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Related Concept Videos

Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

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Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form...
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Transcription Factors02:16

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Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
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Gene transcription is regulated by the synergistic action of several proteins that form a complex at a gene regulatory site. This is observed in eukaryotes, where the regulation of gene expression is a complex process. Regulatory proteins in eukaryotes can broadly be classified into two types – regulators that bind directly to specific DNA sequences and co-regulators that associate with regulatory proteins but cannot directly bind to the DNA. These co-regulators are further divided into...
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Transcription activators are proteins that promote the transcription of genes from DNA to RNA. In most cases, these proteins contain two separate domains ‒ a domain that binds to DNA and a domain for activating transcription; however, in some cases, a single domain is responsible for both binding and activation of transcription, as seen in the glucocorticoid receptor and MyoD.
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General Transcription Factors01:30

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Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
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Related Experiment Video

Updated: Dec 1, 2025

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy
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Transcription Factor Binding Affinities and DNA Shape Readout.

Max Schnepf1, Marc von Reutern1, Claudia Ludwig1

  • 1Gene Center and Department of Biochemistry, Center for Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 München, Germany.

Iscience
|November 9, 2020
PubMed
Summary

Transcription factors (TFs) widely use DNA shape to bind target genes. This study quantines TF-DNA binding affinities, revealing shape readout is crucial for gene regulation.

Keywords:
BiomoleculesMolecular BiologyMolecular Mechanism of Gene Regulation

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Area of Science:

  • Molecular Biology
  • Genetics
  • Bioinformatics

Background:

  • Transcription factor (TF) binding to DNA is vital for gene regulation.
  • DNA geometry influences TF binding, but direct characterization is limited by data availability.
  • Accurate binding affinity data is needed to understand DNA shape's role.

Purpose of the Study:

  • To quantify binding specificities of 13 *Drosophila* TFs using a novel assay.
  • To investigate the contribution of DNA shape to TF binding affinities.
  • To explore amino acid-base interactions and their relation to DNA shape readout.

Main Methods:

  • Established a high-sensitivity binding assay to measure TF-DNA binding specificities.
  • Collected binding affinity data for 13 *Drosophila* TFs, including dinucleotide dependencies.
  • Correlated binding affinities with various DNA shape features.

Main Results:

  • Found that DNA shape readout is a widely utilized mechanism by these TFs.
  • Identified dinucleotide dependencies influencing TF binding specificities.
  • Shape readout/TF-DNA complex structure analysis revealed interactions between charged/polar amino acids and specific DNA shapes.

Conclusions:

  • DNA shape is a significant determinant of transcription factor binding specificity.
  • The developed assay provides a sensitive method for studying TF-DNA interactions.
  • Understanding DNA shape readout offers insights into the mechanisms of gene regulation.