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Related Concept Videos

Transcription Factors02:16

Transcription Factors

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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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Transcription Factors02:16

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General Transcription Factors01:30

General Transcription Factors

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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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Histone Modification02:32

Histone Modification

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The histone proteins have a flexible N-terminal tail extending out from the nucleosome. These histone tails are often subjected to post-translational modifications such as acetylation, methylation, phosphorylation, and ubiquitination. Particular combinations of these modifications form “histone codes” that influence the chromatin folding and tissue-specific gene expression.
Acetylation
The enzyme histone acetyltransferase adds acetyl group to the histones. Another enzyme, histone...
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Histone Modification02:32

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Co-activators and Co-repressors02:04

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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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Updated: Apr 24, 2026

Enhanced Yeast One-hybrid Screens To Identify Transcription Factor Binding To Human DNA Sequences
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Transcription factor binding predicts histone modifications in human cell lines.

Dan Benveniste1, Hans-Joachim Sonntag2, Guido Sanguinetti3

  • 1School of Informatics, University of Edinburgh, Edinburgh EH8 9AB, United Kingdom;

Proceedings of the National Academy of Sciences of the United States of America
|September 5, 2014
PubMed
Summary

Transcription factor binding accurately predicts histone modifications, surpassing DNA sequence analysis. This finding suggests gene expression links to histone marks may be indirect, mediated by transcription factors.

Keywords:
epigeneticsgene regulation

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Area of Science:

  • Genomics
  • Epigenetics
  • Computational Biology

Background:

  • Gene expression regulation involves transcription factors and chromatin modifications.
  • The relative contribution of these factors is debated.
  • Understanding this interplay is crucial for deciphering gene regulation.

Purpose of the Study:

  • To assess the predictive power of transcription factor binding on histone modifications.
  • To compare this predictive power against DNA sequence information.
  • To investigate the role of transcription factors in mediating gene expression changes.

Main Methods:

  • Utilized a computational approach to predict histone modifications.
  • Input features included transcription factor binding sites (TFBS) at promoters and distal elements.
  • Compared prediction accuracy using TFBS versus DNA sequence data.

Main Results:

  • Transcription factor binding accurately predicts histone modifications.
  • This prediction accuracy significantly exceeds that of DNA sequence.
  • Predictions remained accurate across different cell lines.
  • Analysis revealed known transcription factor-histone modifier interactions.

Conclusions:

  • Transcription factor binding is a strong predictor of histone modifications.
  • Histone modification-gene expression associations may be indirect, mediated by transcription factors.
  • Computational models can effectively elucidate gene regulatory mechanisms.