):447-57
20103589
Cell. 2009 Apr 17;137(2):247-58
19361851
Nat Cell Biol. 2006 Feb;8(2):148-55
16429127
Chromosoma. 2007 Aug;116(4):341-7
17404750
Mol Cell. 2006 Mar 3;21(5):719-26
16507369
Mol Biol Evol. 2009 Apr;26(4):729-41
19126867
Genome Res. 2008 Oct;18(10):1562-70
18669478
Nat Cell Biol. 2009 Nov;11(11):1315-24
19838172
Genes Dev. 2003 Aug 1;17(15):1894-908
12897055
Mol Cell Biol. 2002 Jan;22(2):442-52
11756541
Genome Res. 2007 Sep;17(9):1278-85
17675363
Nature. 2008 Sep 25;455(7212):557-60
18716622
Proc Natl Acad Sci U S A. 2005 Jan 11;102(2):337-42
15623550
Epigenetics. 2009 Aug 16;4(6):362-5
19736523
Chromosome Res. 2010 Jan;18(1):115-25
20205353
Science. 2010 May 28;328(5982):1161-4
20508129
Mol Biol Cell. 2010 Feb 1;21(3):393-404
19955211
Mol Cell. 2009 Jun 26;34(6):722-34
19560424
Genes Dev. 2005 Apr 15;19(8):942-54
15833917
PLoS Genet. 2009 Apr;5(4):e1000446
19360092
Genome Res. 2010 Jun;20(6):761-70
20430782
Genome Biol. 2004;5(4):R22
15059255
Genes Dev. 2010 Apr 15;24(8):748-53
20351051
Proc Natl Acad Sci U S A. 2010 Jan 5;107(1):139-44
19966280
EMBO J. 2010 Mar 3;29(5):934-42
20094030
Genome Res. 2010 Feb;20(2):155-69
19952138
Mol Biol Cell. 2001 Nov;12(11):3317-27
11694569
Genes Cells. 1997 Nov;2(11):667-78
9491801
Genome Biol. 2007;8(8):R169
17705870
Mol Cell Biol. 1990 Aug;10(8):4345-55
2164638
Proc Natl Acad Sci U S A. 1966 Mar;55(3):599-606
5221245
Cell. 2009 Mar 6;136(5):852-64
19269364
Chromosome Res. 2010 Jan;18(1):147-61
20205354
Cell. 2003 Aug 8;114(3):385-94
12914702
Mol Cell Biol. 2003 Mar;23(5):1832-42
12589000
Chromosome Res. 2010 Jan;18(1):127-36
20013151
Genome Res. 2010 Jun;20(6):771-80
20435908
Mol Biol Cell. 2006 Jan;17(1):308-16
16251353
Nat Struct Mol Biol. 2004 Nov;11(11):1076-83
15475964
Mol Cell. 2005 Nov 23;20(4):575-87
16307921
Crit Rev Biochem Mol Biol. 2009 Sep-Oct;44(5):343-51
19780641
Curr Opin Cell Biol. 2010 Jun;22(3):277-83
20363609
Genes Dev. 2006 Jul 15;20(14):1874-9
16847347
Genes Cells. 2002 Aug;7(8):781-9
12167157
Nat Cell Biol. 2003 Jul;5(7):668-74
12833066
Methods Mol Biol. 2009;521:105-20
19563103
Mol Cell Biol. 2004 May;24(10):4138-50
15121836
Methods Mol Biol. 2009;521:315-28
19563114
Mol Biol Cell. 2006 Dec;17(12):5337-45
17005913
Nucleic Acids Res. 2010 Nov;38(20):6906-19
20571081
Mol Cell Biol. 1993 May;13(5):2688-96
8386315
J Cell Biol. 2009 Nov 30;187(5):623-35
19951913
EMBO Rep. 2007 Aug;8(8):770-7
17668008
PLoS Comput Biol. 2008 Aug 22;4(8):e1000134
18725940
Anal Chem. 2010 Mar 15;82(6):2480-7
20184350
Mol Cell Biol. 2004 Apr;24(7):2958-67
15024083
Hum Mol Genet. 2004 Jan 15;13(2):191-202
14645202
Proc Natl Acad Sci U S A. 1986 May;83(9):2924-8
3458252
Genes Dev. 2009 May 1;23(9):1077-90
19417103
Chromosome Res. 2010 Jan;18(1):79-89
19921448
Cell. 1993 Jul 2;73(7):1403-9
8324827
Science. 2001 Oct 5;294(5540):96-100
11588251
Epigenetics. 2009 Feb 16;4(2):93-7
19242104
Genome Res. 2007 Jun;17(6):865-76
17568004
BMC Genomics. 2006 Oct 26;7:276
17067396
Chromosome Res. 2010 Jan;18(1):19-34
20012185
Annu Rev Biochem. 2010;79:89-130
20373915
EMBO J. 2005 Jan 12;24(1):120-7
15577942
PLoS Genet. 2010 Jul 01;6(7):e1001011
20617169
Proc Natl Acad Sci U S A. 2005 Dec 20;102(51):18321-5
16352724
Genome Res. 2010 Feb;20(2):201-11
19996087
PLoS Biol. 2004 Jun;2(6):e152
15208711
Mol Cell Biol. 2006 Feb;26(3):1051-62
16428457