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 Packaging02:21

Chromatin Packaging

21.8K
Each human somatic cell contains 6 billion base-pairs of DNA. Each base-pair is 0.34 nm long, which means that each diploid cell contains a staggering 2 meters of DNA. How is such a long DNA strand packed inside a nucleus measuring only 10 - 20 microns in diameter? 
The chromatin
In combination with specialized DNA binding protein called Histones, the DNA double helix forms a compact DNA: protein complex called chromatin. The chromatin itself is further compacted into higher-order...
21.8K
Chromatin Packaging01:32

Chromatin Packaging

18.9K
Each human somatic cell contains 6 billion base pairs of DNA. Each base pair is 0.34 nm long, meaning each diploid cell contains a staggering 2 meters of DNA. This long DNA strand is packed inside a nucleus measuring only 10-20 microns in diameter with the help of specialized DNA-binding proteins called histones. Together they form a compact DNA-protein complex called chromatin. The chromatin is further compacted into higher-order structures. The highest level of compaction is achieved during...
18.9K
Chromatin Packaging02:21

Chromatin Packaging

9.6K
9.6K
Spreading of Chromatin Modifications02:25

Spreading of Chromatin Modifications

9.3K
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...
9.3K
Inheritance of Chromatin Structures03:17

Inheritance of Chromatin Structures

7.3K
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...
7.3K
Chromatin Position Affects Gene Expression02:35

Chromatin Position Affects Gene Expression

24.7K
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...
24.7K

You might also read

Related Articles

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

Sort by
Same author

Recent Progress on Toxicity and Detection Methods of Polychlorinated Biphenyls in Environment and Foodstuffs.

Critical reviews in analytical chemistry·2022
Same author

Identification of an ACK1/TNK2-based prognostic signature for colon cancer to predict survival and inflammatory landscapes.

BMC cancer·2022
Same author

The impact of different IPV-OPV sequential immunization programs on hepatitis A and hepatitis B vaccine efficacy.

Human vaccines & immunotherapeutics·2022
Same author

Establishment of gastric signet ring cell carcinoma organoid for the therapeutic drug testing.

Cell death discovery·2022
Same author

Case Report: Abnormal ECG in a Patient With Acute Pancreatitis.

Frontiers in cardiovascular medicine·2022
Same author

Diurnal RNAPII-tethered chromatin interactions are associated with rhythmic gene expression in rice.

Genome biology·2022

Related Experiment Video

Updated: Jan 21, 2026

Analysis of 18FDG PET/CT Imaging as a Tool for Studying Mycobacterium tuberculosis Infection and Treatment in Non-human Primates
10:04

Analysis of 18FDG PET/CT Imaging as a Tool for Studying Mycobacterium tuberculosis Infection and Treatment in Non-human Primates

Published on: September 5, 2017

19.2K

Chromatin Interaction Analysis with Updated ChIA-PET Tool (V3).

Guoliang Li1, Tongkai Sun2, Huidan Chang2

  • 1National Key Laboratory of Crop Genetic Improvement, Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, No. 1, Shizishan Street, Hongshan District, Wuhan 430070, China. guoliang.li@mail.hzau.edu.cn.

Genes
|July 25, 2019
PubMed
Summary
This summary is machine-generated.

The updated ChIA-PET Tool V3 enhances the analysis of chromatin interactions from sequencing data. This computational package improves the detection and statistics of significant chromatin interactions for transcriptional regulation studies.

Keywords:
ChIA-PETchromatin interaction analysis with paired-end tag data analysischromatin interactionsgenome-widehigh-throughput

More Related Videos

The Other End of the Leash: An Experimental Test to Analyze How Owners Interact with Their Pet Dogs
08:59

The Other End of the Leash: An Experimental Test to Analyze How Owners Interact with Their Pet Dogs

Published on: October 13, 2017

18.2K
Sequential Salt Extractions for the Analysis of Bulk Chromatin Binding Properties of Chromatin Modifying Complexes
07:41

Sequential Salt Extractions for the Analysis of Bulk Chromatin Binding Properties of Chromatin Modifying Complexes

Published on: October 2, 2017

8.8K

Related Experiment Videos

Last Updated: Jan 21, 2026

Analysis of 18FDG PET/CT Imaging as a Tool for Studying Mycobacterium tuberculosis Infection and Treatment in Non-human Primates
10:04

Analysis of 18FDG PET/CT Imaging as a Tool for Studying Mycobacterium tuberculosis Infection and Treatment in Non-human Primates

Published on: September 5, 2017

19.2K
The Other End of the Leash: An Experimental Test to Analyze How Owners Interact with Their Pet Dogs
08:59

The Other End of the Leash: An Experimental Test to Analyze How Owners Interact with Their Pet Dogs

Published on: October 13, 2017

18.2K
Sequential Salt Extractions for the Analysis of Bulk Chromatin Binding Properties of Chromatin Modifying Complexes
07:41

Sequential Salt Extractions for the Analysis of Bulk Chromatin Binding Properties of Chromatin Modifying Complexes

Published on: October 2, 2017

8.8K

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Chromatin interactions are crucial for gene regulation by establishing chromosome conformation.
  • Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing identifies protein-associated chromatin interactions genome-wide.
  • The original ChIA-PET Tool was developed in 2010 for ChIA-PET data analysis.

Purpose of the Study:

  • To present the updated ChIA-PET Tool V3, a computational package for processing next-generation sequencing data from ChIA-PET experiments.
  • To demonstrate the installation and application of ChIA-PET Tool V3 using RNA polymerase II (RNAPII) ChIA-PET data.
  • To compare the performance of ChIA-PET Tool V3 against existing ChIA-PET analysis tools.

Main Methods:

  • ChIA-PET Tool V3 processes both short-read and long-read ChIA-PET data using multithreading.
  • The tool generates comprehensive statistics in an HTML file.
  • Comparative analysis was performed using public datasets and identical computational resources.

Main Results:

  • ChIA-PET Tool V3 demonstrates high overlap in peak detection with other established tools.
  • The tool exhibits higher enrichment for significant chromatin interactions in aggregate peak analysis (APA) plots.
  • The updated version effectively processes diverse ChIA-PET sequencing data.

Conclusions:

  • ChIA-PET Tool V3 is a robust computational package for analyzing ChIA-PET data.
  • The tool offers improved detection and statistical enrichment of significant chromatin interactions.
  • ChIA-PET Tool V3 is publicly available on GitHub for broader research application.