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

Inheritance of Chromatin Structures03:17

Inheritance of Chromatin Structures

6.6K
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...
6.6K
Duplication of Chromatin Structure02:05

Duplication of Chromatin Structure

6.0K
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...
6.0K
Chromatin Position Affects Gene Expression02:35

Chromatin Position Affects Gene Expression

23.7K
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...
23.7K
Chromatin Modification in iPS Cells01:32

Chromatin Modification in iPS Cells

1.9K
Chromatin modification alters gene expression; therefore, scientists can add histone-modifying enzymes, histone variants, and chromatin remodeling complexes to somatic cells to aid reprogramming into pluripotent stem (iPS) cells.
Compact chromatin makes reprogramming difficult. Enzymes, such as histone demethylases and acetyltransferases, are often added during reprogramming to loosen the chromatin, making the DNA more accessible to transcription factors. Molecules that inhibit histone...
1.9K
Lineage Commitment01:21

Lineage Commitment

3.1K
Commitment is the  process whereby stem cells:
3.1K
Chromatin Structure Regulates pre-mRNA Processing02:41

Chromatin Structure Regulates pre-mRNA Processing

7.2K
In eukaryotic cells, nascent mRNA transcripts need to undergo many post-transcriptional modifications to reach the cell cytoplasm and translate into functional proteins. For a long time, transcription and pre-mRNA processing were considered two independent events that occur sequentially in the cell. However, it has now been well established that transcription and pre-mRNA processing are two simultaneous processes that are precisely regulated inside the cell.
The chromatin structure, especially...
7.2K

You might also read

Related Articles

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

Sort by
Same author

R-loops shape the H2A.Z landscape and promote balanced lineage allocation during differentiation.

Genome research·2026
Same author

esBAF and INO80C fine-tune subcompartments and differentially regulate enhancer-promoter interactions.

Genetics·2026
Same author

Mislocalization of FTD3-associated mutant CHMP2B to the nucleus of human neurons due to loss of a nuclear export signal.

Acta neuropathologica communications·2026
Same author

esBAF and INO80C fine-tune subcompartments and differentially regulate enhancer-promoter interactions.

bioRxiv : the preprint server for biology·2025
Same author

The Somatic Mosaicism across Human Tissues Network.

Nature·2025
Same author

The exocyst subunit EXOC2 regulates the toxicity of expanded GGGGCC repeats in C9ORF72-ALS/FTD.

Cell reports·2024
Same journal

A human-specific genetic modifier reconfigures large-scale cortical network dynamics underlying behavioral performance.

bioRxiv : the preprint server for biology·2026
Same journal

<i>Staphylococcus aureus</i> uses a eukaryotic-like uridyltransferase to make UDP-GlcNAc for cell wall synthesis.

bioRxiv : the preprint server for biology·2026
Same journal

Dynamic redistribution of eIF4F controls cap-dependent translation initiation.

bioRxiv : the preprint server for biology·2026
Same journal

When does additional information improve accuracy of RNA secondary structure prediction?

bioRxiv : the preprint server for biology·2026
Same journal

Normative brain-state trajectories reveal deviation from healthy aging in Alzheimer's disease.

bioRxiv : the preprint server for biology·2026
Same journal

Noradrenergic infraslow rhythm during sleep is the critical link between heart-rate dynamics and memory consolidation.

bioRxiv : the preprint server for biology·2026
See all related articles

Related Experiment Video

Updated: Sep 15, 2025

CRISPR-Mediated Reorganization of Chromatin Loop Structure
09:20

CRISPR-Mediated Reorganization of Chromatin Loop Structure

Published on: September 14, 2018

12.7K

R-loops shape chromatin architecture to promote balanced lineage allocation during differentiation.

Chun-Hao Chao1, Thomas G Fazzio1,2

  • 1Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.

Biorxiv : the Preprint Server for Biology
|July 16, 2025
PubMed
Summary
This summary is machine-generated.

RNA:DNA hybrids called R-loops are crucial for genome function. Depleting R-loops in mouse stem cells alters chromatin structure and biases development toward ectodermal fates.

More Related Videos

Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets
11:19

Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets

Published on: July 7, 2010

14.6K
HOX Loci Focused CRISPR/sgRNA Library Screening Identifying Critical CTCF Boundaries
10:10

HOX Loci Focused CRISPR/sgRNA Library Screening Identifying Critical CTCF Boundaries

Published on: March 31, 2019

8.4K

Related Experiment Videos

Last Updated: Sep 15, 2025

CRISPR-Mediated Reorganization of Chromatin Loop Structure
09:20

CRISPR-Mediated Reorganization of Chromatin Loop Structure

Published on: September 14, 2018

12.7K
Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets
11:19

Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets

Published on: July 7, 2010

14.6K
HOX Loci Focused CRISPR/sgRNA Library Screening Identifying Critical CTCF Boundaries
10:10

HOX Loci Focused CRISPR/sgRNA Library Screening Identifying Critical CTCF Boundaries

Published on: March 31, 2019

8.4K

Area of Science:

  • Epigenetics and Developmental Biology
  • Molecular Biology
  • Genomics

Background:

  • R-loops (RNA:DNA hybrids) are increasingly recognized as critical regulators of genome function.
  • Their precise roles in chromatin architecture and developmental potential are not fully understood.

Purpose of the Study:

  • To investigate the impact of acute R-loop depletion on chromatin structure and lineage specification in mouse embryonic stem cells (mESCs).
  • To uncover the function of R-loops in maintaining stem cell fate and developmental trajectories.

Main Methods:

  • Utilized inducible expression of Rnaseh1 in mESCs for acute, global R-loop depletion.
  • Analyzed changes in H2A.Z occupancy, nucleosome density, gene expression, and lineage specification during differentiation.
  • Investigated alterations in transcription factor regulation and cell-cell signaling.

Main Results:

  • R-loop depletion minimally affected steady-state gene expression and self-renewal.
  • Significant reduction in H2A.Z occupancy and increased nucleosome density at promoters were observed.
  • R-loop-depleted mESCs showed a bias toward ectodermal fates during gastruloid differentiation.
  • Dysregulation of lineage-specific transcription factors and impaired cell-cell signaling were noted.

Conclusions:

  • R-loops play a critical, previously unrecognized role in maintaining promoter architecture by influencing H2A.Z occupancy.
  • R-loops are essential for preserving balanced lineage trajectories during early development.
  • These findings provide new insights into the epigenomic regulation of stem cell fate.