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Related Concept Videos

Transcription Factors02:16

Transcription Factors

82.9K
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

Transcription Elongation Factors

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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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Transcription Elongation Factors02:35

Transcription Elongation Factors

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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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Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

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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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Related Experiment Video

Updated: Feb 16, 2026

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy
06:38

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

Published on: February 7, 2019

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DNase-capture reveals differential transcription factor binding modalities.

Daniel Kang1, Richard Sherwood2, Amira Barkal2

  • 1Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.

Plos One
|December 29, 2017
PubMed
Summary

DNase-capture enhances DNase sequencing resolution by targeting specific genomic areas. A new method, BaseNormal, corrects for bias, enabling precise detection of transcription factor binding variations even at limited sites.

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High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy
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Enhanced Yeast One-hybrid Screens To Identify Transcription Factor Binding To Human DNA Sequences
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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • DNase sequencing (DNase-seq) is a powerful tool for identifying open chromatin regions.
  • However, its analytical resolution can be limited, especially for detecting subtle variations in transcription factor binding.
  • Targeted sequencing approaches are needed to improve resolution.

Purpose of the Study:

  • To introduce DNase-capture, an assay that enhances DNase-seq resolution.
  • To develop BaseNormal, a method for correcting capture bias in DNase-capture data.
  • To demonstrate the utility of normalized DNase-capture data for detecting transcription factor binding heterogeneity.

Main Methods:

  • DNase-capture assay design and implementation.
  • Development and application of the BaseNormal algorithm for bias correction.
  • Analysis of DNase-capture data to assess transcription factor protection profiles.

Main Results:

  • DNase-capture successfully focuses sequencing on selected genomic regions, increasing analytical resolution.
  • BaseNormal effectively compensates for capture bias, enabling accurate recovery of transcription factor protection profiles.
  • Normalized DNase-capture data revealed nuanced transcription factor binding heterogeneity with high sensitivity.

Conclusions:

  • DNase-capture is a valuable assay for improving DNase-seq resolution.
  • BaseNormal is a robust method for data normalization in DNase-capture experiments.
  • This approach facilitates sensitive detection of transcription factor binding dynamics.