Abstract
The histone octamer induced bending of DNA into the superhelix structure in nucleosome core particle is important for DNA packing into chromatin, which is directly associated with gene expression and transcription regulation. In this paper, we review current computational methodologies of nucleosome positioning signal recognition based on the sequence and structural features. Sequence-based methods can be effectively applied to genomic nucleosome mapping and genomic texture analysis around the nucleosome regions. The nucleosomal region has been proved to be more flexible than its surrounding regions. Structure-based methods incorporate physical and stereochemical properties of DNA molecules and employ signal processing and pattern recognition techniques to identify the structural significance hidden in the regularity of sequence composition. The special structural information of the specific dinucleotides in the nucleosome structure indicates their important roles in the formation of nucleosome complex. CA/TG shows the greatest flexibility in the structural variation along the DNA path, thus playing the role of “hinge” in the bending of DNA into superhelix. AA/TT and GC, on the other hand, have the highest probability of closely contacting with histone and play the role of facilitating nucleosome positioning.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 112-132 |
| Number of pages | 21 |
| Journal | Current Bioinformatics |
| Volume | 8 |
| Issue number | 1 |
| State | Published - Jan 1 2013 |
| Externally published | Yes |
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Keywords
- Alpha-shape model
- Dimensionality reduction
- DNA stereochemical properties
- Nucleosome positioning
- Sequence features
- Statistical analysis
ASJC Scopus subject areas
- Biochemistry
- Molecular Biology
- Genetics
- Computational Mathematics
Cite this
A survey on structural analysis of nucleosome core particles. / Yang, Xi; Zhou, Weiqiang; Wang, Debby D.; Wu, Qinqin; Yan, Hong.
In: Current Bioinformatics, Vol. 8, No. 1, 01.01.2013, p. 112-132.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - A survey on structural analysis of nucleosome core particles
AU - Yang, Xi
AU - Zhou, Weiqiang
AU - Wang, Debby D.
AU - Wu, Qinqin
AU - Yan, Hong
PY - 2013/1/1
Y1 - 2013/1/1
N2 - The histone octamer induced bending of DNA into the superhelix structure in nucleosome core particle is important for DNA packing into chromatin, which is directly associated with gene expression and transcription regulation. In this paper, we review current computational methodologies of nucleosome positioning signal recognition based on the sequence and structural features. Sequence-based methods can be effectively applied to genomic nucleosome mapping and genomic texture analysis around the nucleosome regions. The nucleosomal region has been proved to be more flexible than its surrounding regions. Structure-based methods incorporate physical and stereochemical properties of DNA molecules and employ signal processing and pattern recognition techniques to identify the structural significance hidden in the regularity of sequence composition. The special structural information of the specific dinucleotides in the nucleosome structure indicates their important roles in the formation of nucleosome complex. CA/TG shows the greatest flexibility in the structural variation along the DNA path, thus playing the role of “hinge” in the bending of DNA into superhelix. AA/TT and GC, on the other hand, have the highest probability of closely contacting with histone and play the role of facilitating nucleosome positioning.
AB - The histone octamer induced bending of DNA into the superhelix structure in nucleosome core particle is important for DNA packing into chromatin, which is directly associated with gene expression and transcription regulation. In this paper, we review current computational methodologies of nucleosome positioning signal recognition based on the sequence and structural features. Sequence-based methods can be effectively applied to genomic nucleosome mapping and genomic texture analysis around the nucleosome regions. The nucleosomal region has been proved to be more flexible than its surrounding regions. Structure-based methods incorporate physical and stereochemical properties of DNA molecules and employ signal processing and pattern recognition techniques to identify the structural significance hidden in the regularity of sequence composition. The special structural information of the specific dinucleotides in the nucleosome structure indicates their important roles in the formation of nucleosome complex. CA/TG shows the greatest flexibility in the structural variation along the DNA path, thus playing the role of “hinge” in the bending of DNA into superhelix. AA/TT and GC, on the other hand, have the highest probability of closely contacting with histone and play the role of facilitating nucleosome positioning.
KW - Alpha-shape model
KW - Dimensionality reduction
KW - DNA stereochemical properties
KW - Nucleosome positioning
KW - Sequence features
KW - Statistical analysis
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M3 - Article
AN - SCOPUS:84930906477
VL - 8
SP - 112
EP - 132
JO - Current Bioinformatics
JF - Current Bioinformatics
SN - 1574-8936
IS - 1
ER -