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

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
Co-activators and Co-repressors02:04

Co-activators and Co-repressors

7.4K
Gene transcription is regulated by the synergistic action of several proteins that form a complex at a gene regulatory site. This is observed in eukaryotes, where the regulation of gene expression is a complex process. Regulatory proteins in eukaryotes can broadly be classified into two types – regulators that bind directly to specific DNA sequences and co-regulators that associate with regulatory proteins but cannot directly bind to the DNA. These co-regulators are further divided into...
7.4K
RNA Polymerase II Accessory Proteins02:36

RNA Polymerase II Accessory Proteins

9.3K
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...
9.3K
Histone Modification02:32

Histone Modification

13.4K
The histone proteins have a flexible N-terminal tail extending out from the nucleosome. These histone tails are often subjected to post-translational modifications such as acetylation, methylation, phosphorylation, and ubiquitination. Particular combinations of these modifications form “histone codes” that influence the chromatin folding and tissue-specific gene expression.
Acetylation
The enzyme histone acetyltransferase adds acetyl group to the histones. Another enzyme, histone...
13.4K
Spreading of Chromatin Modifications02:25

Spreading of Chromatin Modifications

8.3K
The histone proteins in the nucleosomes are post-translationally modified (PTM) to increase or decrease access to DNA. The commonly observed PTMs are methylation, acetylation, phosphorylation, and ubiquitination of lysine amino acids in the histone H3 tail region. These histone modifications have specific meaning for the cell. Hence, they are called "histone code". The protein complex involved in histone modification is termed as "reader-writer" complex.
Writers
The writer...
8.3K
Transcription Factors02:16

Transcription Factors

76.2K
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...
76.2K

You might also read

Related Articles

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

Sort by
Same author

Recognition and silencing of a new transposable element.

Nature communications·2026
Same author

Structural analysis of OCT4 binding to human LIN28B nucleosomes.

Scientific reports·2026
Same author

Mechanisms of chromatin remodeling by the human Snf2-type ATPase SNF2H.

Cell research·2025
Same author

Mechanisms of chromatin remodeling by an Snf2-type ATPase.

bioRxiv : the preprint server for biology·2025
Same author

Illuminating nucleosome interactions.

Cell research·2024
Same author

ISWI catalyzes nucleosome sliding in condensed nucleosome arrays.

Nature structural & molecular biology·2024

Related Experiment Video

Updated: Jul 29, 2025

Isolation and Cultivation of Neural Progenitors Followed by Chromatin-Immunoprecipitation of Histone 3 Lysine 79 Dimethylation Mark
10:09

Isolation and Cultivation of Neural Progenitors Followed by Chromatin-Immunoprecipitation of Histone 3 Lysine 79 Dimethylation Mark

Published on: January 26, 2018

7.5K

Histone modifications regulate pioneer transcription factor cooperativity.

Kalyan K Sinha1, Silvija Bilokapic1, Yongming Du1

  • 1Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.

Nature
|May 24, 2023
PubMed
Summary

Pioneer transcription factors like OCT4 and SOX2 cooperate to access compacted DNA. This study reveals how OCT4 binding alters nucleosome structure, enabling cooperative binding and promoting chromatin decompaction for cell programming.

More Related Videos

Repressing Gene Transcription by Redirecting Cellular Machinery with Chemical Epigenetic Modifiers
10:28

Repressing Gene Transcription by Redirecting Cellular Machinery with Chemical Epigenetic Modifiers

Published on: September 20, 2018

6.5K
Author Spotlight: An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations
11:36

Author Spotlight: An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations

Published on: April 21, 2023

2.2K

Related Experiment Videos

Last Updated: Jul 29, 2025

Isolation and Cultivation of Neural Progenitors Followed by Chromatin-Immunoprecipitation of Histone 3 Lysine 79 Dimethylation Mark
10:09

Isolation and Cultivation of Neural Progenitors Followed by Chromatin-Immunoprecipitation of Histone 3 Lysine 79 Dimethylation Mark

Published on: January 26, 2018

7.5K
Repressing Gene Transcription by Redirecting Cellular Machinery with Chemical Epigenetic Modifiers
10:28

Repressing Gene Transcription by Redirecting Cellular Machinery with Chemical Epigenetic Modifiers

Published on: September 20, 2018

6.5K
Author Spotlight: An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations
11:36

Author Spotlight: An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations

Published on: April 21, 2023

2.2K

Area of Science:

  • Molecular biology
  • Epigenetics
  • Structural biology

Background:

  • Pioneer transcription factors (PTFs) can access compacted chromatin.
  • Cooperation between OCT4 and SOX2 is crucial for pluripotency and reprogramming.
  • Mechanisms of PTF function and cooperation on chromatin are not fully understood.

Purpose of the Study:

  • To elucidate the molecular mechanisms of pioneer transcription factor OCT4 function and cooperation on chromatin.
  • To determine the structural basis for OCT4-mediated nucleosome remodeling and transcription factor binding.

Main Methods:

  • Cryo-electron microscopy (cryo-EM) to determine structures of OCT4 bound to nucleosomes.
  • Biochemical assays to assess nucleosome structure changes and transcription factor binding.
  • Analysis of histone tail interactions and post-translational modifications.

Main Results:

  • OCT4 binding induces nucleosome structural changes and repositions DNA, facilitating cooperative binding of OCT4 and SOX2.
  • OCT4's activation domain interacts with histone H4 N-terminal tail, promoting chromatin decompaction.
  • OCT4's DNA-binding domain interacts with histone H3 N-terminal tail, with H3K27 modifications affecting DNA positioning and transcription factor cooperativity.

Conclusions:

  • OCT4 actively remodels nucleosomes to enable its own binding and that of SOX2, facilitating transcription factor cooperation.
  • Interactions between OCT4 and histone tails (H3 and H4) are key to chromatin modulation.
  • The epigenetic landscape, through histone modifications like H3K27, can regulate OCT4 activity for precise cell programming.