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

24.6K
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...
24.6K
Nucleosome Remodeling02:54

Nucleosome Remodeling

10.7K
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...
10.7K
Inheritance of Chromatin Structures03:17

Inheritance of Chromatin Structures

7.2K
Epigenetics is the study of inherited changes in a cell's phenotype without changing the DNA sequences. It provides a form of memory for the differential gene expression pattern to maintain cell lineage, position-effect variegation, dosage compensation, and maintenance of chromatin structures such as telomeres and centromeres. For example, the structure and location of the centromere on chromosomes are epigenetically inherited. Its functionality is not dictated or ensured by the underlying...
7.2K
Chromatin Immunoprecipitation- ChIP02:36

Chromatin Immunoprecipitation- ChIP

12.1K
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...
12.1K
Duplication of Chromatin Structure02:05

Duplication of Chromatin Structure

7.2K
The process of chromosome duplication during cell division requires genome-wide disruption and re-assembly of chromatin. The chromatin structure must be accurately inherited, reassembled, and maintained in the daughter cells to ensure lineage propagation.
The basic unit of the chromatin is the nucleosome, consisting of DNA wrapped around octameric histone proteins and short stretches of linker DNA separating individual nucleosomes. The histone proteins within the nucleosome have their...
7.2K
Heterochromatin02:38

Heterochromatin

17.8K
The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions that take up more dye are called heterochromatin. Heterochromatin is further classified into two forms – constitutive heterochromatin and facultative heterochromatin.
Constitutive heterochromatin: It is a highly compact region of chromatin that is mostly concentrated in the centromere and telomere. Unlike euchromatin, the amino acid at...
17.8K

You might also read

Related Articles

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

Sort by
Same author

Scalable hypothalamic neuron differentiation from human pluripotent stem cells suitable for modeling metabolic disorders.

Stem cell reports·2026
Same author

Human germline biallelic loss-of-function <i>OSMR</i> variants cause severe allergic disease.

Journal of human immunity·2026
Same author

Associations of Physical Activity and Sedentary Time From Childhood to Adolescence With Cognition in Adolescence: The PANIC Study.

Pediatric exercise science·2026
Same author

Genetics of growth rate in induced pluripotent stem cells.

Stem cell reports·2026
Same author

Genomic analyses implicate hormonal and metabolic dysregulation in polycystic ovary syndrome.

Nature genetics·2026
Same author

Genetic demultiplexing and transcript start site identification from nanopore sequencing of 10x Genomics multiome libraries.

bioRxiv : the preprint server for biology·2026

Related Experiment Video

Updated: Jan 10, 2026

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

2.9K

Genetic integration with cell-specific nucleosome positioning resolves causal relationships underlying chromatin

Xiaoou Wang1, Catherine C Robertson1,2, Arushi Varshney1

  • 1Gilbert S. Omenn Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.

Biorxiv : the Preprint Server for Biology
|November 24, 2025
PubMed
Summary

This study introduces a novel method to map genetic effects on chromatin accessibility, distinguishing nucleosome-free regions (nfrQTLs) from nucleosome occupancy (nucQTLs). Findings reveal nfrQTLs causally influence nucleosome positioning, impacting traits and diseases.

More Related Videos

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis
10:05

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis

Published on: December 12, 2017

22.8K
High-Resolution Mapping of Protein-DNA Interactions in Mouse Stem Cell-Derived Neurons using Chromatin Immunoprecipitation-Exonuclease ChIP-Exo
08:40

High-Resolution Mapping of Protein-DNA Interactions in Mouse Stem Cell-Derived Neurons using Chromatin Immunoprecipitation-Exonuclease ChIP-Exo

Published on: August 14, 2020

5.2K

Related Experiment Videos

Last Updated: Jan 10, 2026

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

2.9K
Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis
10:05

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis

Published on: December 12, 2017

22.8K
High-Resolution Mapping of Protein-DNA Interactions in Mouse Stem Cell-Derived Neurons using Chromatin Immunoprecipitation-Exonuclease ChIP-Exo
08:40

High-Resolution Mapping of Protein-DNA Interactions in Mouse Stem Cell-Derived Neurons using Chromatin Immunoprecipitation-Exonuclease ChIP-Exo

Published on: August 14, 2020

5.2K

Area of Science:

  • Genomics
  • Epigenetics
  • Human Genetics

Background:

  • Cell type-specific chromatin accessibility QTL (caQTL) mapping is crucial for understanding genetic regulation of chromatin and GWAS associations.
  • Existing caQTL studies lack resolution, failing to differentiate nucleosome-free regions (NFRs) from positioned nucleosomes.

Purpose of the Study:

  • To develop and apply a statistical model to decompose ATAC-seq profiles into NFRs and phased nucleosomes.
  • To map cell type-specific genetic effects on NFRs (nfrQTLs) and nucleosome occupancy (nucQTLs) in human skeletal muscle.
  • To investigate the causal relationship between nfrQTLs and nucQTLs in shaping chromatin profiles.

Main Methods:

  • Utilized statistical modeling of ATAC-seq fragment position and length to distinguish NFRs and nucleosomes.
  • Applied single nucleus (sn)ATAC-seq on 281 human muscle biopsies.
  • Performed colocalization and causal inference analyses between nfrQTLs and nucQTLs.

Main Results:

  • Identified 76,027 nfrQTLs and 24,623 nucQTLs across skeletal muscle cell types.
  • Demonstrated that nfrQTLs are significantly more likely to causally influence nucQTLs and adjacent nucleosome phasing.
  • Hundreds of nfrQTLs colocalized with GWAS signals for muscle-related traits, with many mapping to nfrPeaks.

Conclusions:

  • The developed method enhances resolution in caQTL mapping by distinguishing NFRs and nucleosome occupancy.
  • nfrQTLs play a primary role in initiating regulatory effects by altering NFR accessibility, subsequently influencing broader chromatin landscapes.
  • This approach provides mechanistic insights into how genetic variants impact gene expression and complex traits through chromatin modifications.