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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 Elongation Factors02:35

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Transcription elongation is a dynamic process that alters depending upon the sequence heterogeneity of the DNA being transcribed. Hence, it is not surprising that the elongation complex's composition also varies along the way while transcribing a gene.
The transcription elongation is regulated via pausing of RNA polymerase on several occasions during transcription. In bacteria, these halts are necessary because the transcription of DNA into mRNA is coupled to the translation of that mRNA...
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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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From DNA to Protein03:06

From DNA to Protein

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The flow of genetic information in cells from DNA to mRNA to protein is described by the central dogma, which states that genes specify the sequence of mRNAs, which in turn specify the sequence of amino acids making up all proteins. The decoding of one molecule to another is performed by specific proteins and RNAs. Because the information stored in DNA is so central to cellular function, it makes intuitive sense that the cell would make mRNA copies of this information for protein synthesis...
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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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Enhanced Yeast One-hybrid Screens To Identify Transcription Factor Binding To Human DNA Sequences
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Decoding the Inversion Symmetry Underlying Transcription Factor DNA-Binding Specificity and Functionality in the

Laurel A Coons1, Adam B Burkholder2, Sylvia C Hewitt3

  • 1Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences/National Institutes of Health, 111 T.W. Alexander Dr., Research Triangle Park, NC 27709, USA; Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA.

Iscience
|June 2, 2019
PubMed
Summary

Transcription factors (TF) utilize inversion symmetry (IS) to bind specific DNA elements. This DNA-binding code governs target selection and functional activity within the genome.

Keywords:
BioinformaticsEvolutionary BiologyGeneticsMolecular BiologyOmics

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High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy
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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Understanding transcription factor (TF) binding to DNA is crucial for deciphering gene regulation.
  • Predicting which DNA elements TFs bind and how this impacts gene expression remains a significant challenge.

Purpose of the Study:

  • To elucidate the underlying rules governing transcription factor DNA binding.
  • To determine if a universal principle dictates TF-DNA interactions and their functional outcomes.

Main Methods:

  • Analysis of genome-wide TF binding data.
  • Investigation of DNA sequence properties, specifically inversion symmetry (IS).
  • Correlation of IS patterns with TF binding sites and transcriptional activity.

Main Results:

  • TF binding across the genome consistently follows inversion symmetry (IS).
  • Specific DNA elements are selected by TFs based on internal IS patterns.
  • These IS-based rules apply to both active and inactive regulatory elements, differentiating them by TF retention time.

Conclusions:

  • Inversion symmetry (IS) represents a fundamental DNA code used by transcription factors for genome interaction.
  • IS dictates TF target recognition and influences the functional activity of regulatory elements.
  • This finding provides a quantitative framework for understanding TF-DNA interactions and gene regulation.