scholarly journals Role of intrinsic DNA binding specificity in defining target genes of the mammalian transcription factor PDX1

2004 ◽  
Vol 32 (1) ◽  
pp. 54-64 ◽  
Author(s):  
A. Liberzon
Keyword(s):  
Transcription Factor ◽  
Dna Binding ◽  
Target Genes ◽  
Binding Specificity ◽  
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.

scholarly journals Origins of DNA-binding specificity: Role of protein contacts with the DNA backbone

1999 ◽  
Vol 96 (3) ◽  
pp. 811-817 ◽  
Author(s):  
J. F. Schildbach ◽  
A. W. Karzai ◽  
B. E. Raumann ◽  
R. T. Sauer
Keyword(s):  
Dna Binding ◽  
Binding Specificity ◽  
Dna Binding Specificity ◽  
Dna Backbone

DNA binding specificity of cardiac transcription factor complex GATA4 and NKX2‐5

2020 ◽  
Vol 34 (S1) ◽  
pp. 1-1
Author(s):  
Jessica Marie Rodriguez Rios ◽  
Emili Patricia Rosado Rodríguez ◽  
José Arcadio Rodríguez Martínez
Keyword(s):  
Transcription Factor ◽  
Dna Binding ◽  
Binding Specificity ◽  
Dna Binding Specificity ◽  
Transcription Factor Complex

scholarly journals The Role of DNA-binding Specificity in the Evolution of Bacterial Regulatory Networks

2008 ◽  
Vol 379 (3) ◽  
pp. 627-643 ◽  
Author(s):  
Irma Lozada-Chávez ◽  
Vladimir Espinosa Angarica ◽  
Julio Collado-Vides ◽  
Bruno Contreras-Moreira
Keyword(s):  
Dna Binding ◽  
Regulatory Networks ◽  
Binding Specificity ◽  
Dna Binding Specificity

scholarly journals Determinants of DNA-binding specificity of ETS-domain transcription factors.

1996 ◽  
Vol 16 (7) ◽  
pp. 3338-3349 ◽  
Author(s):  
P Shore ◽  
A J Whitmarsh ◽  
R Bhaskaran ◽  
R J Davis ◽  
J P Waltho ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Dna Binding ◽  
Serum Response Factor ◽  
Binding Specificity ◽  
Mitogen Activated Protein Kinase ◽  
Critical Determinant ◽  
Binding Interface ◽  
Dna Binding Specificity ◽  
Mitogen Activated Protein ◽  
Ets Domain

Several mechanisms are employed by members of transcription factor families to achieve sequence-specific DNA recognition. In this study, we have investigated how members of the ETS-domain transcription factor family achieve such specificity. We have used the ternary complex factor (TCF) subfamily as an example. ERK2 mitogen-activated protein kinase stimulates serum response factor-dependent and autonomous DNA binding by the TCFs Elk-1 and SAP-la. Phosphorylated Elk-1 and SAP-la exhibit specificities of DNA binding similar to those of their isolated ETS domains. The ETS domains of Elk-1 and SAP-la and SAP-2 exhibit related but distinct DNA-binding specificities. A single residue, D-69 (Elk-1) or V-68 (SAP-1), has been identified as the critical determinant for the differential binding specificities of Elk-1 and SAP-1a, and an additional residue, D-38 (Elk-1) or Q-37 (SAP-1), further modulates their DNA binding. Creation of mutations D38Q and D69V is sufficient to confer SAP-la DNA-binding specificity upon Elk-1 and thereby allow it to bind to a greater spectrum of sites. Molecular modelling indicates that these two residues (D-38 and D-69) are located away from the DNA-binding interface of Elk-1. Our data suggest a mechanism in which these residues modulate DNA binding by influencing the interaction of other residues with DNA.

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