Related Experiment Video
Updated: Feb 7, 2026
10:23
Genome-wide Snapshot of Chromatin Regulators and States in Xenopus Embryos by ChIP-Seq
Published on: February 26, 2015
12.9K
Assay for Transposase-Accessible Chromatin-Sequencing Using Xenopus Embryos
Ann Rose Bright1, Gert Jan C Veenstra2
1Radboud University, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Nijmegen 6500 HB, The Netherlands.
Cold Spring Harbor Protocols
|July 26, 2018
Summary
This study details a new protocol for Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq) in Xenopus tropicalis embryos. This method maps open chromatin regions, aiding gene regulation studies.
Area of Science:
- Genomics and Molecular Biology
- Developmental Biology
Background:
- Eukaryotic DNA is packaged into chromatin by nucleosomes, influencing gene regulation and cellular identity.
- Regulatory elements like promoters and enhancers are typically nucleosome-free, indicating accessible chromatin.
- Understanding chromatin accessibility is crucial for deciphering gene regulation during development.
Purpose of the Study:
- To describe a robust Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq) protocol.
- To adapt ATAC-seq for use with Xenopus tropicalis embryos.
- To provide a tool for investigating the dynamic regulatory landscape of chromatin in this model organism.
Main Methods:
- Utilizes the hyperactive prokaryotic Tn5-transposase.
- Tn5-transposase preferentially cuts DNA in accessible chromatin regions.
- Tagged DNA fragments are then sequenced to identify open chromatin locations.
Main Results:
- Successfully adapted the ATAC-seq protocol for Xenopus tropicalis embryos.
- The method identifies genomic locations with open chromatin.
- Potential to map DNA-binding protein footprints and nucleosome positioning.
Conclusions:
- The described ATAC-seq protocol is a powerful tool for studying chromatin accessibility in Xenopus tropicalis.
- Facilitates research into gene regulation and developmental processes.
- Enables detailed analysis of the dynamic regulatory landscape of chromatin.
Related Concept Videos
02:21Chromatin Packaging
22.2K
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...
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...
22.2K
01:32Chromatin Packaging
19.3K
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...
19.3K
02:21Chromatin Packaging
9.8K
9.8K
02:25Spreading of Chromatin Modifications
9.5K
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...
Writers
The writer...
9.5K
03:17Inheritance of Chromatin Structures
7.6K
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...
7.6K
02:35Chromatin Position Affects Gene Expression
24.9K
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...
Topologically Associated Domains (TADs)
The 3-dimensional positioning of chromatin in the nucleus influences the...
24.9K