Identification of SOX9 interaction sites in the genome of chondrocytes.
BACKGROUND
Our previous work has provided strong evidence that the transcription factor SOX9 is completely needed for chondrogenic differentiation and cartilage formation acting as a "master switch" in this differentiation. Heterozygous mutations in SOX9 cause campomelic dysplasia, a severe skeletal dysmorphology syndrome in humans characterized by a generalized hypoplasia of endochondral bones. To obtain insights into the logic used by SOX9 to control a network of target genes in chondrocytes, we performed a ChIP-on-chip experiment using SOX9 antibodies.


RESULTS
The ChIP DNA was hybridized to a microarray, which covered 80 genes, many of which are involved in chondrocyte differentiation. Hybridization peaks were detected in a series of cartilage extracellular matrix (ECM) genes including Col2a1, Col11a2, Aggrecan and Cdrap as well as in genes for specific transcription factors and signaling molecules. Our results also showed SOX9 interaction sites in genes that code for proteins that enhance the transcriptional activity of SOX9. Interestingly, a strong SOX9 signal was also observed in genes such as Col1a1 and Osx, whose expression is strongly down regulated in chondrocytes but is high in osteoblasts. In the Col2a1 gene, in addition to an interaction site on a previously identified enhancer in intron 1, another strong interaction site was seen in intron 6. This site is free of nucleosomes specifically in chondrocytes suggesting an important role of this site on Col2a1 transcription regulation by SOX9.


CONCLUSIONS
Our results provide a broad understanding of the strategies used by a "master" transcription factor of differentiation in control of the genetic program of chondrocytes.
Oh
Chun-do
CD
Department of Genetics, M.D. Anderson Cancer Center, The University of Texas, Houston, Texas, United States of America.
Maity
Sankar N
SN
Lu
Jing-Fang
JF
Zhang
Jiexin
J
Liang
Shoudan
S
Coustry
Francoise
F
de Crombrugghe
Benoit
B
Yasuda
Hideyo
H
D000818:Animals; D001665:Binding Sites; D002356:Cartilage / Q000166:cytology; D002454:Cell Differentiation / Q000235:genetics*; D002460:Cell Line; D019902:Chondrocytes / Q000166:cytology*; D024043:Collagen Type II / Q000235:genetics*; D016326:Extracellular Matrix Proteins / Q000235:genetics; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D016678:Genome; D020411:Oligonucleotide Array Sequence Analysis; D051381:Rats; D055758:SOX9 Transcription Factor / Q000235:genetics* / Q000378:metabolism
C511513:COL2A1 protein, rat; D024043:Collagen Type II; D016326:Extracellular Matrix Proteins; D055758:SOX9 Transcription Factor
J Bone Miner Res. 1999 May;14(5):757-63
10320524
J Histochem Cytochem. 1999 Nov;47(11):1351-6
10544208
Cancer Epidemiol Biomarkers Prev. 2007 Aug;16(8):1667-74
17684144
J Biol Chem. 2004 Dec 17;279(51):53848-56
15456762
Development. 1998 Oct;125(19):3831-42
9729491
Cell Tissue Res. 2001 Oct;306(1):107-16
11683172
Proc Natl Acad Sci U S A. 2006 Jan 10;103(2):365-70
16387856
Nucleic Acids Res. 2008 May;36(9):3011-24
18390577
Biochem Biophys Res Commun. 2005 Aug 12;333(4):1300-8
15979579
Development. 1998 Dec;125(24):4977-88
9811582
Curr Biol. 2004 Jul 27;14(14):R546-51
15268870
Osteoarthritis Cartilage. 2003 Jan;11(1):36-43
12505485
Dev Biol. 2001 Apr 15;232(2):372-87
11401399
Biochem Biophys Res Commun. 1986 Dec 30;141(3):904-11
3028392
J Cell Sci. 1995 Dec;108 ( Pt 12):3677-84
8719874
Mol Cell Biol. 2000 Jun;20(11):4149-58
10805756
J Biol Chem. 1991 Dec 5;266(34):23274-81
1744124
Science. 1988 Oct 21;242(4877):405-11
3175662
Cell. 1992 Oct 30;71(3):399-410
1339316
Genes Dev. 2003 Jul 1;17(13):1677-89
12842915
J Biol Chem. 2005 Sep 30;280(39):33132-40
16043491
J Biol Chem. 1995 Nov 17;270(46):27711-9
7499238
Genesis. 2002 Feb;32(2):121-3
11857796
Front Biosci. 1999 Oct 15;4:D694-703
10525480
Nat Neurosci. 2003 Jan;6(1):21-7
12469128
Curr Biol. 2005 Aug 9;15(15):1340-51
16085486
Genes Dev. 2002 Nov 1;16(21):2813-28
12414734
Arthritis Res Ther. 2006;8(2):106
16563183
Genes Dev. 2004 Oct 1;18(19):2404-17
15371327
J Biol Chem. 2001 Feb 16;276(7):4879-85
11098049
Proc Natl Acad Sci U S A. 2001 Jun 5;98(12):6698-703
11371614
Development. 2003 Jun;130(12):2779-91
12736220
Front Biosci. 2008 Jan 01;13:898-903
17981598
Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2414-9
15699338
J Biol Chem. 2000 Feb 4;275(5):3687-92
10652367
Development. 2004 Mar;131(6):1309-18
14973297
Proc Natl Acad Sci U S A. 2005 Oct 11;102(41):14665-70
16203988
Cell. 1989 Feb 24;56(4):607-17
2537150
Nat Genet. 2007 Oct;39(10):1235-44
17873876
J Cell Physiol. 2007 Oct;213(1):1-8
17492773
Mol Cell Biol. 1996 Aug;16(8):4512-23
8754852
Nature. 2008 Jun 12;453(7197):930-4
18454134
J Biol Chem. 2002 Nov 1;277(44):42171-7
12194984
Science. 2000 Dec 22;290(5500):2306-9
11125145
Mol Cell Biol. 2007 Sep;27(18):6497-505
17620412
Proc Natl Acad Sci U S A. 2001 Jan 2;98(1):160-5
11120880
Mol Cell Biol. 1997 Apr;17(4):2336-46
9121483
Arthritis Res Ther. 2006;8(4):R124
16859525
Cell. 2002 Jan 11;108(1):17-29
11792318
Bone. 2004 Jan;34(1):26-36
14751560
Matrix Biol. 1994 Aug;14(4):329-35
7827756
Ann Rheum Dis. 1988 Aug;47(8):684-91
3415368
Genes Dev. 1999 Aug 15;13(16):2072-86
10465785
Gastroenterology. 2007 Aug;133(2):539-46
17681175
J Biol Chem. 1998 Jun 12;273(24):14998-5006
9614107
Arthritis Rheum. 2002 Apr;46(4):961-7
11953973
Development. 1998 Nov;125(21):4175-84
9753672
J Biol Chem. 1995 Nov 17;270(46):27734-41
7499241
Nat Genet. 2006 Oct;38(10):1210-5
16964265
J Biol Chem. 2000 Apr 14;275(15):10738-44
10753864
Nature. 2009 Mar 19;458(7236):362-6
19092803
J Biol Chem. 1997 Jul 25;272(30):18709-17
9228042
Development. 2004 May;131(9):1891-901
15056615
Biochem J. 1998 Feb 15;330 ( Pt 1):549-57
9461555
Bone. 1993 May-Jun;14(3):341-5
8395866
J Biol Chem. 2005 Apr 1;280(13):12758-65
15695815
Dev Biol. 1999 May 15;209(2):239-53
10328918
Proc Natl Acad Sci U S A. 2000 Feb 1;97(3):1113-8
10655493
Hum Mol Genet. 2003 Jul 15;12(14):1755-65
12837698
J Biol Chem. 2004 Feb 13;279(7):6152-62
14630908
Nature. 1994 Dec 8;372(6506):525-30
7990924
Cell. 2009 May 1;137(3):445-58
19410542
Science. 1999 Jul 16;285(5426):409-12
10411504
Nature. 2006 Aug 17;442(7104):772-8
16862119