Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Chromatin Immunoprecipitation- ChIP

Chromatin Immunoprecipitation- ChIP

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...

Euchromatin

Euchromatin

The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions take up more dye, appearing darker, while the less-compact areas take up less dye and appear lighter. Based on the compaction level, chromatins are classified into two primary forms – euchromatin and heterochromatin.
Euchromatin is the less dense region of the chromatin and stains lighter. Euchromatin contains histone H3 extensively...

Heterochromatin

Heterochromatin

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...

Heterochromatin

Heterochromatin

Spreading of Chromatin Modifications

Spreading of Chromatin Modifications

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...

You might also read

Related Articles

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

Sort by

Same author

Cryogenic expansion-induced remodeling of pore architecture in δ-MnO<sub>2</sub>/montmorillonite for enhanced formaldehyde oxidation.

Journal of hazardous materials·2026

Same author

A Novel Naturally Occurring DNA Virus with Significant Potential for Controlling <i>Sclerotinia sclerotiorum</i>.

Plant disease·2026

Same author

Reusable catalytic membrane of defect engineered nitrogen-doped expanded graphite as a metal-free peroxydisulfate activator for bisphenol A removal.

Journal of environmental management·2026

Same author

A DirectView focus reduction assay for high-throughput quantification of neutralizing antibodies against influenza A and B viruses.

Cell reports methods·2026

Same author

Illness Experiences in Young and Middle-Aged Patients With Dilated Cardiomyopathy on Chinese Social Media: Qualitative Study.

Journal of medical Internet research·2026

Same author

Transcriptional regulation in cardiovascular aging.

Frontiers in cardiovascular medicine·2026

Same journal

Neurochondrin promotes U5 snRNP maturation by regulating AAR2 release from PRPF8.

Nucleic acids research·2026

Same journal

Elongationless start-stop elements are stress-resilient translation gates that are more repressive than uTranslons.

Nucleic acids research·2026

Same journal

Evolution of the ribosomal exit tunnel through the eyes of the nascent chain.

Nucleic acids research·2026

Same journal

Enhancing the performance and interpretability of epigenetic clocks.

Nucleic acids research·2026

Same journal

FABIAN-variant 2026: improved prediction of the effects of DNA variants on transcription factor binding.

Nucleic acids research·2026

Same journal

Structural and biochemical characterization of Grimontia hollisae thermostable direct hemolysin with DNA reveals first Vibrio hemolysin with nuclease activity.

Nucleic acids research·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Dec 3, 2025

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq

Published on: November 13, 2017

ATACdb: a comprehensive human chromatin accessibility database.

Fan Wang¹, Xuefeng Bai¹, Yuezhu Wang¹

¹School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China.

Nucleic Acids Research

|October 30, 2020

Summary

This summary is machine-generated.

Researchers created ATACdb, a comprehensive database of human chromatin accessibility data. This resource provides extensive annotations and quality control metrics for regulatory element identification and understanding gene regulation.

More Related Videos

ATAC-Seq Optimization for Cancer Epigenetics Research

ATAC-Seq Optimization for Cancer Epigenetics Research

Published on: June 30, 2022

An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues

An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues

Published on: April 5, 2018

Related Experiment Videos

Last Updated: Dec 3, 2025

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq

Published on: November 13, 2017

ATAC-Seq Optimization for Cancer Epigenetics Research

ATAC-Seq Optimization for Cancer Epigenetics Research

Published on: June 30, 2022

An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues

An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues

Published on: April 5, 2018

Area of Science:

Genomics
Epigenetics
Bioinformatics

Background:

Accessible chromatin regions are key to identifying regulatory elements and understanding gene regulation.
The rapid accumulation of human ATAC-seq data necessitates efficient collection and processing methods.

Purpose of the Study:

To develop a comprehensive human chromatin accessibility database (ATACdb).
To provide a centralized resource for publicly available human chromatin accessibility data.
To annotate and illustrate the functional roles of regulatory elements in a tissue/cell type-specific manner.

Main Methods:

Manual curation of over 2200 chromatin accessibility samples from NCBI GEO/SRA.
Development of ATACdb, incorporating a quality assurance process with four quality control metrics.
Annotation of chromatin accessibility regions with epigenetic data, including enhancers, transcription factors, SNPs, and chromatin interactions.

Main Results:

ATACdb currently contains over 52 million regions from more than 1400 ATAC-seq samples.
The database offers detailed epigenetic annotations and accurate inference of transcription factor footprints.
A robust quality control process ensures data accessibility and reliability for researchers.

Conclusions:

ATACdb serves as a powerful, comprehensive platform for accessible chromatin data.
The database facilitates the study of gene regulatory mechanisms through extensive annotations and quality control.
ATACdb enhances research accessibility to human chromatin accessibility data and TF footprint analysis.