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Related Concept Videos

Transcription Factors02:16

Transcription Factors

75.6K
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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General Transcription Factors01:30

General Transcription Factors

5.2K
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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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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Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

6.3K
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...
6.3K
Transcription Initiation01:47

Transcription Initiation

16.2K
Initiation is the first step of transcription in eukaryotes. Prokaryotic RNA Polymerase (RNAP) can bind to the template DNA and start transcribing. On the other hand, transcription in eukaryotes requires additional proteins, called transcription factors, to first bind to the promoter region in the DNA template. This binding helps recruit the specific RNAP that can assemble on the DNA and start transcription.
The promoters and enhancers and their accessory proteins allow tight regulation of...
16.2K
Transcription Elongation Factors02:35

Transcription Elongation Factors

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Related Experiment Video

Updated: May 31, 2025

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

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TFinder: A Python Web Tool for Predicting Transcription Factor Binding Sites.

Julien Minniti1, Frédéric Checler1, Eric Duplan1

  • 1University Côte d'Azur, INSERM, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, "Laboratory of Excellence (LABEX) Distalz", Valbonne, France.

Journal of Molecular Biology
|January 22, 2025
PubMed
Summary
This summary is machine-generated.

TFinder is a Python web portal that identifies individual motifs, like transcription factor binding sites, in gene regulatory regions across multiple species. This tool simplifies motif discovery for researchers lacking extensive bioinformatics experience.

Keywords:
predictionpromotersoftwaretranscription factor binding sites

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PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins
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PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins
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PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • Transcription is a fundamental cellular process regulating gene expression.
  • Transcription factor binding sites (TFBS) are crucial for specific DNA binding and gene regulation.
  • Identifying TFBS is essential for understanding gene control mechanisms.

Purpose of the Study:

  • To develop an intuitive, all-in-one web portal for identifying individual motifs (IM) and TFBS.
  • To facilitate the retrieval of gene regulatory sequences across multiple species.
  • To enable de novo generation and utilization of Position Weight Matrices (PWMs) for motif analysis.

Main Methods:

  • Utilizes the NCBI API to extract promoter and terminal regulatory regions based on gene name or ID.
  • Searches for IMs using IUPAC codes and JASPAR entries.
  • Supports de novo PWM generation and the use of existing PWMs.
  • Analyzes data across five species simultaneously for unlimited genes.

Main Results:

  • TFinder provides identified motifs in tabular and graphical formats, including P-values and locations relative to the Transcription Start Site (TSS) or terminal regions.
  • Results are emailed to users for easy data analysis and sharing.
  • The tool is freely available as a Python package on GitHub and a Streamlit web application.

Conclusions:

  • TFinder offers a user-friendly solution for identifying gene regulatory elements and transcription factor binding sites.
  • It empowers researchers, including those new to bioinformatics, to perform complex analyses across multiple species.
  • The tool enhances accessibility to motif discovery, aiding in subsequent data analysis and research.