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

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...
Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein.
Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein.
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...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
RNA Polymerase II Accessory Proteins02:36

RNA Polymerase II Accessory Proteins

Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...

You might also read

Related Articles

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

Sort by
Same author

Therapeutic potential of dihydronicotinamide riboside (NRH) on obesity and glucose intolerance in mice.

Nature communications·2026
Same author

MEDAG functions as an A-kinase-anchoring protein in adipocytes.

Molecular cell·2026
Same author

Designing synthetic regulatory elements using the generative AI framework DNA-Diffusion.

Nature genetics·2025
Same author

Inferring binding specificities of human transcription factors with the wisdom of crowds.

bioRxiv : the preprint server for biology·2025
Same author

Cross-platform motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors.

Communications biology·2025
Same author

Lack of single amino acids transcriptionally tunes sensory systems to enhance microbiota intake.

Current biology : CB·2025

Related Experiment Video

Updated: Jun 16, 2026

RNA-Associated Chromatin DNA-DNA Interaction Method
11:01

RNA-Associated Chromatin DNA-DNA Interaction Method

Published on: April 30, 2026

DNA-centered approaches to characterize regulatory protein-DNA interaction complexes.

Jovan Simicevic1, Bart Deplancke

  • 1Ecole Polytechnique Fédérale de Lausanne, School of Life Sciences, Institute of Bioengineering, Station 15, 1015 Lausanne, Switzerland. bart.deplancke@epfl.ch

Molecular Biosystems
|February 23, 2010
PubMed
Summary

This review highlights DNA-centered methods for studying gene regulation by transcription factor complexes. These approaches capture protein complexes on DNA, offering new insights into gene expression control.

More Related Videos

A Quantitative Assay to Study Protein:DNA Interactions, Discover Transcriptional Regulators of Gene Expression, and Identify Novel Anti-tumor Agents
06:43

A Quantitative Assay to Study Protein:DNA Interactions, Discover Transcriptional Regulators of Gene Expression, and Identify Novel Anti-tumor Agents

Published on: August 31, 2013

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

Related Experiment Videos

Last Updated: Jun 16, 2026

RNA-Associated Chromatin DNA-DNA Interaction Method
11:01

RNA-Associated Chromatin DNA-DNA Interaction Method

Published on: April 30, 2026

A Quantitative Assay to Study Protein:DNA Interactions, Discover Transcriptional Regulators of Gene Expression, and Identify Novel Anti-tumor Agents
06:43

A Quantitative Assay to Study Protein:DNA Interactions, Discover Transcriptional Regulators of Gene Expression, and Identify Novel Anti-tumor Agents

Published on: August 31, 2013

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

Area of Science:

  • Molecular Biology
  • Genetics
  • Biochemistry

Background:

  • Gene regulation relies on transcription factors (TFs) forming complexes at DNA regulatory sites.
  • Traditional methods focus on individual TFs, overlooking DNA's role in complex formation.
  • Emerging evidence suggests DNA allosterically influences TF complex assembly.

Purpose of the Study:

  • To review DNA-centered methodologies for studying regulatory DNA-binding protein complexes.
  • To evaluate recent technological advancements in purifying and identifying these complexes.
  • To discuss future directions and the impact of DNA-centered approaches on gene regulation research.

Main Methods:

  • Review of current DNA-centered techniques for capturing protein complexes on regulatory DNA.
  • Evaluation of purification and identification strategies for DNA-binding protein complexes.
  • Analysis of technological improvements in the field.

Main Results:

  • DNA-centered approaches offer a complementary perspective to protein-centered studies.
  • Technological advancements enhance the ability to study complexes in various contexts.
  • These methods correlate complex composition with target gene expression changes.

Conclusions:

  • DNA-centered methodologies are crucial for understanding allosteric regulation of TF complex formation.
  • Further improvements in these techniques will significantly advance gene regulation research.
  • This approach promises deeper insights into the dynamic interplay between DNA and protein complexes.