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Related Concept Videos

Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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...
General Transcription Factors01:30

General 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

Updated: Jul 5, 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

Using TESS to predict transcription factor binding sites in DNA sequence.

Jonathan Schug1

  • 1University of Pennsylvania, Philadelphia, Pennsylvania, USA.

Current Protocols in Bioinformatics
|April 23, 2008
PubMed
Summary

The Transcription Element Search System (TESS) helps identify potential transcription factor binding sites (TFBS) in DNA sequences. This tool aids researchers in understanding gene regulation by predicting where transcription factors may bind.

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Related Experiment Videos

Last Updated: Jul 5, 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

Enhanced Yeast One-hybrid Screens To Identify Transcription Factor Binding To Human DNA Sequences
11:25

Enhanced Yeast One-hybrid Screens To Identify Transcription Factor Binding To Human DNA Sequences

Published on: February 11, 2019

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Gene expression is controlled by the binding of transcription factors to specific DNA sequences.
  • Transcription factors bind sequence-specifically, with varying affinities for different DNA sequences.
  • Identifying potential binding sites is crucial for understanding gene regulation, but random occurrences complicate analysis.

Purpose of the Study:

  • To describe the functionality and usage of the Transcription Element Search System (TESS).
  • To explain how TESS predicts transcription factor binding sites (TFBS) in DNA.
  • To highlight TESS features for evaluating the significance of predicted binding sites.

Main Methods:

  • Utilizes two models for predicting transcription factor binding sites: sequence strings and positional weight matrices.
  • Web-based platform for analyzing DNA sequences.
  • Incorporates features to help researchers sort and assess the statistical significance of predicted sites.

Main Results:

  • TESS can predict potential transcription factor binding sites (TFBS) in DNA sequences.
  • The system employs distinct modeling approaches (strings and PWMs) for prediction.
  • TESS provides tools to evaluate the biological relevance of identified sites.

Conclusions:

  • TESS is a valuable resource for researchers investigating gene regulation.
  • The system facilitates the identification and evaluation of transcription factor binding sites.
  • Accurate prediction of TFBS aids in deciphering the mechanisms controlling gene expression.