Prediction of nucleosome DNA formation potential and nucleosome positioning using increment of diversity combined with quadratic discriminant analysis.
In this work, a novel method was developed to distinguish nucleosome DNA and linker DNA based on increment of diversity combined with quadratic discriminant analysis (IDQD), using k-mer frequency of nucleotides in genome. When used to predict DNA potential for forming nucleosomes, the model achieved a high accuracy of 94.94%, 77.60%, and 86.81%, respectively, for Saccharomyces cerevisiae, Homo sapiens, and Drosophila melanogaster. The area under the receiver operator characteristics curve of our classifier was 0.982 for S. cerevisiae. Our results indicate that DNA sequence preference is critical for nucleosome formation potential and is likely conserved across eukaryotes. The model successfully identified nucleosome-enriched or nucleosome-depleted regions in S. cerevisiae genome, suggesting nucleosome positioning depends on DNA sequence preference. Thus, IDQD classifier is useful for predicting nucleosome positioning.
School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China.
Xiujuan
X
Zhao
Zhiyong
Z
Pei
Jia
J
Liu
Sheng
S
Qin
Lu
L
Cai
D000465:Algorithms; D000818:Animals; D001482:Base Composition; D003198:Computer Simulation; D004247:DNA / Q000378:metabolism*; D016002:Discriminant Analysis; D004331:Drosophila melanogaster / Q000235:genetics / Q000378:metabolism; D016681:Genome, Fungal; D015894:Genome, Human; D049750:Genome, Insect; D006657:Histones / Q000235:genetics / Q000378:metabolism; D006801:Humans; D009707:Nucleosomes / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism
D006657:Histones; D009707:Nucleosomes; D004247:DNA