TBP paralogs accommodate metazoan- and vertebrate-specific developmental gene regulation.
In addition to TATA-binding protein (TBP), a key factor for transcription initiation, the metazoan-specific TBP-like factor TLF/TRF2 and the vertebrate-specific factor TBP2/TRF3 are known to be required for transcription of specific subsets of genes. We have combined an antisense-knockdown approach with transcriptome profiling to determine the significance and biological role of TBP-independent transcription in early gastrula-stage Xenopus laevis embryos. Here, we report that, although each of the TBP family members is essential for embryonic development, relatively few genes depend on TBP in the embryo. Most of the transcripts that depend on TBP in the embryo are also expressed maternally and in adult stages, and show no functional specialization. In contrast, TLF is linked to preferential expression in embryos and shows functional specialization in catabolism. A requirement for TBP2 is linked to vertebrate-specific embryonic genes and ventral-specific expression. Therefore TBP paralogs are essential for the gene-regulatory repertoire that is directly linked to early embryogenesis.
Jacobi
Ulrike G
UG
Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands.
Akkers
Robert C
RC
Pierson
Elisabeth S
ES
Weeks
Daniel L
DL
Dagle
John M
JM
Veenstra
Gert Jan C
GJ
D000818:Animals; D005775:Gastrula / Q000378:metabolism; D018507:Gene Expression Regulation, Developmental; D035182:TATA Box Binding Protein-Like Proteins / Q000378:metabolism*; D035181:TATA-Box Binding Protein / Q000378:metabolism*; D029867:Xenopus Proteins / Q000378:metabolism*; D014982:Xenopus laevis / Q000235:genetics / Q000378:metabolism*
D035182:TATA Box Binding Protein-Like Proteins; D035181:TATA-Box Binding Protein; C492584:TBPL2 protein, Xenopus; D029867:Xenopus Proteins
Science. 2000 Dec 22;290(5500):2312-5
11125147
Cell. 2000 Sep 29;103(1):5-8
11051541
Curr Biol. 2001 Feb 20;11(4):282-7
11250159
Science. 2001 May 11;292(5519):1153-5
11352070
Mech Dev. 2001 Aug;106(1-2):203-5
11472857
Mol Cell. 2001 Mar;7(3):509-15
11463376
Trends Biochem Sci. 2001 Nov;26(11):665-71
11701325
Differentiation. 2001 Dec;69(2-3):75-82
11798068
Development. 2002 Feb;129(4):945-55
11861477
Science. 2002 Nov 1;298(5595):1036-9
12411709
Mol Cell. 2002 Dec;10(6):1467-77
12504020
Genes Dev. 2003 Jun 1;17(11):1309-20
12782648
Trends Biochem Sci. 2003 Jul;28(7):391-8
12878007
Proc Natl Acad Sci U S A. 2003 Dec 9;100(25):14887-91
14634207
Curr Biol. 2004 Apr 6;14(7):593-8
15062100
Mol Cell Biol. 2004 Sep;24(18):8104-12
15340072
Proc Natl Acad Sci U S A. 2004 Sep 14;101(37):13525-30
15345743
Cell. 1982 Oct;30(3):675-86
6183003
Biochem Genet. 1985 Feb;23(1-2):73-88
3994660
Cell. 1991 May 31;65(5):775-83
2040014
Cell. 1992 May 15;69(4):685-96
1586947
Cell. 1992 May 15;69(4):697-702
1586948
Nature. 1993 Feb 11;361(6412):557-61
8429912
Oligonucleotides. 2006 Spring;16(1):26-42
16584293
Mol Cell Biol. 2006 Oct;26(20):7492-505
17015475
Genes Dev. 1993 Jul;7(7B):1291-308
8330735
EMBO J. 1994 Sep 15;13(18):4321-8
7925276
Cell. 1995 Apr 21;81(2):269-78
7736579
Mech Dev. 1995 Apr;50(2-3):103-17
7542467
Trends Biochem Sci. 1996 Sep;21(9):327-35
8870495
Dev Biol. 1997 Sep 15;189(2):335-46
9299125
Cell. 1997 Oct 3;91(1):71-83
9335336
Proc Natl Acad Sci U S A. 1999 Apr 27;96(9):4791-6
10220372
Trends Biochem Sci. 1999 Sep;24(9):335-9
10470030
Mol Cell Biol. 1999 Nov;19(11):7610-20
10523649
Mech Dev. 2005 Mar;122(3):355-63
15763212
Mech Dev. 2005 Mar;122(3):441-75
15763214
Mol Cell Biol. 2005 Apr;25(7):2632-43
15767669
Nucleic Acids Res. 2006;34(1):185-200
16397297
Proc Natl Acad Sci U S A. 1999 Nov 23;96(24):13720-5
10570139
Mol Cell Biol. 1999 Dec;19(12):7972-82
10567523
Nucleic Acids Res. 2006;34(3):986-95
16464828
Science. 2000 May 5;288(5467):867-70
10797011
Nucleic Acids Res. 2000 May 15;28(10):2153-7
10773085
Mol Cell. 2000 Sep;6(3):705-13
11030349
Mol Cell. 2000 Sep;6(3):715-22
11030350
Nucleic Acids Res. 2001 Jan 1;29(1):159-64
11125077