71 Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape

ABSTRACT For a particular functional family of basic helix-loop-helix (bHLH) transcription factors, there is ample evidence that different factors regulate different target genes but little idea of how these different target genes are distinguished. We investigated the contribution of DNA binding site differences to the specificities of two functionally related proneural bHLH transcription factors required for the genesis of Drosophila sense organ precursors (Atonal and Scute). We show that the proneural target gene, Bearded, is regulated by both Scute and Atonal via distinct E-box consensus binding sites. By comparing with other Ato-dependent enhancer sequences, we define an Ato-specific binding consensus that differs from the previously defined Scute-specific E-box consensus, thereby defining distinct EAto and ESc sites. These E-box variants are crucial for function. First, tandem repeats of 20-bp sequences containing EAto and ESc sites are sufficient to confer Atonal- and Scute-specific expression patterns, respectively, on a reporter gene in vivo. Second, interchanging EAto and ESc sites within enhancers almost abolishes enhancer activity. While the latter finding shows that enhancer context is also important in defining how proneural proteins interact with these sites, it is clear that differential utilization of DNA binding sites underlies proneural protein specificity.

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

Journal of Endocrinology ◽

10.1530/joe-11-0010 ◽

2011 ◽

Vol 210 (1) ◽

pp. 15-27 ◽

Cited By ~ 20

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).

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DNA-binding specificity of GATA family transcription factors.

Molecular and Cellular Biology ◽

10.1128/mcb.13.7.3999 ◽

1993 ◽

Vol 13 (7) ◽

pp. 3999-4010 ◽

Cited By ~ 448

Author(s):

M Merika ◽

S H Orkin

Keyword(s):

Transcription Factors ◽

Dna Binding ◽

Mammalian Cells ◽

Chimeric Protein ◽

Binding Specificity ◽

Mobility Shift ◽

Binding Domains ◽

Dna Binding Specificity ◽

Mobility Shift Assay ◽

Gata Family

GATA-binding proteins constitute a family of transcription factors that recognize a target site conforming to the consensus WGATAR (W = A or T and R = A or G). Here we have used the method of polymerase chain reaction-mediated random site selection to assess in an unbiased manner the DNA-binding specificity of GATA proteins. Contrary to our expectations, we show that GATA proteins bind a variety of motifs that deviate from the previously assigned consensus. Many of the nonconsensus sequences bind protein with high affinity, equivalent to that of conventional GATA motifs. By using the selected sequences as probes in the electrophoretic mobility shift assay, we demonstrate overlapping, but distinct, sequence preferences for GATA family members, specified by their respective DNA-binding domains. Furthermore, we provide additional evidence for interaction of amino and carboxy fingers of GATA-1 in defining its binding site. By performing cotransfection experiments, we also show that transactivation parallels DNA binding. A chimeric protein containing the finger domain of areA and the activation domains of GATA-1 is capable of activating transcription in mammalian cells through GATA motifs. Our findings suggest a mechanism by which GATA proteins might selectively regulate gene expression in cells in which they are coexpressed.

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DNA-binding specificity and molecular functions of NAC transcription factors

Plant Science ◽

10.1016/j.plantsci.2005.05.035 ◽

2005 ◽

Vol 169 (4) ◽

pp. 785-797 ◽

Cited By ~ 104

Author(s):

Addie N. Olsen ◽

Heidi A. Ernst ◽

Leila Lo Leggio ◽

Karen Skriver

Keyword(s):

Transcription Factors ◽

Dna Binding ◽

Binding Specificity ◽

Nac Transcription Factors ◽

Dna Binding Specificity ◽

Molecular Functions

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DNA binding by MADS-box transcription factors: a molecular mechanism for differential DNA bending.

Molecular and Cellular Biology ◽

10.1128/mcb.17.5.2876 ◽

1997 ◽

Vol 17 (5) ◽

pp. 2876-2887 ◽

Cited By ~ 59

Author(s):

A G West ◽

P Shore ◽

A D Sharrocks

Keyword(s):

Transcription Factors ◽

Dna Binding ◽

Serum Response Factor ◽

Dna Bending ◽

Binding Specificity ◽

Single Amino Acid ◽

Specific Gene ◽

Mads Box ◽

Dna Binding Specificity ◽

Single Amino Acid Residue

The serum response factor (SRF) and myocyte enhancer factor 2A (MEF2A) represent two human members of the MADS-box transcription factor family. Each protein has a distinct biological function which is reflected by the distinct specificities of the proteins for coregulatory protein partners and DNA-binding sites. In this study, we have investigated the mechanism of DNA binding utilized by these two related transcription factors. Although SRF and MEF2A belong to the same family and contain related DNA-binding domains, their DNA-binding mechanisms differ in several key aspects. In contrast to the dramatic DNA bending induced by SRF, MEF2A induces minimal DNA distortion. A combination of loss- and gain-of-function mutagenesis identified a single amino acid residue located at the N terminus of the recognition helices as the critical mediator of this differential DNA bending. This residue is also involved in determining DNA-binding specificity, thus indicating a link between DNA bending and DNA-binding specificity determination. Furthermore, different basic residues within the putative recognition alpha-helices are critical for DNA binding, and the role of the C-terminal extensions to the MADS box in dimerization between SRF and MEF2A also differs. These important differences in the molecular interactions of SRF and MEF2A are likely to contribute to their differing roles in the regulation of specific gene transcription.

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Correlated Evolutionary Pressure at Interacting Transcription Factors and DNA Response Elements Can Guide the Rational Engineering of DNA Binding Specificity

Journal of Molecular Biology ◽

10.1016/j.jmb.2005.04.054 ◽

2005 ◽

Vol 350 (3) ◽

pp. 402-415 ◽

Cited By ~ 21

Author(s):

Michele Raviscioni ◽

Peili Gu ◽

Minawar Sattar ◽

Austin J. Cooney ◽

Olivier Lichtarge

Keyword(s):

Transcription Factors ◽

Dna Binding ◽

Binding Specificity ◽

Response Elements ◽

Rational Engineering ◽

Dna Binding Specificity

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Structural determinants of DNA recognition by plant MADS-domain transcription factors

Nucleic Acids Research ◽

10.1093/nar/gkt1172 ◽

2013 ◽

Vol 42 (4) ◽

pp. 2138-2146 ◽

Cited By ~ 21

Author(s):

Jose M. Muiño ◽

Cezary Smaczniak ◽

Gerco C. Angenent ◽

Kerstin Kaufmann ◽

Aalt D.J. van Dijk

Keyword(s):

Transcription Factors ◽

Dna Binding ◽

Binding Site ◽

Structural Characteristics ◽

Binding Specificity ◽

Structural Motif ◽

Dna Binding Specificity ◽

Dna Binding Site ◽

Carg Box

Abstract Plant MADS-domain transcription factors act as key regulators of many developmental processes. Despite the wealth of information that exists about these factors, the mechanisms by which they recognize their cognate DNA-binding site, called CArG-box (consensus CCW6GG), and how different MADS-domain proteins achieve DNA-binding specificity, are still largely unknown. We used information from in vivo ChIP-seq experiments, in vitro DNA-binding data and evolutionary conservation to address these important questions. We found that structural characteristics of the DNA play an important role in the DNA binding of plant MADS-domain proteins. The central region of the CArG-box largely resembles a structural motif called ‘A-tract’, which is characterized by a narrow minor groove and may assist bending of the DNA by MADS-domain proteins. Periodically spaced A-tracts outside the CArG-box suggest additional roles for this structure in the process of DNA binding of these transcription factors. Structural characteristics of the CArG-box not only play an important role in DNA-binding site recognition of MADS-domain proteins, but also partly explain differences in DNA-binding specificity of different members of this transcription factor family and their heteromeric complexes.

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