Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Transcription Factors02:16

Transcription Factors

76.4K
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...
76.4K
Conserved Binding Sites01:49

Conserved Binding Sites

4.3K
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...
4.3K
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

6.5K
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...
6.5K
General Transcription Factors01:30

General Transcription Factors

5.5K
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...
5.5K
The Eukaryotic Promoter Region02:40

The Eukaryotic Promoter Region

16.6K
The eukaryotic promoter region is a segment of DNA located upstream of a gene. It contains an RNA polymerase binding site, a transcription start site, and several cis-regulatory sequences.  The proximal promoter region is located in the vicinity of the gene and has cis-regulatory sequences and the core promoter. The core promoter is the binding site for RNA polymerase and is usually located between -35 and +35 nucleotides from the transcription start site. The distal promoter regions are...
16.6K
Ligand Binding Sites02:40

Ligand Binding Sites

7.8K
7.8K

You might also read

Related Articles

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

Sort by
Same author

Lipidomic profiling of plasma triglyceride species reveals distinct signatures and dietary associations in drug-refractory hypertriglyceridemia.

Clinical nutrition (Edinburgh, Scotland)·2026
Same author

Integration of AHRR methylation, heavy metals, and clinical characteristics for urothelial carcinoma risk stratification: An explainable artificial intelligence approach.

Environmental pollution (Barking, Essex : 1987)·2026
Same author

Evaluation of hematocrit-adjusted conversion strategies for mycophenolic acid and tacrolimus monitoring using volumetric absorptive microsampling in lung and renal transplant recipients.

Journal of pharmacy & pharmaceutical sciences : a publication of the Canadian Society for Pharmaceutical Sciences, Societe canadienne des sciences pharmaceutiques·2026
Same author

Peanut genome resource: a functional genomics platform for Arachis hypogaea.

Plant & cell physiology·2025
Same author

A novel approach for quantifying therapeutic monoclonal antibodies in blood through liquid chromatography-tandem mass spectrometry.

Analytica chimica acta·2025
Same author

Five-days-on-two-days-off (FOTO) versus daily bictegravir/emtricitabine/tenofovir alafenamide in virologically suppressed people with HIV: a pilot randomized clinical trial.

The Journal of antimicrobial chemotherapy·2025
Same journal

Isolation of Mesenchymal Stem Cell-Derived Extracellular Vesicles.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Modeling Melanoma Immune Surveillance by CAR-T Cells in Human Skin Organoids.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Stepwise Optimization of a Matrigel-Based In Vitro Angiogenesis Assay for Reproducible and Quantifiable 2D-Tube Formation Using HUVECs.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Quantifying Mechanical Properties of Fresh Ovarian Tissue with Optical Brillouin Microscopy.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

3D Chromatin Architecture During Early Development: New Methods and New Findings.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Metabolic Plasticity in Embryogenesis Throughout the Lens of NAD<sup></sup>.

Methods in molecular biology (Clifton, N.J.)·2026
See all related articles

Related Experiment Video

Updated: Aug 24, 2025

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

8.1K

Database for Plant Transcription Factor Binding Sites.

Wen-Chi Chang1, Chi-Nga Chow2

  • 1Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, Taiwan. sarah321@mail.ncku.edu.tw.

Methods in Molecular Biology (Clifton, N.J.)
|October 20, 2022
PubMed
Summary
This summary is machine-generated.

Reconstructing plant gene regulatory networks is challenging. Databases like PlantPAN 3.0, which map transcription factor binding sites, are crucial for advancing plant science research.

Keywords:
BioinformaticsDatabasePromoterRegulatory networkTranscription factorTranscription factor binding site

More Related Videos

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

8.8K
Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFR&#945;+ 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

9.4K

Related Experiment Videos

Last Updated: Aug 24, 2025

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

8.1K
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

8.8K
Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFR&#945;+ 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

9.4K

Area of Science:

  • Plant biology
  • Bioinformatics
  • Genomics

Background:

  • Reconstructing gene regulatory networks is essential but difficult in plant sciences.
  • High-throughput techniques like ChIP-seq and DAP-seq identify regulatory factor binding landscapes.
  • Understanding transcription factor (TF) and binding site relationships is key to elucidating gene regulation.

Purpose of the Study:

  • To highlight the importance of plant TF and transcription factor binding site (TFBS) databases.
  • To demonstrate how bioinformatics systems facilitate gene regulation research using PlantPAN 3.0 as an example.

Main Methods:

  • Utilized PlantPAN (version 3.0) database.
  • Explained the role of bioinformatics in analyzing TF-TFBS interactions.

Main Results:

  • PlantPAN 3.0 serves as a valuable resource for plant TF and TFBS data.
  • Bioinformatics systems significantly advance the study of gene regulation.

Conclusions:

  • Accessible databases like PlantPAN are vital for initiating complex gene regulatory studies.
  • Bioinformatics tools are indispensable for unraveling plant gene regulatory mechanisms.