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

Chromatin Position Affects Gene Expression02:35

Chromatin Position Affects Gene Expression

23.5K
Chromatin is the massive complex of DNA and proteins packaged inside the nucleus. The complexity of chromatin folding and how it is packaged inside the nucleus greatly influences  access to genetic information. Generally, the nucleus' periphery is considered transcriptionally repressive, while the cell's interior is considered a transcriptionally active area. 
Topologically Associated Domains (TADs)
The 3-dimensional positioning of chromatin in the nucleus influences the...
23.5K
Nucleosome Remodeling02:54

Nucleosome Remodeling

9.3K
Nucleosomes are the basic units of chromatin compaction. Each nucleosome consists of the DNA bound tightly around a histone core, which makes the DNA inaccessible to DNA binding proteins such as DNA polymerase and RNA polymerase. Hence, the fundamental problem is to ensure access to DNA when appropriate, despite the compact and protective chromatin structure.
Nucleosome remodeling complex
Eukaryotic cells have specialized enzymes called ATP-dependent nucleosome remodeling enzymes. These enzymes...
9.3K
Position-effect Variegation02:32

Position-effect Variegation

6.4K
In 1928, a German botanist Emil Heitz observed the moss nuclei with a DNA binding dye. He observed that while some chromatin regions decondense and spread out in the interphase nucleus, others do not. He termed them euchromatin and heterochromatin, respectively. He proposed that the heterochromatin regions reflect a functionally inactive state of the genome. It was later confirmed that heterochromatin is transcriptionally repressed, and euchromatin is transcriptionally active chromatin.
6.4K
Forces Acting on Chromosomes02:11

Forces Acting on Chromosomes

3.4K
During mitosis, chromosome movements occur through the interplay of multiple piconewton level forces. In prometaphase, these forces help in chromosome assembly or congression at the equatorial plane, eventually leading to their alignment at the metaphase plate. The forces acting on the chromosomes are space and time-dependent; therefore, they vary with the position of the chromosomes as the cell progresses through mitosis. 
Microtubules and motor proteins exert two types of forces on...
3.4K
The Nucleosome Core Particle02:10

The Nucleosome Core Particle

12.3K
Nucleosomes are the DNA-histone complex, where the DNA strand is wound around the histone core. The histone core is an octamer containing two copies of H2A, H2B, H3, and H4 histone proteins.
The paradox
Nucleosomes, paradoxically, perform two opposite functions simultaneously. On the one hand, their main responsibility is to protect the delicate DNA strands from physical damage and help achieve a higher compaction ratio. While on the other hand, they must allow polymerase enzymes to access DNA...
12.3K
Histone Variants at the Centromere02:30

Histone Variants at the Centromere

4.4K
Histone variants are the histone proteins with structural and sequence variations. These variants may be regarded as “mutant” forms that replace their canonical histone counterparts in the nucleosomes. Specific post-translational modifications on the histone variants enable further chromatin complexity and regulate tissue-specific gene expression. The most common histone variants are from histone H2A, H2B, and linker histone H1 families. However, several variants of histone H3...
4.4K

You might also read

Related Articles

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

Sort by
Same author

Retraction Note: Could Intensive Blood Pressure Control Really Reduce Diabetic Retinopathy Outcomes? Evidence from Meta-Analysis and Trial Sequential Analysis from Randomized Controlled Trials.

Diabetes therapy : research, treatment and education of diabetes and related disorders·2023
Same author

Bibliometric Analysis of 100 Most Highly Cited Publications on Acupuncture for Migraine.

Journal of pain research·2023
Same author

Using a Multi-isotope Approach and Isotope Mixing Models to Trace and Quantify Phosphorus Sources in the Tuojiang River, Southwest China.

Environmental science & technology·2023
Same author

Pharmacokinetic analysis of 6-O-[<sup>18</sup>F]FEE for PET imaging of EGFR mutation.

Bioorganic & medicinal chemistry letters·2023
Same author

Unmanipulated haploidentical hematopoietic stem cell transplantation for pediatric <i>de novo</i> acute megakaryoblastic leukemia without Down syndrome in China: A single-center study.

Frontiers in oncology·2023
Same author

Hypermethylation of <i>Smad7</i> in CD4<sup>+</sup> T cells is associated with the disease activity of rheumatoid arthritis.

Frontiers in immunology·2023
Same journal

Computational protocol for modeling supported nanoparticle catalysts with strong metal-support interactions.

STAR protocols·2026
Same journal

Protocol for genomic mapping of chromatin targets using high-throughput CUT&RUN.

STAR protocols·2026
Same journal

A protocol for noninvasive quantification of dietary fat absorption in mice.

STAR protocols·2026
Same journal

Protocol for an AlCl<sub>3</sub>-induced Alzheimer's model in zebrafish larvae with optimized pH and behavioral assessment.

STAR protocols·2026
Same journal

Protocol for live cell barcoding and immunophenotyping of human hematological malignancies using cytometry by time of flight.

STAR protocols·2026
Same journal

Generating drug resistance models in human and murine cancer cell lines and assessing cross-resistance to chemotherapeutics and KRAS inhibitors.

STAR protocols·2026
See all related articles

Related Experiment Video

Updated: Aug 17, 2025

Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method
08:53

Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method

Published on: May 2, 2025

463

Predicting nucleosome positioning using statistical equilibrium models in budding yeast.

Hungyo Kharerin1, Lu Bai2

  • 1Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA; Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, USA.

STAR Protocols
|December 15, 2022
PubMed
Summary
This summary is machine-generated.

This study introduces a thermodynamic modeling protocol to predict how transcription factors (TFs) and chromatin remodelers influence nucleosome positioning. The method accurately identifies TFs that displace nucleosomes and predicts nucleosome-depleted regions (NDRs) using DNA sequence and TF motifs.

Keywords:
BioinformaticsBiophysicsComputer sciencesGenomicsModel OrganismsMolecular Biology

More Related Videos

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

11.2K
Use of Time-Lapse Microscopy and Stage-Specific Nuclear Depletion of Proteins to Study Meiosis in S. cerevisiae
07:48

Use of Time-Lapse Microscopy and Stage-Specific Nuclear Depletion of Proteins to Study Meiosis in S. cerevisiae

Published on: October 11, 2022

1.9K

Related Experiment Videos

Last Updated: Aug 17, 2025

Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method
08:53

Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method

Published on: May 2, 2025

463
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

11.2K
Use of Time-Lapse Microscopy and Stage-Specific Nuclear Depletion of Proteins to Study Meiosis in S. cerevisiae
07:48

Use of Time-Lapse Microscopy and Stage-Specific Nuclear Depletion of Proteins to Study Meiosis in S. cerevisiae

Published on: October 11, 2022

1.9K

Area of Science:

  • Genomics
  • Molecular Biology
  • Computational Biology

Background:

  • Nucleosome positioning is crucial for gene regulation.
  • Transcription factors (TFs) and chromatin remodelers play key roles in modulating nucleosome occupancy.
  • Predicting these interactions is essential for understanding genome organization and function.

Purpose of the Study:

  • To develop a protocol for predicting nucleosome positioning influenced by TFs and chromatin remodelers.
  • To enable genome-wide annotation of nucleosome-depleted regions (NDRs).
  • To identify nucleosome-displacing TFs and predict NDR characteristics.

Main Methods:

  • Utilized thermodynamic models to simulate nucleosome positioning.
  • Developed step-by-step approaches for annotating NDRs.
  • Computed nucleosome and TF occupancy.
  • Optimized model parameters and evaluated performance.

Main Results:

  • Successfully identified nucleosome-displacing TFs in the budding yeast genome.
  • Predicted locations and sizes of NDRs using only DNA sequence and TF motifs.
  • Demonstrated the protocol's ability to model TF-nucleosome interactions.

Conclusions:

  • The presented protocol provides a robust framework for predicting nucleosome positioning.
  • It can be applied across various organisms with known TF motifs.
  • This approach aids in understanding genome regulation by TFs and chromatin remodelers.