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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
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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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Cooperative Binding of Transcription Regulators02:13

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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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Chromatin Immunoprecipitation- ChIP02:36

Chromatin Immunoprecipitation- ChIP

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Chromatin immunoprecipitation, or ChIP, is an antibody-based technique used to identify sites on DNA that bind to transcription factors of interest or histone proteins. It also helps determine the type of histone modifications such as acetylation, phosphorylation, or methylation.
Types of ChIP
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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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Ligand Binding Sites02:40

Ligand Binding Sites

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Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
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Related Experiment Video

Updated: Jul 14, 2025

Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFR&#945;+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis
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Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis

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Prediction and Analysis of Transcription Factor Binding Sites: Practical Examples and Case Studies Using R

Vijaykumar Yogesh Muley1,2

  • 1Independent Researcher, Hingoli, India.

Methods in Molecular Biology (Clifton, N.J.)
|October 6, 2023
PubMed
Summary

This study introduces a practical method for identifying transcription factor binding sites (TFBSs) in DNA sequences. It demonstrates how to analyze gene regulation in development and response to viral infections.

Keywords:
EOMES geneGene regulationLHX9Regulatory elementsSTAT1 and STAT2 heterodimerTranscription factor binding sitesTranscription factors

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High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy
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Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation
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Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

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High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy
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Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation
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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Transcription factors (TFs) regulate gene expression by binding to specific DNA sites (TFBSs).
  • Understanding TFBSs is crucial for deciphering gene regulatory networks in various biological processes.
  • Current methods require accessible protocols for TFBS identification and analysis.

Purpose of the Study:

  • To provide a practical protocol for identifying transcription factor binding sites (TFBSs) in genomic DNA.
  • To demonstrate the application of TFBS analysis in studying gene regulation during embryonic development and viral response.
  • To facilitate the interpretation of results and generation of publication-ready figures.

Main Methods:

  • Extraction of upstream gene regions from genomic data.
  • Identification of TFBSs using the PWMEnrich R/Bioconductor package.
  • Case studies involving single DNA sequence analysis (EOMES promoter) and group gene analysis (HPIV1 infection).

Main Results:

  • Identified potential regulation of EOMES by the LHX9-FOXP1 complex during embryonic development.
  • Revealed key regulators, including STAT1:STAT2 heterodimer and IRF family proteins, in response to HPIV1 infection.
  • Demonstrated the utility of the protocol for analyzing TFBSs in specific gene contexts.

Conclusions:

  • The presented protocol offers an accessible approach to TFBS identification and analysis.
  • This method provides insights into transcriptional regulation in developmental biology and immunology.
  • Understanding TFBSs is vital for research in disease mechanisms and potential therapeutic targets.