A multiplicity of CCAAT box-binding proteins

Dorn, Arnulf; Bollekens, Jacques; Staub, Adrian; Benoist, Christophe; Mathis, Diane

doi:10.1016/0092-8674(87)90513-7

Cited by 722 publications

(491 citation statements)

References 41 publications

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“…This strengthens the conclusions of previous studies (Kabe et al, 2005) about the critical role of NF-Y as a regulator of transcription of many bidirectional promoters (Mantovani, 1998), and of CCAAT boxes as binding sites for several other TFs (Dorn et al, 1987).…”

Section: Discussionsupporting

confidence: 89%

“…it allows different pairs of genes to differ in total and relative expression of the two genes and might facilitate interactions with other TFs, as suggested in (Dorn et al, 1987).…”

Section: Discussionmentioning

confidence: 99%

“…We note that this is only applies to unidirectional promoters, since in bidirectional promoters the orientation of the box is ambiguous. As certain mismatches in the sequences do not affect the binding significantly (Mantovani, 1998;Zanotto et al, 2009), we allow mismatches to some extent in all positions but the CCAAT box, as evidence suggest that this box is strictly required for NF-Y to bind (Dorn et al, 1987;van Huijsduijnen et al, 1987). In case of overlapping matches, only the first is recorded.…”

Section: Search Of Nf-y Type Ccaat Boxesmentioning

confidence: 99%

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Genome wide study of NF-Y type CCAAT boxes in unidirectional and bidirectional promoters in human and mouse

Häkkinen

Healy

Jacobs

et al. 2011

Journal of Theoretical Biology

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International audienceA subset of CCAAT boxes are known binding sites for the transcription factor NF-Y. We characterize their number, mismatches to the consensus sequence, and locations in bidirectional and unidirectional promoter sequences in human and mouse. We confront the findings with an analytical null model of DNA sequences and find that NF-Y type CCAAT boxes play key, but distinct roles in the two types of promoters. They are found above chance in both, but in unidirectional only when having few mismatches. In bidirectional, the relative positions of multiple boxes differ from what is expected by chance, suggesting the need for contiguity. In agreement, when there are four boxes (four-box configurations), these have much lower number of mismatches than expected in bidirectional promoters alone. Positioning of the first box differs in the two types of promoters and the null model, and mismatches and positioning are found to be correlated. Finally, four-box configurations are conserved between human and mouse, supporting the relevance of the findings. We conclude that bidirectional and unidirectional promoters, while sharing some similarities, appear to possess distinct regulatory mechanisms at the sequence level

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Section: Discussionsupporting

confidence: 89%

“…it allows different pairs of genes to differ in total and relative expression of the two genes and might facilitate interactions with other TFs, as suggested in (Dorn et al, 1987).…”

Section: Discussionmentioning

confidence: 99%

Section: Search Of Nf-y Type Ccaat Boxesmentioning

confidence: 99%

See 1 more Smart Citation

Genome wide study of NF-Y type CCAAT boxes in unidirectional and bidirectional promoters in human and mouse

Häkkinen

Healy

Jacobs

et al. 2011

Journal of Theoretical Biology

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“…For example, in the lysis/lysogeny switch of bacteriophage λ, cro and repressor compete for related sites in the rightward operator 28 . In eukaryotes, a number of regulatory proteins have been shown to be members of protein families with related DNA-binding specificities [29][30][31][32][33][34][35][36][37] . In fact, a member of the nuclear hormone receptor family, thyroid hormone receptor, was recently shown to mediate negative effects on transcription from oestrogen-responsive DNA elements, apparently by competing with oestrogen receptor for binding to the elements 38 .…”

Section: Discussionmentioning

confidence: 99%

Activation and repression of transcription by homoeodomain-containing proteins that bind a common site

Jaynes

O’Farrell

1988

Nature

223

148

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The product of the fushi tarazu (ftz) gene is shown to be a site-dependent activator of transcription. In vitro-defined binding sites act as ftz-dependent enhancers in cultured cells. Another homoeodomain-containing protein, the engrailed gene product, competes for homoeodomainbinding sites and counteracts ftz activation.GENETIC analysis in Drosophila melanogaster has identified a group of regulatory genes that participate in embryonic pattern formation 1,2 . Many of these genes encode a 60 amino-acid sequence, the homoeodomain, that is highly conserved through evolution [3][4][5] . This domain contains a putative helix-turn-helix motif 6 such as that found in a number of bacterial regulators 7 , and possesses a sequence-specific DNA-binding activity 8,9 . Numerous regulatory interactions occur among homoeodomain-encoding genes during development. For example, a combination of segmentation and homoeotic gene products, many of which contain homoeodomains 1 , specify the developmental fates of cells in striped patterns 10,11 . Furthermore, homoeodomain-containing proteins (homoeodomain proteins) regulate both each other 12 and downstream (`cytodifferentiation' 13 ) genes. Consequently, it has been attractive to think of homoeodomain proteins as direct regulators of transcription. Due to the complexity of cross-regulatory interactions however, mutations altering or eliminating one homoeodomain protein generally change the expression patterns of many other regulators, confounding efforts to distinguish direct from indirect regulation. Additionally, suspected target genes contain large cis-acting control regions that respond, directly or indirectly, to complex combinations of regulators [14][15][16][17] . As a result, identification of target genes directly regulated by homoeodomain proteins has been problematic.Previous studies have documented instances in which homoeodomain proteins control transcription. The enhancer activity of a DNA fragment from the ftz gene, a homoeodomaincontaining member of the pair-rule class of segmentation genes, suggested that the ftz gene product (ftz) activates its own expression in the embryo 18 . In a different approach a Drosophila tissue culture system was used to show that the Ultrabithorax (Ubx) gene product induces expression of its own promoter, and inhibits the Antennapedia (Antp) (P1) promoter (M. Krasnow and D. S. Hogness, personal communication, see ref. 19 for summary). In these cases however, the complexity of the regulatory circuitry and of the responding control regions leaves open the possibility that the homoeodomain proteins produce these transcriptional effects through intermediaries. To circumvent the complexities of natural target genes, we chose to use binding sites identified in vitro to build homoeodomain-responsive promoters. We find that ftz is a potent activator of transcription from these promoters in cultured cells.During sequential subdivision of the Drosophila embryo to produce segmentally repeating patterns, combinations of regulatory gene prod...

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“…Other recent studies have demonstrated separate binding sites for NF1 and CAAT binding factors (36) and provided evidence for the recognition of CAAT sequences by multiple factors (7). The data reported here suggest that rat liver nuclear extracts contain an NFllike factor that binds to the wild-type promoter and to the 5'-end NFl-mutated promoter, pID1, over the CAAT sequence, as would be suggested by the results of Jones et al (i.e., NF1 is identical to CTF [20]).…”

Section: Discussionmentioning

confidence: 99%

Identification of basal and cyclic AMP regulatory elements in the promoter of the phosphoenolpyruvate carboxykinase gene.

Quinn¹,

Wong²,

Magnuson³

et al. 1988

Mol. Cell. Biol.

174

110

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Promoter elements important for basal and cyclic AMP (cAMP)-regulated expression of the phosphoenolpyruvate carboxykinase (PEPCK) Analysis of the expression of fusion genes, in which the coding sequence of a reporter gene is placed under the control of putative regulatory elements of a test gene, has resulted in the identification of various cis-acting elements of eucaryotic and viral genes which interact with trans-acting factors to control transcription in mammalian cells (8,28,30). The two classes of cis-acting elements which have been identified are termed promoter and enhancer elements. Promoter elements are characterized by their dependence on position and orientation with respect to the transcription start site (8,28,30). These are typified by the CAAT, SP1, and TATA elements. Enhancer elements are characterized by their ability to exert effects relatively independently of distance from and orientation to the transcription start site (41). Enhancers may be constitutively active, as in the cases of the simian virus 40 enhancer (34) and the basal-level enhancers of the human metallothionein Ila gene (16, 40), or they may be regulatable, as exemplified by the metalregulatory elements of the human metallothionein IIa gene (22,23) and the steroid hormone response elements (22,23,37). Typically, deletion of a regulatable enhancer sequence affects regulated expression but has little or no effect on basal expression of the gene.The gene encoding phosphoenolpyruvate carboxykinase (PEPCK) is regulated at the transcriptional level by a number of hormones (3,10,24,39

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A multiplicity of CCAAT box-binding proteins

Cited by 722 publications

References 41 publications

Genome wide study of NF-Y type CCAAT boxes in unidirectional and bidirectional promoters in human and mouse

Genome wide study of NF-Y type CCAAT boxes in unidirectional and bidirectional promoters in human and mouse

Activation and repression of transcription by homoeodomain-containing proteins that bind a common site

Identification of basal and cyclic AMP regulatory elements in the promoter of the phosphoenolpyruvate carboxykinase gene.

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