scholarly journals Protein Binding Microarrays for the Characterization of DNA–Protein Interactions

2006 ◽  
pp. 65-85 ◽  
Author(s):  
Martha L. Bulyk
Keyword(s):  
Protein Binding ◽  
Protein Interactions ◽  
Protein Binding Microarrays ◽  
Dna Protein Interactions

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 Genome-wide identification of protein binding sites in mammalian cells

2021 ◽  
Author(s):  
Fenglin Liu ◽  
Tianyu Ma ◽  
Yu-Xiang Zhang
Keyword(s):  
Transcription Factors ◽  
Protein Binding ◽  
Protein Interactions ◽  
Binding Sites ◽  
Mammalian Cells ◽  
Protein Binding Sites ◽  
Genome Wide ◽  
Transcription Binding Sites ◽  
Dna Protein Interactions

AbstractWe present GWPBS-Cap, a method to capture genome-wide protein binding sites (PBSs) without using antibodies. Using this technique, we identified many protein binding sites with different binding strengths between proteins and DNA. The PBSs can be useful to predict transcription binding sites and the co-localization of multiple transcription factors in the genome. The results also revealed that active promoters contained more protein binding sites with lower NaCl tolerances. Taken together, GWPBS-Cap can be used to efficiently identify protein binding sites and reveal genome-wide landscape of DNA-protein interactions.

Single-Molecule Characterization of DNA–Protein Interactions Using Nanopore Biosensors

2017 ◽  
pp. 353-385 ◽  
Author(s):  
A.H. Squires ◽  
T. Gilboa ◽  
C. Torfstein ◽  
N. Varongchayakul ◽  
A. Meller
Keyword(s):  
Single Molecule ◽  
Protein Interactions ◽  
Dna Protein Interactions
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