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

Histone Modification02:32

Histone Modification

13.7K
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...
13.7K
Histone Variants at the Centromere02:30

Histone Variants at the Centromere

4.5K
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...
4.5K
Spreading of Chromatin Modifications02:25

Spreading of Chromatin Modifications

8.5K
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...
8.5K
Tagging and Fusion Proteins01:24

Tagging and Fusion Proteins

6.9K
Proteins are involved in several cellular processes and biochemical reactions. Analyzing a specific protein of interest requires it to be isolated from the other proteins in the cell. This is achieved by overexpressing the specific gene in a suitable host to produce large quantities of the target protein. A tag or label is recombined with the gene to produce a fusion protein containing the target protein and the tag. The tags on these fusion proteins can then be used for easy detection and...
6.9K
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

You might also read

Related Articles

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

Sort by
Same author

Azacytidine restores T cell function in AML by modulating DNA methylation.

bioRxiv : the preprint server for biology·2026
Same author

Attenuation of Immune Senescence Markers After Intensive Cancer Therapy Through Resistance Training: A Pilot Study.

Cancers·2026
Same author

Astrocyte reactivity by alcohol dependence in the central amygdala.

Brain, behavior, and immunity·2026
Same author

MYST Acetyltransferases Interact with SETBP1 and Are a Targetable Therapeutic Vulnerability in SETBP1-Mutant Leukemia.

Blood cancer discovery·2026
Same author

Astrocyte Reactivity by Alcohol Dependence in the Central Amygdala.

bioRxiv : the preprint server for biology·2026
Same author

A Perturb-seq map of a differentiation hub reveals synergistic vulnerabilities in KMT2A-rearranged acute myeloid leukemia.

Leukemia·2026

Related Experiment Video

Updated: Sep 5, 2025

Author Spotlight: Navigating Challenges and Innovations in Muscle Stem Cell Studies
07:09

Author Spotlight: Navigating Challenges and Innovations in Muscle Stem Cell Studies

Published on: March 1, 2024

859

GoPeaks: histone modification peak calling for CUT&Tag.

William M Yashar1,2, Garth Kong1, Jake VanCampen1

  • 1Knight Cancer Institute, Oregon Health & Science University, Portland, USA.

Genome Biology
|July 5, 2022
PubMed
Summary
This summary is machine-generated.

GoPeaks is a new computational tool for analyzing histone modifications using CUT&Tag technology. It offers improved detection of genome-wide epigenetic marks, especially H3K27ac, compared to existing methods.

Keywords:
ATAC-seqCUT&RUNCUT&TagChIP-seqEpigeneticsGoPeaksHistone modificationsMACS2Peak callingSEACR

More Related Videos

Profiling of H3K4me3 Modification in Plants using Cleavage under Targets and Tagmentation
09:48

Profiling of H3K4me3 Modification in Plants using Cleavage under Targets and Tagmentation

Published on: April 22, 2022

4.1K
Author Spotlight: Enhanced Histone PTM Isomer Identification Through LC-TIMS-ToF MS/MS and PASEF
05:52

Author Spotlight: Enhanced Histone PTM Isomer Identification Through LC-TIMS-ToF MS/MS and PASEF

Published on: January 12, 2024

1.2K

Related Experiment Videos

Last Updated: Sep 5, 2025

Author Spotlight: Navigating Challenges and Innovations in Muscle Stem Cell Studies
07:09

Author Spotlight: Navigating Challenges and Innovations in Muscle Stem Cell Studies

Published on: March 1, 2024

859
Profiling of H3K4me3 Modification in Plants using Cleavage under Targets and Tagmentation
09:48

Profiling of H3K4me3 Modification in Plants using Cleavage under Targets and Tagmentation

Published on: April 22, 2022

4.1K
Author Spotlight: Enhanced Histone PTM Isomer Identification Through LC-TIMS-ToF MS/MS and PASEF
05:52

Author Spotlight: Enhanced Histone PTM Isomer Identification Through LC-TIMS-ToF MS/MS and PASEF

Published on: January 12, 2024

1.2K

Area of Science:

  • Epigenetics and Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Histone modifications are crucial for regulating gene expression.
  • Current methods like ChIP-seq for profiling histone modifications can be costly and less sensitive.
  • CUT&Tag technology offers a more sensitive and cost-effective alternative for mapping histone modifications.

Purpose of the Study:

  • To introduce GoPeaks, a novel peak calling algorithm tailored for CUT&Tag data.
  • To evaluate the performance of GoPeaks in detecting various histone modification patterns.
  • To demonstrate GoPeaks' superior sensitivity in identifying H3K27ac peaks.

Main Methods:

  • Development of the GoPeaks algorithm for analyzing CUT&Tag sequencing data.
  • Comparative analysis of GoPeaks against established peak calling tools (e.g., for ChIP-seq).
  • Assessment of peak detection accuracy across different histone modification profiles.

Main Results:

  • GoPeaks demonstrates robust genome-wide detection of histone modifications.
  • The algorithm shows significantly improved sensitivity for identifying H3K27ac peaks.
  • GoPeaks outperforms standard algorithms in detecting histone modifications with diverse peak profiles.

Conclusions:

  • GoPeaks is an effective and sensitive tool for analyzing histone modification CUT&Tag data.
  • This method enhances the ability to study epigenetic regulation and transcriptional control.
  • GoPeaks provides a valuable advancement for epigenetic research and discovery.