scholarly journals REL Domain of NFATc2 Binding to Five Types of DNA Using Protein Binding Microarrays

ACS Omega ◽  
2021 ◽  
Vol 6 (6) ◽  
pp. 4147-4154
Author(s):  
Sreejana Ray ◽  
Desiree Tillo ◽  
Stewart R. Durell ◽  
Syed Khund-Sayeed ◽  
Charles Vinson
Keyword(s):  
Protein Binding ◽  
Protein Binding Microarrays

scholarly journals Cytokinin induces genome-wide binding of the type-B response regulator ARR10 to regulate growth and development in Arabidopsis

2017 ◽  
Vol 114 (29) ◽  
pp. E5995-E6004 ◽  
Author(s):  
Yan O. Zubo ◽  
Ivory Clabaugh Blakley ◽  
Maria V. Yamburenko ◽  
Jennifer M. Worthen ◽  
Ian H. Street ◽  
...  
Keyword(s):  
Protein Binding ◽  
Binding Sites ◽  
Growth And Development ◽  
Abiotic Factors ◽  
Physiological Responses ◽  
Physiological Role ◽  
Primary Response ◽  
Type B ◽  
Protein Binding Microarrays

The plant hormone cytokinin affects a diverse array of growth and development processes and responses to the environment. How a signaling molecule mediates such a diverse array of outputs and how these response pathways are integrated with other inputs remain fundamental questions in plant biology. To this end, we characterized the transcriptional network initiated by the type-B ARABIDOPSIS RESPONSE REGULATORs (ARRs) that mediate the cytokinin primary response, making use of chromatin immunoprecipitation sequencing (ChIP-seq), protein-binding microarrays, and transcriptomic approaches. By ectopic overexpression of ARR10, Arabidopsis lines hypersensitive to cytokinin were generated and used to clarify the role of cytokinin in regulation of various physiological responses. ChIP-seq was used to identify the cytokinin-dependent targets for ARR10, thereby defining a crucial link between the cytokinin primary-response pathway and the transcriptional changes that mediate physiological responses to this phytohormone. Binding of ARR10 was induced by cytokinin with binding sites enriched toward the transcriptional start sites for both induced and repressed genes. Three type-B ARR DNA-binding motifs, determined by use of protein-binding microarrays, were enriched at ARR10 binding sites, confirming their physiological relevance. WUSCHEL was identified as a direct target of ARR10, with its cytokinin-enhanced expression resulting in enhanced shooting in tissue culture. Results from our analyses shed light on the physiological role of the type-B ARRs in regulating the cytokinin response, mechanism of type-B ARR activation, and basis by which cytokinin regulates diverse aspects of growth and development as well as responses to biotic and abiotic factors.

scholarly journals Integrated approach for the identification of human hepatocyte nuclear factor 4α target genes using protein binding microarrays

Hepatology ◽  
2009 ◽  
Vol 51 (2) ◽  
pp. 642-653 ◽  
Author(s):  
Eugene Bolotin ◽  
Hailing Liao ◽  
Tuong Chi Ta ◽  
Chuhu Yang ◽  
Wendy Hwang-Verslues ◽  
...  
Keyword(s):  
Protein Binding ◽  
Target Genes ◽  
Integrated Approach ◽  
Human Hepatocyte ◽  
Nuclear Factor ◽  
Hepatocyte Nuclear Factor ◽  
Hepatocyte Nuclear Factor 4Α ◽  
Protein Binding Microarrays

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 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.

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