Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Master Transcription Regulators

Master Transcription Regulators

Master transcription regulators are regulatory proteins that are predominantly responsible for regulating the expression of multiple genes. Often these genes work in concert to drive a complex process. Activation of a master transcription regulator can lead to a cascade of transcriptional activation necessary for that outcome. These regulators can directly bind to the regulatory sequences of the various genes involved, or they can indirectly regulate transcription by binding to regulatory...

Conserved Binding Sites

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...

Cooperative Binding of Transcription Regulators

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...

Cooperative Binding of Transcription Regulators

Cooperative Binding of Transcription Regulators

Transcription Factors

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 Factors

Transcription Factors

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

JASPAR 2026: expansion of transcription factor binding profiles and integration of deep learning models.

Nucleic acids research·2025

Same author

Synthetic deconvolution of an auxin-dependent transcriptional code.

Cell·2025

Same author

SEPALLATA-driven MADS transcription factor tetramerization is required for inner whorl floral organ development.

The Plant cell·2024

Same author

The ALOG domain defines a family of plant-specific transcription factors acting during Arabidopsis flower development.

Proceedings of the National Academy of Sciences of the United States of America·2024

Same author

JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles.

Nucleic acids research·2023

Same author

Identification of Plant Transcription Factor DNA-Binding Sites Using seq-DAP-seq.

Methods in molecular biology (Clifton, N.J.)·2023

Search research articles

Related Experiment Video

Updated: Apr 5, 2026

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

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

Published on: February 7, 2019

MORPHEUS, a Webtool for Transcription Factor Binding Analysis Using Position Weight Matrices with Dependency.

Eugenio Gómez Minguet¹, Stéphane Segard², Céline Charavay²

¹Laboratoire de Physiologie Cellulaire Végétale, Unité Mixte de Recherche 5168, Centre National de la Recherche Scientifique, Commissariat à l'Énergie Atomique, Institut National de la Recherche Agronomique, Université Joseph Fourier Grenoble I, 38054, Grenoble, France.

|August 19, 2015

Summary

This summary is machine-generated.

We developed Morpheus, a user-friendly web tool for predicting transcription factor binding sites (TFBS) using Position Weight Matrices. This tool aids in understanding gene regulation and evolution, even with complex sequence dependencies.

More Related Videos

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

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

Published on: February 11, 2019

Author Spotlight: Impact of Intergenic Interactions on Disease-Identifying Dark Biomarkers

Author Spotlight: Impact of Intergenic Interactions on Disease-Identifying Dark Biomarkers

Published on: March 1, 2024

Related Experiment Videos

Last Updated: Apr 5, 2026

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

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

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

Published on: February 11, 2019

Author Spotlight: Impact of Intergenic Interactions on Disease-Identifying Dark Biomarkers

Author Spotlight: Impact of Intergenic Interactions on Disease-Identifying Dark Biomarkers

Published on: March 1, 2024

Area of Science:

Genomics
Evolutionary Biology
Bioinformatics

Background:

Transcriptional networks regulate biological processes, and changes in transcription factors or their binding sites drive evolution.
Predicting transcription factor binding sites (TFBS) from genomic sequences is crucial as sequencing efforts expand.
Existing TFBS discovery algorithms lack user-friendly tools for analyzing DNA binding models.

Purpose of the Study:

To develop a flexible and user-friendly suite of web tools (Morpheus) for predicting TFBS presence and affinity.
To incorporate advanced features like nucleotide position dependencies and biophysical models for regulatory region occupancy.
To demonstrate the utility of Morpheus in functional and evolutionary analyses of plant gene regulation.

Main Methods:

Developed Morpheus, a web tool suite based on Position Weight Matrices (PWM) formalism.
Implemented features for nucleotide position dependencies and biophysical modeling of regulatory region occupancy.
Applied Morpheus to analyze the regulatory link between LEAFY and APETALA1 in Brassicales.

Main Results:

Morpheus provides a user-friendly platform for TFBS prediction without programming skills.
The tool successfully analyzed the regulatory link between a key plant transcription factor (LEAFY) and its target gene (APETALA1).
Demonstrated the potential of Morpheus in evolutionary analysis of gene regulation within the Brassicales clade.

Conclusions:

Morpheus offers a powerful and accessible solution for TFBS prediction and analysis.
The tool facilitates functional and evolutionary studies of gene regulation.
Morpheus simplifies the investigation of transcription factor binding and its impact on biological processes.