scholarly journals Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors

2009 ◽  
Vol 4 (3) ◽  
pp. 393-411 ◽  
Author(s):  
Michael F Berger ◽  
Martha L Bulyk
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Protein Binding ◽  
Protein Binding Microarrays ◽  
Comprehensive Characterization ◽  
Universal Protein

scholarly journals Improved protein-binding microarrays for the identification of DNA-binding specificities of transcription factors

2011 ◽  
Vol 66 (4) ◽  
pp. 700-711 ◽  
Author(s):  
Marta Godoy ◽  
José M. Franco-Zorrilla ◽  
Julián Pérez-Pérez ◽  
Juan C. Oliveros ◽  
Óscar Lorenzo ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Protein Binding ◽  
Protein Binding Microarrays

scholarly journals Functional analysis of the endothelial cell-specific Tie2/Tek promoter identifies unique protein-binding elements

1998 ◽  
Vol 330 (1) ◽  
pp. 335-343 ◽  
Author(s):  
M. Bahaa FADEL ◽  
C. Stephane BOUTET ◽  
Thomas QUERTERMOUS
Keyword(s):  
Gene Expression ◽  
Endothelial Cell ◽  
Dna Binding ◽  
Protein Binding ◽  
Dna Sequences ◽  
Molecular Basis ◽  
Proximal Promoter ◽  
Specific Gene ◽  
Specific Gene Expression

To investigate the molecular basis of endothelial cell-specific gene expression, we have examined the DNA sequences and the cognate DNA-binding proteins that mediate transcription of the murine tie2/tek gene. Reporter transfection experiments conformed with earlier findings in transgenic mice, indicating that the upstream promoter of Tie2/Tek is capable of activating transcription in an endothelial cell-specific fashion. These experiments have also allowed the identification of a single upstream inhibitory region (region I) and two positive regulatory regions (regions U and A) in the proximal promoter. Electrophoretic mobility-shift assays have allowed further characterization of three novel DNA-binding sequences associated with these regions and have provided preliminary characterization of the protein factors binding to these elements. Two of the elements (U and A) confer increased transcription on a heterologous promoter, with element U functioning in an endothelial-cell-selective manner. By employing embryonic endothelial-like yolk sac cells in parallel with adult-derived endothelial cells, we have identified differences in functional activity and protein binding that may reflect mechanisms for specifying developmental regulation of tie2/tek expression. Further study of the DNA and protein elements characterized in these experiments is likely to provide new insight into the molecular basis of developmental- and cell-specific gene expression in the endothelium.

scholarly journals VOZ; Isolation and Characterization of Novel Vascular Plant Transcription Factors with a One-Zinc Finger from Arabidopsis thaliana

2004 ◽  
Vol 45 (7) ◽  
pp. 845-854 ◽  
Author(s):  
Nobutaka Mitsuda ◽  
Toru Hisabori ◽  
Kunio Takeyasu ◽  
Masa H. Sato
Keyword(s):  
Arabidopsis Thaliana ◽  
Transcription Factors ◽  
Dna Binding ◽  
Physcomitrella Patens ◽  
Cultured Cells ◽  
Vascular Plant ◽  
Amino Acid Sequence Similarity ◽  
Cis Acting ◽  
Isolation And Characterization

Abstract A 38-bp pollen-specific cis-acting region of the AVP1 gene is involved in the expression of the Arabidopsis thaliana V-PPase during pollen development. Here, we report the isolation and structural characterization of AtVOZ1 and AtVOZ2, novel transcription factors that bind to the 38-bp cis-acting region of A. thaliana V-PPase gene, AVP1. AtVOZ1 and AtVOZ2 show 53% amino acid sequence similarity. Homologs of AtVOZ1 and AtVOZ2 are found in various vascular plants as well as a moss, Physcomitrella patens. Promoter-β-glucuronidase reporter analysis shows that AtVOZ1 is specifically expressed in the phloem tissue and AtVOZ2 is strongly expressed in the root. In vivo transient effector-reporter analysis in A. thaliana suspension-cultured cells demonstrates that AtVOZ1 and AtVOZ2 function as transcriptional activators in the Arabidopsis cell. Two conserved regions termed Domain-A and Domain-B were identified from an alignment of AtVOZ proteins and their homologs of O. sativa and P. patens. AtVOZ2 binds as a dimer to the specific palindromic sequence, GCGTNx7ACGC, with Domain-B, which is comprised of a functional novel zinc coordinating motif and a conserved basic region. Domain-B is shown to function as both the DNA-binding and the dimerization domains of AtVOZ2. From highly the conservative nature among all identified VOZ proteins, we conclude that Domain-B is responsible for the DNA binding and dimerization of all VOZ-family proteins and designate it as the VOZ-domain.

scholarly journals MotifMark: Finding Regulatory Motifs in DNA Sequences

2017 ◽  
Author(s):  
Hamid Reza Hassanzadeh ◽  
Pushkar Kolhe ◽  
Charles L. Isbell ◽  
May D. Wang
Keyword(s):  
Protein Binding ◽  
High Throughput ◽  
Dna Sequences ◽  
Binding Sites ◽  
Biological Activities ◽  
Inaccurate Data ◽  
Dna Binding Sites ◽  
Protein Binding Microarrays ◽  
Downstream Analysis

AbstractThe interaction between proteins and DNA is a key driving force in a significant number of biological processes such as transcriptional regulation, repair, recombination, splicing, and DNA modification. The identification of DNA-binding sites and the specificity of target proteins in binding to these regions are two important steps in understanding the mechanisms of these biological activities. A number of high-throughput technologies have recently emerged that try to quantify the affinity between proteins and DNA motifs. Despite their success, these technologies have their own limitations and fall short in precise characterization of motifs, and as a result, require further downstream analysis to extract useful and interpretable information from a haystack of noisy and inaccurate data. Here we propose MotifMark, a new algorithm based on graph theory and machine learning, that can find binding sites on candidate probes and rank their specificity in regard to the underlying transcription factor. We developed a pipeline to analyze experimental data derived from compact universal protein binding microarrays and benchmarked it against two of the most accurate motif search methods. Our results indicate that MotifMark can be a viable alternative technique for prediction of motif from protein binding microarrays and possibly other related high-throughput techniques.

scholarly journals Principles of dimer-specific gene regulation revealed by a comprehensive characterization of NF-κB family DNA binding

2011 ◽  
Vol 13 (1) ◽  
pp. 95-102 ◽  
Author(s):  
Trevor Siggers ◽  
Abraham B Chang ◽  
Ana Teixeira ◽  
Daniel Wong ◽  
Kevin J Williams ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Dna Binding ◽  
Specific Gene ◽  
Comprehensive Characterization

scholarly journals A Rice Promoter Protein Binding Microarray for Cis-Acting Elements for Rice Transcription Factors

2020 ◽  
Author(s):  
JOUNG SUG KIM ◽  
SongHwa Chae ◽  
Kyong Mi Jun ◽  
Gang-Seob Lee ◽  
Jong-Seong Jeon ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Protein Binding ◽  
Target Genes ◽  
Specific Protein ◽  
Transcriptional Level ◽  
Binding Motifs ◽  
Putative Target ◽  
Protein Binding Microarray ◽  
Dna Binding Motifs

Abstract BackgroundTranscription factors (TFs) regulate the expression of genes at the transcriptional level by binding a specific DNA sequence. Thus, predicting the DNA-binding motifs of TFs is one of the most important areas for the functional analysis of TFs in the postgenomic era. Although many methods have been developed for this challenge, there are still many TFs with unknown DNA-binding motifs.FindingsIn this paper, we designed an rice (Oryza sativa)-specific protein binding microarray (RPBM), and its probes are 40 bp long with 20 bp of overlap; there are 49 probes spanning the 1 kb promoter region before the translation start site of each gene. To confirm the efficiency of RPBM technology, we selected two TFs, OsWOX13 and OsSMF1. We identified the ATTGATTG DNA-binding sequence and 635 putative target genes of OsWOX13. OsSMF1 bound to GCTGACTCA and GGATGCC sequences and bound especially strongly to CCACGTCA. A total of 932 putative target genes were identified for OsSMF1.ConclusionsRPBM can be applicable in the analysis of DNA-binding motifs for TFs where binding is evaluated in extended natural promoter regions. The analysis can also be applicable to TFs that have single or multiple binding motifs. The technology might even be expanded for application to TFs that are heterodimers or form higher-order complexes.

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