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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...
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...
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...

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Related Experiment Video

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Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
11:34

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

Published on: August 9, 2019

Predicting transcription factor binding sites using local over-representation and comparative genomics.

Matthieu Defrance1, Hélène Touzet

  • 1LIFL, UMR CNRS 8022, Université des Sciences et Technologies de Lille, Villeneuve d'Ascq, France. defrance@lifl.fr

BMC Bioinformatics
|September 2, 2006
PubMed
Summary

TFM-Explorer identifies transcription factor binding sites (TFBSs) in coregulated genes using a novel method that considers spatial conservation and multiple species. This tool efficiently detects regulatory signals in complex genomic data.

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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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Area of Science:

  • Genomics
  • Computational Biology
  • Bioinformatics

Background:

  • Identifying cis-regulatory elements is vital for understanding gene expression.
  • Computational detection of overrepresented transcription factor binding sites (TFBSs) in coregulated genes is challenging, particularly in higher eukaryotes.

Purpose of the Study:

  • To develop an efficient computational method for detecting overrepresented TFBSs in coregulated genes.
  • To address the challenges of TFBS detection in complex genomic data and higher organisms.

Main Methods:

  • Developed TFM-Explorer, a method that models coregulated genes using position weight matrices.
  • Incorporated spatial conservation within sequences and multi-species support into the TFBS detection algorithm.
  • Utilized an efficient and robust algorithm capable of handling noisy and large datasets.

Main Results:

  • TFM-Explorer successfully identifies locally overrepresented TFBSs in sets of coregulated genes.
  • The method demonstrates efficiency and robustness, enabling the detection of weak regulatory signals.
  • Promising results were achieved across human, mouse, and rat genomes.

Conclusions:

  • TFM-Explorer offers an efficient approach for predicting TFBS overrepresentation in related sequences.
  • The software provides a valuable tool for genomic research, aiding in the understanding of gene regulation.
  • TFM-Explorer is publicly available for use in biological research.