Related Experiment Video
Updated: Jun 2, 2026
10:40
Assembly of Nucleosomal Arrays from Recombinant Core Histones and Nucleosome Positioning DNA
Published on: September 10, 2013
Nucleosome DNA sequence structure of isochores
Zakharia M Frenkel1, Thomas Bettecken, Edward N Trifonov
1Genome Diversity Center, Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel.
BMC Genomics
|April 23, 2011
Summary
Nucleosome positioning patterns vary significantly across DNA isochore types, primarily due to differences in guanine-cytosine (G+C) content, not species. This G+C dependency influences dominant DNA sequence motifs and dinucleotide periodicities observed in various species.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Isochores, large DNA regions with distinct G+C content, exhibit variations suggesting differences in nucleosome positioning.
- Nucleosome positioning is crucial for DNA accessibility and gene regulation.
Purpose of the Study:
- To investigate the relationship between DNA G+C content and nucleosome positioning patterns across different isochore types.
- To determine if observed variations in nucleosome positioning are species-specific or G+C content-dependent.
Main Methods:
- Shannon N-gram extension was used to extract DNA positioning patterns from isochore sequences.
- Dinucleotide periodicity analyses were performed on isochore sequences from human, mouse, and chicken.
Main Results:
- A general motif (YRRRRRYYYYYR) was identified across all isochore types.
- Dominant positioning patterns varied significantly, correlating with G+C content differences (e.g., TAAAAATTTTTA vs. CGGGGGCCCCCG).
- Species-specific variations in dinucleotide periodicity (CG in humans, AG/CT in chickens, weak CG in mice) were observed, indicating subtle species-specificity.
Conclusions:
- Nucleosome positioning patterns are strongly influenced by G+C content, leading to distinct patterns in different isochores.
- Species-specificity in nucleosome positioning patterns is subtle and reflected in preferred dinucleotide periodicities.
Related Concept Videos
01:19The Nucleosome
Human DNA is almost two meters long. However, it is compressed inside a tiny nucleus measuring only a few microns in diameter. To make this degree of compaction possible, DNA is organized into several sequential levels so that it can 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.
In a chromosome, DNA is wound twice around a protein complex called a histone octamer core, which consists of 8 histone proteins. This...
In a chromosome, DNA is wound twice around a protein complex called a histone octamer core, which consists of 8 histone proteins. This...
02:33The Nucleosome
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...
02:33The Nucleosome
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...
01:12The Nucleosome Core Particle
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...
02:10The Nucleosome Core Particle
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.
The paradox
Nucleosomes, paradoxically, perform two opposite functions simultaneously. On the one hand, their main responsibility is to protect the delicate DNA strands from physical damage and help achieve a higher compaction ratio. While on the other hand, they must allow polymerase enzymes to access DNA...
The paradox
Nucleosomes, paradoxically, perform two opposite functions simultaneously. On the one hand, their main responsibility is to protect the delicate DNA strands from physical damage and help achieve a higher compaction ratio. While on the other hand, they must allow polymerase enzymes to access DNA...
02:21Chromatin Packaging
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 structures.
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 structures.