The distribution of inverted repeat sequences in the Saccharomyces cerevisiae genome.
Although a variety of possible functions have been proposed for inverted repeat sequences (IRs), it is not known which of them might occur in vivo. We investigate this question by assessing the distributions and properties of IRs in the Saccharomyces cerevisiae (SC) genome. Using the IRFinder algorithm we detect 100,514 IRs having copy length greater than 6 bp and spacer length less than 77 bp. To assess statistical significance we also determine the IR distributions in two types of randomization of the S. cerevisiae genome. We find that the S. cerevisiae genome is significantly enriched in IRs relative to random. The S. cerevisiae IRs are significantly longer and contain fewer imperfections than those from the randomized genomes, suggesting that processes to lengthen and/or correct errors in IRs may be operative in vivo. The S. cerevisiae IRs are highly clustered in intergenic regions, while their occurrence in coding sequences is consistent with random. Clustering is stronger in the 3' flanks of genes than in their 5' flanks. However, the S. cerevisiae genome is not enriched in those IRs that would extrude cruciforms, suggesting that this is not a common event. Various explanations for these results are considered.
Strawbridge
Eva M
EM
Department of Mathematics, University of Chicago, IL 60637, USA. emstrawb@math.uchicago.edu
Benson
Gary
G
Gelfand
Yevgeniy
Y
Benham
Craig J
CJ
D024509:3' Flanking Region; D024506:5' Flanking Region; D000465:Algorithms; D001483:Base Sequence; D016681:Genome, Fungal / Q000235:genetics*; D055029:Inverted Repeat Sequences; D012441:Saccharomyces cerevisiae / Q000235:genetics*
Genetics. 1997 Jul;146(3):835-47
9215890
Cell. 1983 Jul;33(3):817-29
6871994
Mol Cell Biol. 2000 May;20(10):3449-58
10779335
Cell. 1996 Dec 13;87(6):1115-22
8978615
Proc Natl Acad Sci U S A. 1982 Jul;79(13):4128-32
7051004
Nucleic Acids Res. 1996 Jan 1;24(1):238-41
8594589
J Virol. 2007 Oct;81(20):11290-303
17686840
J Mol Biol. 2000 Mar 10;296(5):1169-73
10698623
Proc Natl Acad Sci U S A. 1983 Nov;80(22):6785-9
6316325
Nucleic Acids Res. 1995 Jun 11;23(11):1977-83
7596826
Biopolymers. 1982 Mar;21(3):679-96
7066478
Phys Rev E Stat Nonlin Soft Matter Phys. 2007 Oct;76(4 Pt 1):041914
17995033
Proc Natl Acad Sci U S A. 1983 Sep;80(18):5545-9
6577442
J Mol Biol. 2002 Feb 22;316(3):563-81
11866518
Genome Res. 2004 Oct;14(10A):1861-9
15466286
Nat Struct Mol Biol. 2008 Feb;15(2):146-54
18193062
Proc Natl Acad Sci U S A. 1997 May 13;94(10):5237-42
9144221
Nat Genet. 2005 Mar;37(3):320-7
15711546
Funct Integr Genomics. 2007 Jul;7(3):221-7
17340149
Front Biosci. 2007 May 01;12:4409-23
17485385
Proc Natl Acad Sci U S A. 1980 Nov;77(11):6468-72
6256738
Nat Struct Mol Biol. 2004 Nov;11(11):1092-100
15502847
Genes Dev. 2005 Jun 1;19(11):1390-9
15937224
Nucleic Acids Res. 1998 Apr 1;26(7):1793-800
9512554
J Cell Biochem. 1996 Oct;63(1):1-22
8891900
Mol Cell. 2008 Mar 14;29(5):644-51
18342610
J Biol Chem. 2002 Mar 29;277(13):11174-83
11805087
Mol Cell Biol. 2002 Apr;22(7):2068-77
11884595
J Bacteriol. 1997 Nov;179(22):7046-54
9371452
Nucleic Acids Res. 2007;35(4):1198-208
17264116
Nucleic Acids Res. 1997 Aug 1;25(15):3009-16
9224600
Curr Genet. 2005 May;47(5):289-97
15776233
Nat Genet. 1997 Nov;17(3):298-304
9354793
Proc Natl Acad Sci U S A. 1996 Jan 23;93(2):819-23
8570641
Mol Cell Biol. 2007 Mar;27(6):1993-2002
17242211
Genome Res. 2000 Sep;10(9):1381-92
10984456
Mol Cell Biol. 1997 Sep;17(9):5559-70
9271431
Bioinformatics. 2002 Jul;18(7):971-9
12117795
FEBS Lett. 2006 Feb 20;580(5):1277-84
16466723
J Comput Biol. 2005 Apr;12(3):331-54
15857246
J Mol Biol. 1985 Oct 5;185(3):461-78
2997451
Mol Microbiol. 2004 Jul;53(2):665-74
15228542
Nucleic Acids Res. 2005 Sep 01;33(15):e134
16141192
Front Biosci. 2007 May 01;12:4208-20
17485368
Genetics. 1998 Apr;148(4):1507-24
9560370
DNA Repair (Amst). 2009 Mar 1;8(3):383-9
19124276
J Mol Biol. 2006 Feb 17;356(2):300-11
16376936
Mol Biol Evol. 2000 Aug;17(8):1268-75
10908647
DNA Repair (Amst). 2006 Sep 8;5(9-10):1146-60
16807136
Trends Biochem Sci. 2008 Jan;33(1):44-50
18054234
Genetics. 2002 Jul;161(3):1065-75
12136011
Mol Cell Biol. 1993 Sep;13(9):5315-22
8395002
Proc Natl Acad Sci U S A. 2008 Jul 22;105(29):9936-41
18632578
Genetics. 2003 Aug;164(4):1279-89
12930739
Nucleic Acids Res. 1992 Nov 25;20(22):5991-7
1461732
J Virol. 1995 Dec;69(12):7489-96
7494255
Proc Natl Acad Sci U S A. 1997 Mar 18;94(6):2174-9
9122167
J Mol Biol. 1993 Dec 20;234(4):1184-96
8263920
J Biol Chem. 1997 Dec 26;272(52):33145-52
9407101
Genetics. 1991 Dec;129(4):991-1005
1783300
J Cell Biochem. 2002;87(2):194-207
12244572
Trends Genet. 2003 Jul;19(7):365-9
12850440
Proc Natl Acad Sci U S A. 1999 Feb 16;96(4):1504-9
9990053
Genetics. 1993 Feb;133(2):143-8
8436264
Nucleic Acids Res. 1987 Dec 10;15(23):9641-54
3697079