scholarly journals Differences in DNA Binding Specificity of Floral Homeotic Protein Complexes Predict Organ-Specific Target Genes

2017 ◽  
Vol 29 (8) ◽  
pp. 1822-1835 ◽  
Author(s):  
Cezary Smaczniak ◽  
Jose M. Muiño ◽  
Dijun Chen ◽  
Gerco C. Angenent ◽  
Kerstin Kaufmann
Keyword(s):  
Dna Binding ◽  
Target Genes ◽  
Protein Complexes ◽  
Binding Specificity ◽  
Specific Target ◽  
Dna Binding Specificity ◽  
Organ Specific ◽  
Floral Homeotic

scholarly journals In vitro DNA-binding profile of transcription factors: methods and new insights

2011 ◽  
Vol 210 (1) ◽  
pp. 15-27 ◽  
Author(s):  
Jinke Wang ◽  
Jie Lu ◽  
Guangming Gu ◽  
Yingxun Liu
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Dna Sequences ◽  
Binding Sites ◽  
Target Genes ◽  
Binding Specificity ◽  
Cell Physiology ◽  
Binding Profile ◽  
Dna Binding Specificity

The DNA-binding specificity of transcription factors (TFs) has broad impacts on cell physiology, cell development and in evolution. However, the DNA-binding specificity of most known TFs still remains unknown. The specificity of a TF protein is determined by its relative affinity to all possible binding sites. In recent years, the development of several in vitro techniques permits high-throughput determination of relative binding affinity of a TF to all possible k bp-long DNA sequences, thus greatly promoting the characterization of DNA-binding specificity of many known TFs. All DNA sequences that can be bound by a TF with various binding affinities form their DNA-binding profile (DBP). The DBP is important to generate an accurate DNA-binding model, identify all DNA-binding sites and target genes of TFs in the whole genome, and build transcription regulatory network. This study reviewed these techniques, especially two master techniques: double-stranded DNA microarray and systematic evolution of ligands by exponential enrichment in combination with parallel DNA sequencing techniques (SELEX-seq).

scholarly journals Binding of the Vestigial co-factor switches the DNA-target selectivity of the Scalloped selector protein

Development ◽  
2001 ◽  
Vol 128 (17) ◽  
pp. 3295-3305 ◽  
Author(s):  
Georg Halder ◽  
Sean B. Carroll
Keyword(s):  
Dna Binding ◽  
Target Genes ◽  
Binding Specificity ◽  
General Mechanism ◽  
Binding Selectivity ◽  
Binding Domains ◽  
Dna Binding Specificity ◽  
Selector Protein

The formation and identity of organs and appendages are regulated by specific selector genes that encode transcription factors that regulate potentially large sets of target genes. The DNA-binding domains of selector proteins often exhibit relatively low DNA-binding specificity in vitro. It is not understood how the target selectivity of most selector proteins is determined in vivo. The Scalloped selector protein controls wing development in Drosophila by regulating the expression of numerous target genes and forming a complex with the Vestigial protein. We show that binding of Vestigial to Scalloped switches the DNA-binding selectivity of Scalloped. Two conserved domains of the Vestigial protein that are not required for Scalloped binding in solution are required for the formation of the heterotetrameric Vestigial-Scalloped complex on DNA. We suggest that Vestigial affects the conformation of Scalloped to create a wing cell-specific DNA-binding selectivity. The modification of selector protein DNA-binding specificity by co-factors appears to be a general mechanism for regulating their target selectivity in vivo.

scholarly journals Identification of the DNA Binding Specificity and Potential Target Genes for the Farnesoid X-activated Receptor

2000 ◽  
Vol 275 (14) ◽  
pp. 10638-10647 ◽  
Author(s):  
Bryan A. Laffitte ◽  
Heidi Rachelle Kast ◽  
Catherine M. Nguyen ◽  
Ann Marie Zavacki ◽  
David D. Moore ◽  
...  
Keyword(s):  
Dna Binding ◽  
Target Genes ◽  
Binding Specificity ◽  
Potential Target ◽  
Dna Binding Specificity

scholarly journals Role of the PAS Domain in Regulation of Dimerization and DNA Binding Specificity of the Dioxin Receptor

1998 ◽  
Vol 18 (7) ◽  
pp. 4079-4088 ◽  
Author(s):  
Ingemar Pongratz ◽  
Camilla Antonsson ◽  
Murray L. Whitelaw ◽  
Lorenz Poellinger
Keyword(s):  
Dna Binding ◽  
Target Genes ◽  
Binding Specificity ◽  
Pas Domain ◽  
Bhlh Domain ◽  
Dna Binding Specificity ◽  
Dioxin Receptor

ABSTRACT The dioxin receptor is a ligand-regulated transcription factor that mediates signal transduction by dioxin and related environmental pollutants. The receptor belongs to the basic helix-loop-helix (bHLH)–Per-Arnt-Sim (PAS) family of factors, which, in addition to the bHLH motif, contain a PAS region of homology. Upon activation, the dioxin receptor dimerizes with the bHLH-PAS factor Arnt, enabling the receptor to recognize xenobiotic response elements in the vicinity of target genes. We have studied the role of the PAS domain in dimerization and DNA binding specificity of the dioxin receptor and Arnt by monitoring the abilities of the individual bHLH domains and different bHLH-PAS fragments to dimerize and bind DNA in vitro and recognize target genes in vivo. The minimal bHLH domain of the dioxin receptor formed homodimeric complexes, heterodimerized with full-length Arnt, and together with Arnt was sufficient for recognition of target DNA in vitro and in vivo. In a similar fashion, only the bHLH domain of Arnt was necessary for DNA binding specificity in the presence of the dioxin receptor bHLH domain. Moreover, the bHLH domain of the dioxin receptor displayed a broad dimerization potential, as manifested by complex formation with, e.g., the unrelated bHLH-Zip transcription factor USF. In contrast, a construct spanning the dioxin receptor bHLH domain and an N-terminal portion of the PAS domain failed to form homodimers and was capable of dimerizing only with Arnt. Thus, the PAS domain is essential to confer dimerization specificity of the dioxin receptor.

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