Related Experiment Video
Updated: Sep 13, 2025
06:32
Deciphering Molecular Mechanism of Histone Assembly by DNA Curtain Technique
Published on: March 9, 2022
1.9K
Structural basis of nucleosome binding and destabilization by the extended DNA binding domain of RFX5
Wanqiang Xue1, Yaoyao Han2,3, Ying Tian1
1Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai 200434, China.
Nucleic Acids Research
|July 31, 2025
Summary
Regulatory factor X 5 (RFX5) binds nucleosomes, remodeling them to potentially increase DNA accessibility and gene transcription. This study reveals the RFX5-nucleosome structure and its destabilizing effects.
Area of Science:
- Structural Biology
- Molecular Biology
- Epigenetics
Background:
- Regulatory factor X 5 (RFX5) is a transcription factor implicated in various diseases.
- RFX5 is unique in its ability to bind nucleosomes and induce remodeling in vivo.
Purpose of the Study:
- To determine the structure of the RFX5-nucleosome complex using cryo-EM.
- To elucidate the mechanism by which RFX5 interacts with and remodels nucleosomes.
Main Methods:
- Cryogenic electron microscopy (cryo-EM) to determine the structure of the RFX5-nucleosome complex.
- Structural analysis of RFX5 binding to nucleosomal DNA and histones.
Main Results:
- The extended DNA binding domain (eDBD) of RFX5 binds to nucleosomes at superhelical location +2.
- RFX5 eDBD interacts extensively with both nucleosomal DNA and histones.
- RFX5 binding induces DNA distortion and detachment of adjacent DNA gyres, destabilizing the nucleosome.
Conclusions:
- RFX5 binding alters nucleosome structure, potentially increasing DNA accessibility.
- These findings provide insights into RFX5-mediated nucleosome destabilization and its role in gene regulation.
Related Concept Videos
02:54Nucleosome Remodeling
9.5K
Nucleosomes are the basic units of chromatin compaction. Each nucleosome consists of the DNA bound tightly around a histone core, which makes the DNA inaccessible to DNA binding proteins such as DNA polymerase and RNA polymerase. Hence, the fundamental problem is to ensure access to DNA when appropriate, despite the compact and protective chromatin structure.
Nucleosome remodeling complex
Eukaryotic cells have specialized enzymes called ATP-dependent nucleosome remodeling enzymes. These enzymes...
Nucleosome remodeling complex
Eukaryotic cells have specialized enzymes called ATP-dependent nucleosome remodeling enzymes. These enzymes...
9.5K
01:49Conserved Binding Sites
4.4K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
4.4K
01:12The Nucleosome Core Particle
1.3K
Nucleosomes are the DNA-histone complex, where the DNA strand is wound around the histone core. The histone core is an octamer containing two copies of H2A, H2B, H3, and H4 histone proteins.
Nucleosomes, paradoxically, perform two opposite functions simultaneously. On the one hand, their primary aim is to protect the delicate DNA strands from physical damage and help achieve a higher compaction ratio. On the other hand, they must allow polymerase enzymes to access histone-bound DNA during...
Nucleosomes, paradoxically, perform two opposite functions simultaneously. On the one hand, their primary aim is to protect the delicate DNA strands from physical damage and help achieve a higher compaction ratio. On the other hand, they must allow polymerase enzymes to access histone-bound DNA during...
1.3K
02:33The Nucleosome
16.8K
DNA in a human cell is almost 2m long and it is packed inside a tiny nucleus that is only a few microns in diameter. The level of compaction of DNA inside the nucleus is astonishing. It is organized into several sequentially higher levels of compaction to fit into such a tiny space. The most compact form of DNA is a chromosome that can be seen under a microscope in a dividing cell.
DNA is wound twice around a protein complex called histone core, that consist of 8 histone proteins. This complex...
DNA is wound twice around a protein complex called histone core, that consist of 8 histone proteins. This complex...
16.8K
02:21Chromatin Packaging
16.5K
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...
16.5K
02:13Cooperative Binding of Transcription Regulators
6.6K
Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome. Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form...
6.6K