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...

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...

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

Quantitative detection of gut microbial eukaryotes with EukDetect2 reveals global distribution of commensal protists and association with distinct microbial community structure.

bioRxiv : the preprint server for biology·2026

Same author

Expanding vaginal microbiome pangenomes via a custom MIDAS database reveals <i>Lactobacillus crispatus</i> accessory genes associated with cervical dysplasia.

mSystems·2026

Same author

Linkage of nucleotide and functional diversity varies across gut bacteria.

Proceedings of the National Academy of Sciences of the United States of America·2026

Same author

VUStruct: A compute pipeline for high throughput and personalized structural biology.

PLoS computational biology·2026

Same author

Use of Paracervical Blocks for Patients Who Undergo Intrauterine Device Insertion.

JAMA network open·2026

Same author

Gut microbiome-dependent IL-1 signaling is a mediator of ACVR1<sup>R206H</sup>-driven heterotopic ossification.

bioRxiv : the preprint server for biology·2026

Search research articles

Related Experiment Video

Updated: Aug 2, 2025

Capturing Chromosome Conformation Across Length Scales

Capturing Chromosome Conformation Across Length Scales

Published on: January 20, 2023

Comparing chromatin contact maps at scale: methods and insights.

Laura M Gunsalus^1,2, Evonne McArthur^2,3,4, Ketrin Gjoni^1,2

¹Gladstone Institute of Data Science and Biotechnology, San Francisco, CA.

Biorxiv : the Preprint Server for Biology

|April 17, 2023

Summary

Comparing 3D genome organization requires robust methods for analyzing chromatin contact maps. This study introduces new techniques and benchmarks existing ones to better understand genome structure in development and disease.

More Related Videos

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Published on: May 6, 2010

Mapping Mammalian 3D Genome Interactions with Micro-C-XL

Mapping Mammalian 3D Genome Interactions with Micro-C-XL

Published on: November 3, 2023

Related Experiment Videos

Last Updated: Aug 2, 2025

Capturing Chromosome Conformation Across Length Scales

Capturing Chromosome Conformation Across Length Scales

Published on: January 20, 2023

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Published on: May 6, 2010

Mapping Mammalian 3D Genome Interactions with Micro-C-XL

Mapping Mammalian 3D Genome Interactions with Micro-C-XL

Published on: November 3, 2023

Area of Science:

Genomics
Computational Biology
Epigenetics

Background:

Comparing three-dimensional (3D) genome organization via chromatin contact maps is crucial for understanding development, evolution, and disease.
Existing methods for comparing these maps lack a gold standard and often yield conflicting results.

Approach:

Developed and evaluated novel comparison methods alongside existing approaches using genome-wide Hi-C data and 22,500 in silico predicted contact maps.
Assessed method robustness against biological and technical variations like boundary size and noise.

Key Points:

Simple difference-based methods (e.g., mean squared error) are useful for initial screening of chromatin contact maps.
Biologically informed methods are essential for identifying reasons behind map divergence and formulating functional hypotheses.
A comprehensive benchmark, reference guide, and codebase are provided for scalable comparison of chromatin contact maps.

Conclusions:

The study offers a standardized framework for comparing chromatin contact maps, facilitating deeper biological insights into 3D genome organization.
The developed resources enable researchers to rapidly and reliably assess differences in genome architecture across various biological contexts.