Comparing anterior and posterior Hox complex formation reveals guidelines for predicting cis-regulatory elements.
Hox transcription factors specify numerous cell fates along the anterior-posterior axis by regulating the expression of downstream target genes. While expression analysis has uncovered large numbers of de-regulated genes in cells with altered Hox activity, determining which are direct versus indirect targets has remained a significant challenge. Here, we characterize the DNA binding activity of Hox transcription factor complexes on eight experimentally verified cis-regulatory elements. Hox factors regulate the activity of each element by forming protein complexes with two cofactor proteins, Extradenticle (Exd) and Homothorax (Hth). Using comparative DNA binding assays, we found that a number of flexible arrangements of Hox, Exd, and Hth binding sites mediate cooperative transcription factor complexes. Moreover, analysis of a Distal-less regulatory element (DMXR) that is repressed by abdominal Hox factors revealed that suboptimal binding sites can be combined to form high affinity transcription complexes. Lastly, we determined that the anterior Hox factors are more dependent upon Exd and Hth for complex formation than posterior Hox factors. Based upon these findings, we suggest a general set of guidelines to serve as a basis for designing bioinformatics algorithms aimed at identifying Hox regulatory elements using the wealth of recently sequenced genomes.
Uhl
Juli D
JD
Division of Developmental Biology, Cincinnati Children's Hospital, 3333 Burnet Ave, MLC 7007, Cincinnati, OH 45229, USA.
Cook
Tiffany A
TA
Gebelein
Brian
B
D000818:Animals; D001665:Binding Sites; D029721:Drosophila Proteins / Q000235:genetics / Q000378:metabolism; D004331:Drosophila melanogaster / Q000378:metabolism; D018507:Gene Expression Regulation, Developmental; D018398:Homeodomain Proteins / Q000235:genetics* / Q000378:metabolism; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism
D029721:Drosophila Proteins; D018398:Homeodomain Proteins; D014157:Transcription Factors
Dev Cell. 2002 Oct;3(4):487-98
12408801
Development. 2000 Jan;127(1):155-66
10654609
Dev Biol. 2008 May 15;317(2):497-507
18407260
Development. 2001 Sep;128(18):3595-607
11566863
Nucleic Acids Res. 2003 Jul 1;31(13):3589-92
12824372
Mol Cell Biol. 2001 Feb;21(3):928-39
11154279
Mol Hum Reprod. 2008 Jun;14(6):357-66
18456676
Dev Biol. 2007 Feb 15;302(2):646-60
17113575
Blood. 1997 Mar 15;89(6):1922-30
9058712
Proc Natl Acad Sci U S A. 2006 Jul 5;103(27):10305-10309
16793922
Nature. 2004 Oct 7;431(7009):653-9
15470419
Cell. 2008 Jun 27;133(7):1277-89
18585360
Nat Rev Genet. 2005 Dec;6(12):881-92
16341069
Cell. 1994 Aug 26;78(4):603-15
7915199
Development. 2007 Jan;134(2):381-92
17166915
Science. 2006 Sep 29;313(5795):1918-22
17008523
Development. 2005 Apr;132(7):1591-600
15753213
Dev Biol. 1989 Oct;135(2):376-91
2570723
J Biol Chem. 2004 Jan 9;279(2):866-75
14561764
Cell. 1995 Jun 30;81(7):1031-42
7600572
Cell. 2007 Nov 2;131(3):530-43
17981120
Cancer Res. 2006 Dec 15;66(24):11781-91
17178874
Mol Cell Biol. 1997 Nov;17(11):6448-58
9343407
Dev Biol. 2005 Mar 15;279(2):462-80
15733672
Nucleic Acids Res. 1997 Nov 1;25(21):4173-80
9336443
Genes Dev. 1990 Jul;4(7):1209-23
1976570
Cell. 1989 Nov 3;59(3):573-80
2572329
Genes Dev. 1995 Mar 15;9(6):663-74
7729685
Leukemia. 1999 Dec;13(12):1993-9
10602420
Development. 1993 Aug;118(4):1063-75
7903632
Dev Biol. 2006 Mar 15;291(2):193-206
16515781
Curr Opin Genet Dev. 1998 Aug;8(4):423-9
9729718
Cell. 1999 Feb 19;96(4):587-97
10052460
Annu Rev Biochem. 1994;63:487-526
7979246
Cell. 2008 Jun 27;133(7):1133-5
18585344
Genes Dev. 2003 Aug 15;17(16):2060-72
12923056
Nature. 2002 Feb 21;415(6874):910-3
11859369
Cell. 2008 Jun 27;133(7):1266-76
18585359
Mol Cell Biol. 2005 Oct;25(19):8541-52
16166636
Proc Natl Acad Sci U S A. 1993 Aug 15;90(16):7666-70
8102800
Genes Dev. 1999 Jul 1;13(13):1704-16
10398683
Blood. 2005 Dec 1;106(12):3988-94
16091451
EMBO J. 1996 May 15;15(10):2476-87
8665855
Development. 2004 Aug;131(16):4071-83
15289435
Dev Cell. 2008 Aug;15(2):298-308
18694568
Genes Dev. 1996 Jan 15;10(2):176-84
8566751
Mol Cell Biol. 1999 Jul;19(7):5134-42
10373562
Nature. 1999 Feb 25;397(6721):714-9
10067897
Mol Cell Biol. 1997 Oct;17(10):5679-87
9315626
Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2420-4
15699330
Nat Rev Genet. 2005 Dec;6(12):893-904
16341070
J Mol Biol. 1993 Dec 20;234(4):1070-83
7903397
Mol Cell Biol. 1996 Apr;16(4):1632-40
8657138
Proc Natl Acad Sci U S A. 2007 Oct 23;104(43):16946-51
17942685
Development. 1997 May;124(10):2007-14
9169847
Mol Cell Biol. 1995 Aug;15(8):3989-97
7623795
Curr Top Dev Biol. 2009;88:63-101
19651302
Cell. 1992 Jan 24;68(2):283-302
1346368
Cancer Res. 2006 Jul 1;66(13):6628-37
16818636
Cell. 1997 Oct 17;91(2):171-83
9346235
Mol Cell Biol. 1996 Apr;16(4):1734-45
8657149
Genes Dev. 1999 Apr 15;13(8):935-45
10215621
Nature. 2002 Feb 21;415(6874):914-7
11859370
C R Acad Sci III. 1993 Sep;316(9):995-1008
7915637
Front Biosci. 2008 May 01;13:4297-308
18508512
Development. 1999 Nov;126(22):5137-48
10529430
Bioessays. 1995 Oct;17(10):855-63
7487967
EMBO J. 1994 Aug 1;13(15):3551-60
7914870
Annu Rev Cell Dev Biol. 2000;16:243-71
11031237
Development. 2007 Jul;134(14):2549-60
17553908