Identification of novel protein/DNA interactions within the promoter of the bone-related transcription factor Runx2/Cbfa1

2002 ◽  
Vol 86 (2) ◽  
pp. 403-412 ◽  
Author(s):  
Hicham Drissi ◽  
Arlyssa Pouliot ◽  
Janet L. Stein ◽  
Andre J. van Wijnen ◽  
Gary S. Stein ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Dna Interactions ◽  
Protein Dna Interactions ◽  
Related Transcription Factor ◽  
Novel Protein

scholarly journals Molecular dynamics studies on the DNA-binding process of ERG

2016 ◽  
Vol 12 (12) ◽  
pp. 3600-3610 ◽  
Author(s):  
Matthias G. Beuerle ◽  
Neil P. Dufton ◽  
Anna M. Randi ◽  
Ian R. Gould
Keyword(s):  
Molecular Dynamics ◽  
Transcription Factor ◽  
Dna Binding ◽  
Sequence Specificity ◽  
Dna Interactions ◽  
Binding Process ◽  
Protein Dna Interactions

Molecular dynamics study elucidating the mechanistic background of the DNA-binding process and the sequence specificity of the transcription factor ERG. Along with the biological findings the capabilities of unbiased DNA-binding simulations in combination with various means of analysis in the field of protein DNA-interactions are shown.

Ets Domain Transcription Factor PE1 Suppresses Human Interstitial Collagenase Promoter Activity by Antagonizing Protein−DNA Interactions at a Critical AP1 Element†

Biochemistry ◽  
2000 ◽  
Vol 39 (30) ◽  
pp. 8917-8928 ◽  
Author(s):  
Miri Bidder ◽  
Arleen P. Loewy ◽  
Tammy Latifi ◽  
Elizabeth P. Newberry ◽  
Glenda Ferguson ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Promoter Activity ◽  
Dna Interactions ◽  
Protein Dna Interactions ◽  
Ets Domain ◽  
Interstitial Collagenase

Tilling the chromatin landscape: emerging methods for the discovery and profiling of protein–DNA interactions

2005 ◽  
Vol 83 (4) ◽  
pp. 525-534 ◽  
Author(s):  
Benjamin A.T Rodriguez ◽  
Tim H.-M Huang
Keyword(s):  
Transcription Factor ◽  
Histone Modification ◽  
Transcription Factor Binding ◽  
Dna Interactions ◽  
Factor Binding ◽  
Protein Dna Interactions ◽  
Chromatin Profiling ◽  
Chip Chip

Interactions between protein and DNA are essential for cellular function. The incremental process of developing global approaches to study chromatin began with the in vitro characterization of chromatin structural components and modifications of the versatile chromatin immunoprecipitation (ChIP) assay, capable of analyzing protein–DNA interactions in vivo. Among the emerging global approaches are ChIP cloning, ChIP display, differential chromatin scanning, ChIP–chip, DamID chromatin profiling, and chromatin array. These methods have been used to assess transcription-factor binding and (or) histone modification. This review describes these global methods and illustrates their potential in answering biological questions.Key words: ChIP, transcription factor binding, histone modification, ChIP display, differential chromatin scanning, ChIP-chip, DamID chromatin profiling, chromatin array.

scholarly journals Assembly of the Hap2p/Hap3p/Hap4p/Hap5p-DNA Complex in Saccharomyces cerevisiae

2005 ◽  
Vol 4 (11) ◽  
pp. 1829-1839 ◽  
Author(s):  
David S. McNabb ◽  
Inés Pinto
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Transcription Factor ◽  
Dna Binding ◽  
Transcriptional Activation ◽  
Target Genes ◽  
Dna Interactions ◽  
Activation Domain ◽  
Binding Factor ◽  
Protein Dna Interactions ◽  
Dna Complex

ABSTRACT The CCAAT-binding factor (CBF) is an evolutionarily conserved multimeric transcriptional activator in eukaryotes. In Saccharomyces cerevisiae, the CCAAT-binding factor is composed of four subunits, termed Hap2p, Hap3p, Hap4p, and Hap5p. The Hap2p/Hap3p/Hap5p heterotrimer is the DNA-binding component of the complex that binds to the consensus 5′-CCAAT-3′ sequence in the promoter of target genes. The Hap4p subunit contains the transcriptional activation domain necessary for stimulating transcription after interacting with Hap2p/Hap3p/Hap5p. In this report, we demonstrate that Hap2p, Hap3p, and Hap5p assemble via a one-step pathway requiring all three subunits simultaneously, as opposed to the mammalian CCAAT-binding factor which has been shown to assemble via a two-step pathway with CBF-A (Hap3p homolog) and CBF-C (Hap5p homolog) forming a stable dimer before CBF-B (Hap2p homolog) can interact. We have also found that the interaction of Hap4p with Hap2p/Hap3p/Hap5p requires DNA binding as a prerequisite. To further understand the protein-protein and protein-DNA interactions of this transcription factor, we identified the minimal domain of Hap4p necessary for interaction with the Hap2p/Hap3p/Hap5p-DNA complex, and we demonstrate that this domain is sufficient to complement the respiratory deficiency of a hap4Δ mutant and activate transcription when fused with the VP16 activation domain. These studies provide a further understanding of the assembly of the yeast CCAAT-binding factor at target promoters and raise a number of questions concerning the protein-protein and protein-DNA interactions of this multisubunit transcription factor.

scholarly journals An improved ChEC-seq method accurately maps the genome-wide binding of transcription coactivators and sequence-specific transcription factors

2021 ◽  
Author(s):  
Rafal Donczew ◽  
Amélia Lalou ◽  
Didier Devys ◽  
Laszlo Tora ◽  
Steven Hahn
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Dna Sequence ◽  
Dna Interactions ◽  
Experimental Conditions ◽  
Genome Wide ◽  
Protein Dna Interactions ◽  
Cleavage Step ◽  
Computational Analyses ◽  
Active Genes

AbstractMittal and colleagues have raised questions about mapping transcription factor locations on DNA using the MNase-based ChEC-seq method (Mittal et al., 2021). Partly due to this concern, we modified the experimental conditions of the MNase cleavage step and subsequent computational analyses, resulting in more stringent conditions for mapping protein-DNA interactions (Donczew et al., 2020). The revised method (dx.doi.org/10.17504/protocols.io.bizgkf3w) answers questions raised by Mittal et al. and, without changing earlier conclusions, identified widespread promoter binding of the transcription coactivators TFIID and SAGA at active genes. The revised method is also suitable for accurately mapping the genome-wide locations of DNA sequence-specific transcription factors.

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