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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

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 analyses the...
Conserved Binding Sites01:49

Conserved Binding Sites

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 analyses the...
Transcription Factors02:16

Transcription Factors

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...
Transcription Factors02:16

Transcription Factors

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...
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

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 dimers that...
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

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 dimers that...

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Related Experiment Video

Updated: May 23, 2026

Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis
12:29

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

Published on: April 16, 2018

Transcription factor binding sites detection by using alignment-based approach.

Ghasem Mahdevar1, Mehdi Sadeghi, Abbas Nowzari-Dalini

  • 1Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran. mahdevar@ibb.ut.ac.ir

Journal of Theoretical Biology
|April 17, 2012
PubMed
Summary
This summary is machine-generated.

Discovering transcription factor binding sites (TFBSs) computationally is crucial for understanding gene expression. This study introduces a novel method that improves TFBS identification accuracy by incorporating biological knowledge.

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Last Updated: May 23, 2026

Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis
12:29

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

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Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Gene expression dictates phenotypic variation by translating DNA information into observable traits.
  • Transcription factors (TFs) binding to specific DNA sites (TFBSs) regulate gene expression.
  • Computational identification of TFBSs is challenging yet vital due to experimental costs.

Purpose of the Study:

  • To develop a novel computational method for identifying transcription factor binding sites (TFBSs).
  • To enhance the accuracy of TFBS discovery by integrating known biological characteristics.
  • To provide a more efficient alternative to costly experimental methods for TFBS identification.

Main Methods:

  • A new computational approach for TFBS discovery was developed.
  • The method accepts DNA sequences of variable lengths as input.
  • The output identifies potential TFBS locations within the sequences.

Main Results:

  • The proposed method demonstrates higher accuracy in TFBS discovery compared to previous approaches.
  • Performance was validated using both biological and simulated datasets.
  • The integration of biological facts improved prediction reliability.

Conclusions:

  • The novel computational method offers a significant advancement in TFBS identification.
  • This approach can accelerate research in gene regulation and molecular biology.
  • Accurate TFBS discovery is essential for understanding the mechanisms of gene expression.