scholarly journals A phage display combined with DNA affinity magnetic system can be applied to a screening of DNA binding proteins, such as transcription factors

2010 ◽  
Vol 13 (1) ◽  
Author(s):  
Kusumadewi Sri Yulita ◽  
Takafumi Kouno ◽  
Bunichi Ezaki
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Phage Display ◽  
Binding Proteins ◽  
Magnetic System ◽  
Dna Binding Proteins

scholarly journals Regulation of glioblastoma multiforme stem-like cells by inhibitor of DNA binding proteins and oligodendroglial lineage-associated transcription factors

2012 ◽  
Vol 103 (6) ◽  
pp. 1028-1037 ◽  
Author(s):  
Yanjue Wu ◽  
Jean-Philippe Richard ◽  
Shervin D. Wang ◽  
Prakash Rath ◽  
John Laterra ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Glioblastoma Multiforme ◽  
Dna Binding ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Inhibitor Of Dna Binding

scholarly journals Photoaffinity labeling of transcription factors by DNA-templated crosslinking

2015 ◽  
Vol 6 (1) ◽  
pp. 745-751 ◽  
Author(s):  
Ying Liu ◽  
Wenlu Zheng ◽  
Wan Zhang ◽  
Nan Chen ◽  
Yang Liu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Binding Site ◽  
Binding Proteins ◽  
Photoaffinity Labeling ◽  
Dna Binding Proteins ◽  
Probe System ◽  
Dual Probe

A dual-probe system can specifically capture DNA-binding proteins with an unmodified binding site.

scholarly journals Regulation of Transcription by Hypoxia Requires a Multiprotein Complex That Includes Hypoxia-Inducible Factor 1, an Adjacent Transcription Factor, and p300/CREB Binding Protein

1998 ◽  
Vol 18 (7) ◽  
pp. 4089-4096 ◽  
Author(s):  
Benjamin L. Ebert ◽  
H. Franklin Bunn
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Dna Binding ◽  
Binding Proteins ◽  
Binding Protein ◽  
Hypoxia Inducible Factor ◽  
Dna Binding Proteins ◽  
Creb Binding Protein ◽  
Multiprotein Complex ◽  
Hypoxia Inducible Factor 1

ABSTRACT Molecular adaptation to hypoxia depends on the binding of hypoxia-inducible factor 1 (HIF-1) to cognate response elements in oxygen-regulated genes. In addition, adjacent sequences are required for hypoxia-inducible transcription. To investigate the mechanism of interaction between these cis-acting sequences, the multiprotein complex binding to the lactate dehydrogenase A (LDH-A) promoter was characterized. The involvement of HIF-1, CREB-1/ATF-1, and p300/CREB binding protein (CBP) was demonstrated by techniques documenting in vitro binding, in combination with transient transfections that test the in vivo functional importance of each protein. In both the LDH-A promoter and the erythropoietin 3′ enhancer, formation of multiprotein complexes was analyzed by using biotinylated probes encompassing functionally critical cis-acting sequences. Strong binding of p300/CBP required interactions with multiple DNA binding proteins. Thus, the necessity of transcription factor binding sites adjacent to a HIF-1 site for hypoxically inducible transcription may be due to the requirement of p300 to interact with multiple transcription factors for high-affinity binding and activation of transcription. Since it has been found to interact with a wide range of transcription factors, p300 is likely to play a similar role in other genes, mediating interactions between DNA binding proteins, thereby activating stimulus-specific and tissue-specific gene transcription.

scholarly journals Natural selection driven by DNA binding proteins shapes genome-wide motif statistics

2016 ◽  
Author(s):  
Long Qian ◽  
Edo Kussell
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Large Collection ◽  
Functional Sites ◽  
Genome Wide ◽  
A Genome ◽  
Global Selection

AbstractEctopic DNA binding by transcription factors and other DNA binding proteins can be detrimental to cellular functions and ultimately to organismal fitness. The frequency of protein-DNA binding at non-functional sites depends on the global composition of a genome with respect to all possible short motifs, or k-mer words. To determine whether weak yet ubiquitous protein-DNA interactions could exert significant evolutionary pressures on genomes, we correlate in vitro measurements of binding strengths on all 8-mer words from a large collection of transcription factors, in several different species, against their relative genomic frequencies. Our analysis reveals a clear signal of purifying selection to reduce the large number of weak binding sites genome-wide. This evolutionary process, which we call global selection, has a detectable hallmark in that similar words experience similar evolutionary pressure, a consequence of the biophysics of protein-DNA binding. By analyzing a large collection of genomes, we show that global selection exists in all domains of life, and operates through tiny selective steps, maintaining genomic binding landscapes over long evolutionary timescales.

Affinity Selection of DNA-Binding Proteins from Yeast Genomic DNA Libraries by Improved   Phage Display Vector

2002 ◽  
Vol 132 (6) ◽  
pp. 975-982 ◽  
Author(s):  
H. Hagiwara ◽  
S. Kunihiro ◽  
K. Nakajima ◽  
M. Sano ◽  
H. Masaki ◽  
...  
Keyword(s):  
Dna Binding ◽  
Phage Display ◽  
Genomic Dna ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Affinity Selection ◽  
Dna Libraries ◽  
Selection Of

Degradation of constitutive transcription factors during apoptosis in rat thymocytes

1994 ◽  
Vol 72 (11-12) ◽  
pp. 639-648 ◽  
Author(s):  
Ian de Belle ◽  
Lucia Testolin ◽  
Siyaram Pandey ◽  
Christine Carson ◽  
P. Roy Walker ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Dna Binding ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Binding Activity ◽  
Significant Loss ◽  
Dna Binding Activity ◽  
The Stability ◽  
Induced Apoptosis

Dexamethasone (Dex) accelerates the rate of apoptosis in thymocytes by a process thought to require gene expression. Among the genes implicated in the regulation of this phenomenon are the immediate early genes such as c-fos and c-jun, whose expression is modulated by a complement of preexisting transcription factors. We have analyzed the DNA-binding activity of these constitutive transcription factors during Dex-induced apoptosis in thymocytes to assess their functionality. We observed a progressive loss of the DNA-binding proteins in parallel with the appearance of the characteristic morphological and biochemical features of apoptosis. At the same time we have found a general increase in the nuclear proteolytic activity concomitant with a significant loss of the nuclear nonhistone chromosomal proteins. Indeed, cotreatment of thymocytes with the nonspecific serine protease inhibitor phenyl-methylsulphonyl fluoride was able to partially protect the stability of the DNA-binding proteins and alter the expression of the c-fos and c-jun genes but did not inhibit apoptosis. Our results suggest that the action of a protease(s) is responsible for the degradation of constitutive transcription factors during Dex-induced apoptosis, rendering the death pathway irreversible.Key words: apoptosis, thymocytes, proteolysis, transcription factors, gene expression.

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