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

Combinatorial Gene Control02:33

Combinatorial Gene Control

8.6K
Combinatorial gene control is the synergistic action of several transcriptional factors to regulate the expression of a single gene. The absence of one or more of these factors may lead to a significant difference in the level of gene expression or repression.
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
8.6K
Chromatin Immunoprecipitation- ChIP02:36

Chromatin Immunoprecipitation- ChIP

9.5K
Chromatin immunoprecipitation, or ChIP, is an antibody-based technique used to identify sites on DNA that bind to transcription factors of interest or histone proteins. It also helps determine the type of histone modifications such as acetylation, phosphorylation, or methylation.
Types of ChIP
ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...
9.5K

You might also read

Related Articles

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

Sort by
Same author

A safe and effective mucosal RSV vaccine in mice consisting of RSV phosphoprotein and flagellin variant.

Cell reports·2021
Same author

In vivo liquid biopsy for glioblastoma malignancy by the AFM and LSPR based sensing of exosomal CD44 and CD133 in a mouse model.

Biosensors & bioelectronics·2021
Same author

Genomic evidence for the Chinese mountain cat as a wildcat conspecific (<i>Felis silvestris bieti</i>) and its introgression to domestic cats.

Science advances·2021
Same author

Optimization and visualization of phase modulation with filtered and amplified maximal-length sequence for SBS suppression in a short fiber system: a theoretical treatment.

Optics express·2021
Same author

The nearly complete genome of Ginkgo biloba illuminates gymnosperm evolution.

Nature plants·2021
Same author

All Binder-Free Electrodes for High-Performance Wearable Aqueous Rechargeable Sodium-Ion Batteries.

Nano-micro letters·2021

Related Experiment Video

Updated: May 6, 2026

Generation of High Quality Chromatin Immunoprecipitation DNA Template for High-throughput Sequencing ChIP-seq
09:52

Generation of High Quality Chromatin Immunoprecipitation DNA Template for High-throughput Sequencing ChIP-seq

Published on: April 19, 2013

23.8K

Discover context-specific combinatorial transcription factor interactions by integrating diverse ChIP-Seq data sets.

Li Teng1, Bing He, Peng Gao

  • 1Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA, Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA and Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USA.

Nucleic Acids Research
|November 13, 2013
PubMed
Summary

Discovering transcription factor (TF) interactions at enhancers is key for understanding gene regulation. This study introduces a new method to find TF combinations, revealing cell-specific patterns and the role of transposable elements in regulatory evolution.

More Related Videos

The ChIP-exo Method: Identifying Protein-DNA Interactions with Near Base Pair Precision
09:27

The ChIP-exo Method: Identifying Protein-DNA Interactions with Near Base Pair Precision

Published on: December 23, 2016

16.2K
Genome-wide Mapping of Protein-DNA Interactions with ChEC-seq in Saccharomyces cerevisiae
10:43

Genome-wide Mapping of Protein-DNA Interactions with ChEC-seq in Saccharomyces cerevisiae

Published on: June 3, 2017

10.5K

Related Experiment Videos

Last Updated: May 6, 2026

Generation of High Quality Chromatin Immunoprecipitation DNA Template for High-throughput Sequencing ChIP-seq
09:52

Generation of High Quality Chromatin Immunoprecipitation DNA Template for High-throughput Sequencing ChIP-seq

Published on: April 19, 2013

23.8K
The ChIP-exo Method: Identifying Protein-DNA Interactions with Near Base Pair Precision
09:27

The ChIP-exo Method: Identifying Protein-DNA Interactions with Near Base Pair Precision

Published on: December 23, 2016

16.2K
Genome-wide Mapping of Protein-DNA Interactions with ChEC-seq in Saccharomyces cerevisiae
10:43

Genome-wide Mapping of Protein-DNA Interactions with ChEC-seq in Saccharomyces cerevisiae

Published on: June 3, 2017

10.5K

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Combinatorial interactions among transcription factors (TFs) are crucial for cellular regulation but are poorly understood.
  • Existing ChIP-Seq data for TFs and chromatin marks offer potential for discovery but are underutilized.
  • Novel bioinformatics tools are needed to integrate these data types for deeper insights into gene regulation.

Purpose of the Study:

  • To develop and apply a novel computational method for identifying frequent combinatorial TF occupancy patterns at enhancers.
  • To analyze TF interactions across multiple human cell types using ChIP-Seq data.
  • To investigate the relationship between TF combinatorial patterns, enhancer architecture, and transposable elements.

Main Methods:

  • Probabilistic item set mining to discover TF combinatorial patterns.
  • Integration of genome-wide ChIP-Seq data for transcription factors and chromatin modifications.
  • Analysis of 108 TFs across four human cell types to identify cell-type-specific regulatory interactions.

Main Results:

  • Identified abundant cell-type-specific combinatorial TF interactions at enhancers.
  • Revealed that most enhancers exhibit flexible combinatorial architectures.
  • Found disproportionate overlap between transposable elements and enhancers with combinatorial TF patterns.

Conclusions:

  • The novel method effectively discovers TF combinatorial patterns at enhancers, accounting for data uncertainty.
  • TF combinatorial regulation is highly dynamic and cell-type-specific.
  • Transposable elements may have played a significant role in the evolutionary development of combinatorial gene regulation.