scholarly journals Novel DNA-binding protein fromDrosophilaembryos identified by binding site selection

FEBS Letters ◽  
1996 ◽  
Vol 396 (1) ◽  
pp. 99-102
Author(s):  
Vesna Todorović ◽  
Snežana Kojić ◽  
Miloš Vujanac ◽  
Ana Savić ◽  
Dragana Stefanović
Keyword(s):  
Dna Binding ◽  
Binding Site ◽  
Site Selection ◽  
Binding Protein ◽  
Dna Binding Protein

scholarly journals Evi-1, a murine zinc finger proto-oncogene, encodes a sequence-specific DNA-binding protein.

1991 ◽  
Vol 11 (5) ◽  
pp. 2665-2674 ◽  
Author(s):  
A S Perkins ◽  
R Fishel ◽  
N A Jenkins ◽  
N G Copeland
Keyword(s):  
Dna Binding ◽  
Binding Site ◽  
Zinc Finger ◽  
Sequence Data ◽  
Binding Protein ◽  
Consensus Sequence ◽  
Dna Binding Protein ◽  
Polymerase Chain Reaction Method ◽  
Nucleotide Sequence Data ◽  
Carboxy Terminal

Evi-1 was originally identified as a common site of viral integration in murine myeloid tumors. Evi-1 encodes a 120-kDa polypeptide containing 10 zinc finger motifs located in two domains 380 amino acids apart and an acidic domain located carboxy terminal to the second set of zinc fingers. These features suggest that Evi-1 is a site-specific DNA-binding protein involved in the regulation of RNA transcription. We have purified Evi-1 protein from E. coli and have employed a gel shift-polymerase chain reaction method using random oligonucleotides to identify a high-affinity binding site for Evi-1. The consensus sequence for this binding site is TGACAAGATAA. Evi-1 protein specifically protects this motif from DNase I digestion. By searching the nucleotide sequence data bases, we have found this binding site both in sequences 5' to genes in putative or known regulatory regions and within intron sequences.

scholarly journals COUP-TF (chicken ovalbumin upstream promoter transcription factor)-interacting protein 1 (CTIP1) is a sequence-specific DNA binding protein

2002 ◽  
Vol 368 (2) ◽  
pp. 555-563 ◽  
Author(s):  
Dorina AVRAM ◽  
Andrew FIELDS ◽  
Thanaset SENAWONG ◽  
Acharawan TOPARK-NGARM ◽  
Mark LEID
Keyword(s):  
Transcription Factor ◽  
Immune System ◽  
Dna Binding ◽  
Binding Site ◽  
Binding Protein ◽  
Family Members ◽  
Dna Binding Protein ◽  
Cell Leukaemia ◽  
Upstream Promoter ◽  
Chicken Ovalbumin

Chicken ovalbumin upstream promoter transcription factor (COUP-TF)-interacting proteins 1 and 2 [CTIP1/Evi9/B cell leukaemia (Bcl) l1a and CTIP2/Bcl11b respectively] are highly related C2H2 zinc finger proteins that are abundantly expressed in brain and the immune system, and are associated with immune system malignancies. A selection procedure was employed to isolate high-affinity DNA binding sites for CTIP1. The core binding site on DNA identified in these studies, 5′-GGCCGG-3′ (upper strand), is highly related to the canonical GC box and was bound by a CTIP1 oligomeric complex(es) in vitro. Furthermore, both CTIP1 and CTIP2 repressed transcription of a reporter gene harbouring a multimerized CTIP binding site, and this repression was neither reversed by trichostatin A (an inhibitor of known class I and II histone deacetylases) nor stimulated by co-transfection of a COUP-TF family member. These results demonstrate that CTIP1 is a sequence-specific DNA binding protein and a bona fide transcriptional repressor that is capable of functioning independently of COUP-TF family members. These findings may be relevant to the physiological and/or pathological action(s) of CTIPs in cells that do not express COUP-TF family members, such as cells of the haematopoietic and immune systems.

scholarly journals The release element of the yeast polymerase I transcription terminator can function independently of Reb1p.

1995 ◽  
Vol 15 (11) ◽  
pp. 5929-5936 ◽  
Author(s):  
S W Jeong ◽  
W H Lang ◽  
R H Reeder
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Dna Binding ◽  
Binding Site ◽  
Mutational Analysis ◽  
Binding Protein ◽  
Dna Binding Protein ◽  
Lac Repressor ◽  
Transcription Terminator ◽  
Polymerase I ◽  
Apparent Ability

The Saccharomyces cerevisiae polymerase I (polI) transcription terminator utilizes a DNA-binding protein (Reb1p) as part of a signal that causes the polymerase to pause prior to release from the template. To study the release element of the terminator, independent of the Reb1p pause signal, we have replaced the Reb1p binding site with the binding site for the lac repressor, which acts as a self-contained heterologous pause signal for polI. Release efficiency is maximal when the lac repressor causes polI to pause in exactly the same position that Reb1p would have caused it to pause, suggesting that polI must be precisely positioned for transcript release to occur. Mutational analysis shows that the release element is a region rich in T residues which codes for the extreme 3' end of the transcript and which has no apparent ability to form hairpins when transcribed into RNA. We discuss possible mechanisms whereby this polI release element might function.

scholarly journals A lipopolysaccharide-induced DNA-binding protein for a class II gene in B cells is distinct from NF-kappa B

1989 ◽  
Vol 9 (8) ◽  
pp. 3184-3192
Author(s):  
E M Gravallese ◽  
M R Boothby ◽  
C M Smas ◽  
L H Glimcher
Keyword(s):  
B Cells ◽  
Dna Binding ◽  
Binding Site ◽  
Binding Protein ◽  
Regulatory Region ◽  
Dna Binding Protein ◽  
Class Ii ◽  
Nf Kappa B ◽  
Inducible Protein ◽  
Lps Treatment

Class II (Ia) major histocompatibility complex molecules are cell surface proteins normally expressed by a limited subset of cells of the immune system. These molecules regulate the activation of T cells and are required for the presentation of antigens and the initiation of immune responses. The expression of Ia in B cells is determined by both the developmental stage of the B cell and by certain external stimuli. It has been demonstrated previously that treatment of B cells with lipopolysaccharide (LPS) results in increased surface expression of Ia protein. However, we have confirmed that LPS treatment results in a significant decrease in mRNA encoding the Ia proteins which persists for at least 18 h. Within the upstream regulatory region of A alpha k, an NF-kappa B-like binding site is present. We have identified an LPS-induced DNA-binding protein in extracts from athymic mice whose spleens consist predominantly of B cells. Binding activity is present in low levels in unstimulated spleen cells and is increased by LPS treatment. This protein binds to two sites in a regulatory region of the Ia A alpha k gene, one of which contains the NF-kappa B-like binding site. DNA fragments containing these sites cross-compete for protein binding. Analysis by DNase I footprinting identified a target binding sequence, named the LPS-responsive element. Although this target sequence contains an NF-kappa B-like binding site, competition with a mutant oligonucleotide demonstrated that bases critical for NF-kappa B binding are not required for binding of the LPS-inducible protein. Therefore, we hypothesized that this inducible protein represents a new mediator of LPS action, distinct from NF-kappa B, and may be one mechanism to account for the decrease in mRNA encoding the Ia proteins.

scholarly journals Tumor suppressor Smad4 is a transforming growth factor beta-inducible DNA binding protein.

1997 ◽  
Vol 17 (12) ◽  
pp. 7019-7028 ◽  
Author(s):  
J M Yingling ◽  
M B Datto ◽  
C Wong ◽  
J P Frederick ◽  
N T Liberati ◽  
...  
Keyword(s):  
Growth Factor ◽  
Dna Binding ◽  
Binding Site ◽  
Transforming Growth Factor Beta ◽  
Transcriptional Activation ◽  
Transforming Growth Factor ◽  
Binding Protein ◽  
Dna Binding Protein ◽  
Tgf Beta ◽  
Growth Factor Beta

Members of the Smad family of proteins are thought to play important roles in transforming growth factor beta (TGF-beta)-mediated signal transduction. In response to TGF-beta, specific Smads become inducibly phosphorylated, form heteromers with Smad4, and undergo nuclear accumulation. In addition, overexpression of specific Smad combinations can mimic the transcriptional effect of TGF-beta on both the plasminogen activator inhibitor 1 (PAI-1) promoter and the reporter construct p3TP-Lux. Although these data suggest a role for Smads in regulating transcription, the precise nuclear function of these heteromeric Smad complexes remains largely unknown. Here we show that in Mv1Lu cells Smad3 and Smad4 form a TGF-beta-induced, phosphorylation-dependent, DNA binding complex that specifically recognizes a bipartite binding site within p3TP-Lux. Furthermore, we demonstrate that Smad4 itself is a DNA binding protein which recognizes the same sequence. Interestingly, mutations which eliminate the Smad DNA binding site do not interfere with either TGF-beta-dependent transcriptional activation or activation by Smad3/Smad4 cooverexpression. In contrast, mutation of adjacent AP1 sites within this context eliminates both TGF-beta-dependent transcriptional activation and activation in response to Smad3/Smad4 cooverexpression. Furthermore, concatemerized AP1 sites, in isolation, are activated by Smad3/Smad4 cooverexpression and, to a certain extent, by TGF-beta. Taken together, these data suggest that the Smad3/Smad4 complex has at least two separable nuclear functions: it forms a rapid, yet transient sequence-specific DNA binding complex, and it potentiates AP1-dependent transcriptional activation.

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