scholarly journals The Electronic Behavior of Zinc-Finger Protein Binding Sites in the Context of the DNA Extended Ladder Model

2016 ◽  
Vol 4 ◽  
Author(s):  
Nestor N. Oiwa ◽  
Claudette E. Cordeiro ◽  
Dieter W. Heermann
Keyword(s):  
Protein Binding ◽  
Zinc Finger ◽  
Binding Sites ◽  
Zinc Finger Protein ◽  
Protein Binding Sites ◽  
Ladder Model ◽  
Finger Protein ◽  
Electronic Behavior

scholarly journals The Cardiac Tissue-Restricted Homeobox Protein Csx/Nkx2.5 Physically Associates with the Zinc Finger Protein GATA4 and Cooperatively Activates Atrial Natriuretic Factor Gene Expression

1998 ◽  
Vol 18 (6) ◽  
pp. 3120-3129 ◽  
Author(s):  
Youngsook Lee ◽  
Tetsuo Shioi ◽  
Hideko Kasahara ◽  
Shawn M. Jobe ◽  
Russell J. Wiese ◽  
...  
Keyword(s):  
Gene Expression ◽  
Zinc Finger ◽  
Protein Interaction ◽  
Binding Sites ◽  
Atrial Natriuretic Factor ◽  
Target Gene ◽  
Cardiac Tissue ◽  
Zinc Finger Protein ◽  
Finger Protein ◽  
Homeobox Protein

ABSTRACT Specification and differentiation of the cardiac muscle lineage appear to require a combinatorial network of many factors. The cardiac muscle-restricted homeobox protein Csx/Nkx2.5 (Csx) is expressed in the precardiac mesoderm as well as the embryonic and adult heart. Targeted disruption of Csx causes embryonic lethality due to abnormal heart morphogenesis. The zinc finger transcription factor GATA4 is also expressed in the heart and has been shown to be essential for heart tube formation. GATA4 is known to activate many cardiac tissue-restricted genes. In this study, we tested whether Csx and GATA4 physically associate and cooperatively activate transcription of a target gene. Coimmunoprecipitation experiments demonstrate that Csx and GATA4 associate intracellularly. Interestingly, in vitro protein-protein interaction studies indicate that helix III of the homeodomain of Csx is required to interact with GATA4 and that the carboxy-terminal zinc finger of GATA4 is necessary to associate with Csx. Both regions are known to directly contact the cognate DNA sequences. The promoter-enhancer region of the atrial natriuretic factor (ANF) contains several putative Csx binding sites and consensus GATA4 binding sites. Transient-transfection assays indicate that Csx can activate ANF reporter gene expression to the same extent that GATA4 does in a DNA binding site-dependent manner. Coexpression of Csx and GATA4 synergistically activates ANF reporter gene expression. Mutational analyses suggest that this synergy requires both factors to fully retain their transcriptional activities, including the cofactor binding activity. These results demonstrate the first example of homeoprotein and zinc finger protein interaction in vertebrates to cooperatively regulate target gene expression. Such synergistic interaction among tissue-restricted transcription factors may be an important mechanism to reinforce tissue-specific developmental pathways.

scholarly journals Repression of hsp70 heat shock gene transcription by the suppressor of hairy-wing protein of Drosophila melanogaster.

1991 ◽  
Vol 11 (4) ◽  
pp. 1894-1900 ◽  
Author(s):  
C Holdridge ◽  
D Dorsett
Keyword(s):  
Drosophila Melanogaster ◽  
Heat Shock ◽  
Protein Binding ◽  
Protein Interactions ◽  
Binding Sites ◽  
Zinc Finger Protein ◽  
Gene Promoter ◽  
Heat Shock Gene ◽  
Protein Binding Sites ◽  
Shock Gene

The suppressor of hairy-wing [su(Hw)] locus of Drosophila melanogaster encodes a zinc finger protein that binds a repeated motif in the gypsy retroposon. Mutations of su(Hw) suppress the phenotypes associated with mutations caused by gypsy insertions. To examine the mechanisms by which su(Hw) alters gene expression, a fragment of gypsy containing multiple su(Hw) protein-binding sites was inserted into various locations in the well-characterized Drosophila hsp70 heat shock gene promoter. We found no evidence for activation of basal hsp70 transcription by su(Hw) protein in cultured Drosophila cells but observed that it can repress heat shock-induced transcription. Repression occurred only when su(Hw) protein-binding sites were positioned between binding sites for proteins required for heat shock transcription. We propose that su(Hw) protein interferes nonspecifically with protein-protein interactions required for heat shock transcription, perhaps sterically, or by altering the ability of DNA to bend or twist.

Identification of a KRAB-Zinc Finger Protein Binding to theRpe65Gene Promoter

2006 ◽  
Vol 31 (5) ◽  
pp. 457-466 ◽  
Author(s):  
Zhongjian Lu ◽  
Eugenia Poliakov ◽  
T. Michael Redmond
Keyword(s):  
Protein Binding ◽  
Zinc Finger ◽  
Zinc Finger Protein ◽  
Finger Protein

DNA Unwinding Induced by Zinc Finger Protein Binding†

Biochemistry ◽  
1996 ◽  
Vol 35 (12) ◽  
pp. 3845-3848 ◽  
Author(s):  
Yigong Shi ◽  
Jeremy M. Berg
Keyword(s):  
Protein Binding ◽  
Zinc Finger ◽  
Zinc Finger Protein ◽  
Dna Unwinding ◽  
Finger Protein

scholarly journals The zinc finger protein CLAMP promotes long-range chromatin interactions that mediate dosage compensation of the Drosophila male X-chromosome

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
William Jordan ◽  
Erica Larschan
Keyword(s):  
Long Range ◽  
Zinc Finger ◽  
X Chromosome ◽  
Dosage Compensation ◽  
Binding Sites ◽  
Zinc Finger Protein ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Active Chromatin ◽  
Finger Protein

Abstract Background Drosophila dosage compensation is an important model system for defining how active chromatin domains are formed. The male-specific lethal dosage compensation complex (MSLc) increases transcript levels of genes along the length of the single male X-chromosome to equalize with that expressed from the two female X-chromosomes. The strongest binding sites for MSLc cluster together in three-dimensional space largely independent of MSLc because clustering occurs in both sexes. CLAMP, a non-sex specific, ubiquitous zinc finger protein, binds synergistically with MSLc to enrich the occupancy of both factors on the male X-chromosome. Results Here, we demonstrate that CLAMP promotes the observed three-dimensional clustering of MSLc binding sites. Moreover, the X-enriched CLAMP protein more strongly promotes longer-range three-dimensional interactions on the X-chromosome than autosomes. Genome-wide, CLAMP promotes three-dimensional interactions between active chromatin regions together with other insulator proteins. Conclusion Overall, we define how long-range interactions which are modulated by a locally enriched ubiquitous transcription factor promote hyper-activation of the X-chromosome to mediate dosage compensation.

scholarly journals Gfi-1 encodes a nuclear zinc finger protein that binds DNA and functions as a transcriptional repressor.

1996 ◽  
Vol 16 (8) ◽  
pp. 4024-4034 ◽  
Author(s):  
P A Zweidler-Mckay ◽  
H L Grimes ◽  
M M Flubacher ◽  
P N Tsichlis
Keyword(s):  
T Cell ◽  
Binding Site ◽  
Electrophoretic Mobility ◽  
Zinc Finger ◽  
Binding Sites ◽  
Zinc Finger Protein ◽  
Zinc Fingers ◽  
Mobility Shift ◽  
Finger Protein ◽  
Electrophoretic Mobility Shift Assays

The Gfi-1 proto-oncogene encodes a zinc finger protein with six C2H2-type, C-terminal zinc finger motifs and is activated by provirus integration in T-cell lymphoma lines selected for interleukin-2 independence in culture and in primary retrovirus-induced thymomas. Gfi-1 expression in adult animals is restricted to the thymus, spleen, and testis and is enhanced in mitogen-stimulated splenocytes. In this report, we show that Gfi-1 is a 55-kDa nuclear protein that binds DNA in a sequence-specific manner. The Gfi-1 binding site, TAAATCAC(A/T)GCA, was defined via random oligonucleotide selection utilizing a bacterially expressed glutathione S-transferase-Gfi-1 fusion protein. Binding to this site was confirmed by electrophoretic mobility shift assays and DNase I footprinting. Methylation interference analysis and electrophoretic mobility shift assays with mutant oliginucleotides defined the relative importance of specific bases at the consensus binding site. Deletion of individual zinc fingers demonstrated that only zinc fingers 3, 4, and 5 are required for sequence-specific DNA binding. Potential Gfi-1 binding sites were detected in a large number of eukaryotic promoter-enhancers, including the enhancers of several proto-oncogenes and cytokine genes and the enhancer of the human cytomegalovirus (HCMV) major immediate-early promoter, which contains two such sites. HCMV major immediate-early-chloramphenicol acetyltransferase reporter constructs, transfected into NIH 3T3 fibroblasts, were repressed by Gfi-1, and the repression was abrogated by mutation of critical residues in the two Gfi-1 binding sites. These results suggest that Gfi-1 may play a role in HCMV biology and may contribute to oncogenesis and T-cell activation by repressing the expression of genes that inhibit these processes.

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