Genomic mapping of Suppressor of Hairy-wing binding sites in Drosophila.
BACKGROUND
Insulator elements are proposed to play a key role in the organization of the regulatory architecture of the genome. In Drosophila, one of the best studied is the gypsy retrotransposon insulator, which is bound by the Suppressor of Hairy-wing (Su [Hw]) transcriptional regulator. Immunolocalization studies suggest that there are several hundred Su(Hw) sites in the genome, but few of these endogenous Su(Hw) binding sites have been identified.


RESULTS
We used chromatin immunopurification with genomic microarray analysis to identify in vivo Su(Hw) binding sites across the 3 megabase Adh region. We find 60 sites, and these enabled the construction of a robust new Su(Hw) binding site consensus. In contrast to the gypsy insulator, which contains tightly clustered Su(Hw) binding sites, endogenous sites generally occur as isolated sites. These endogenous sites have three key features. In contrast to most analyses of DNA-binding protein specificity, we find that strong matches to the binding consensus are good predictors of binding site occupancy. Examination of occupancy in different tissues and developmental stages reveals that most Su(Hw) sites, if not all, are constitutively occupied, and these isolated Su(Hw) sites are generally highly conserved. Analysis of transcript levels in su(Hw) mutants indicate widespread and general changes in gene expression. Importantly, the vast majority of genes with altered expression are not associated with clustering of Su(Hw) binding sites, emphasizing the functional relevance of isolated sites.


CONCLUSIONS
Taken together, our in vivo binding and gene expression data support a role for the Su(Hw) protein in maintaining a constant genomic architecture.
Adryan
Boris
B
Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK. boris@mrc-lmb.cam.ac.uk
Woerfel
Gertrud
G
Birch-Machin
Ian
I
Gao
Shan
S
Quick
Marie
M
Meadows
Lisa
L
Russell
Steven
S
White
Robert
R
D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D047369:Chromatin Immunoprecipitation; D002874:Chromosome Mapping; D016384:Consensus Sequence; D004268:DNA-Binding Proteins / Q000378:metabolism*; D004330:Drosophila / Q000235:genetics*; D029721:Drosophila Proteins / Q000378:metabolism*; D005786:Gene Expression Regulation; D049750:Genome, Insect; D038101:Insulator Elements; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D012097:Repressor Proteins / Q000378:metabolism*
D004268:DNA-Binding Proteins; D029721:Drosophila Proteins; D012097:Repressor Proteins; C083738:su(Hw) protein, Drosophila
Proc Natl Acad Sci U S A. 2000 Mar 28;97(7):3347-51
10716700
Mol Cell Biol. 2006 Aug;26(16):5983-93
16880510
Development. 2000 Nov;127(21):4619-30
11023865
Science. 2000 Dec 22;290(5500):2306-9
11125145
Nature. 2001 Jan 25;409(6819):533-8
11206552
EMBO J. 2001 May 15;20(10):2518-27
11350941
Bioinformatics. 2001 Jun;17(6):509-19
11395427
Mol Cell Biol. 2001 Jul;21(14):4807-17
11416154
Trends Genet. 2001 Sep;17(9):520-7
11525835
Proc Natl Acad Sci U S A. 2001 Dec 18;98(26):15050-5
11742088
Mol Cell. 2000 Nov;6(5):1025-35
11106742
Bioinformatics. 2002;18 Suppl 1:S96-104
12169536
Cell. 2002 Oct 18;111(2):151-4
12408858
Dev Cell. 2002 Nov;3(5):659-71
12431373
Genes Dev. 2003 Mar 1;17(5):664-75
12629048
Development. 2003 Jul;130(14):3249-58
12783795
Proc Natl Acad Sci U S A. 2003 Aug 5;100(16):9428-33
12876199
J Cell Biol. 2003 Aug 18;162(4):565-74
12925706
Proc Natl Acad Sci U S A. 2003 Nov 11;100(23):13436-41
14597701
Mol Cell Biol. 2003 Dec;23(24):9338-48
14645543
Curr Opin Cell Biol. 2004 Jun;16(3):256-62
15145349
Genome Res. 2004 Jun;14(6):1188-90
15173120
Genetics. 2004 Jun;167(2):797-813
15238529
J Biol. 2002;1(1):5
12144710
J Mol Biol. 2004 Sep 17;342(3):775-85
15342236
EMBO J. 1990 Aug;9(8):2579-85
1973385
Genes Dev. 1990 Sep;4(9):1505-15
2174809
Cell. 1991 Mar 8;64(5):941-50
1848159
Genes Dev. 1992 Oct;6(10):1865-73
1327958
Proc Int Conf Intell Syst Mol Biol. 1994;2:28-36
7584402
Proc Natl Acad Sci U S A. 1996 Sep 3;93(18):9378-83
8790337
Genetics. 1996 Sep;144(1):159-70
8878682
Cell. 1998 Feb 20;92(4):511-21
9491892
Cell. 1999 Aug 6;98(3):387-96
10458613
Genetics. 1999 Sep;153(1):179-219
10471707
Bioinformatics. 1999 Jul-Aug;15(7-8):563-77
10487864
Genetics. 1999 Oct;153(2):787-98
10511558
Mol Cell. 2004 Dec 3;16(5):737-48
15574329
EMBO Rep. 2005 Feb;6(2):165-70
15678159
Nucleic Acids Res. 2005;33(5):1445-53
15760844
Heredity (Edinb). 2005 Jun;94(6):571-6
15815711
Genome Biol. 2005;6(7):R63
15998452
BMC Mol Biol. 2005;6:16
15985163
Mol Cell. 2005 Oct 7;20(1):105-16
16209949
Genetics. 2006 Apr;172(4):2337-49
16452134
EMBO J. 2000 May 15;19(10):2315-22
10811622