Name
Abstract | ||
|---|---|---|
Our recent investigation in the protist Trichomonas vaginalis suggested a DNA sequence periodicity with a unit length of 120.9 nt, which represents a sequence signature for nucleosome positioning. We now extended our observation in higher eukaryotes and identified a similar periodicity of 175 nt in length in Caenorhabditis elegans. In the process of defining the sequence compositional characteristics, we found that the 10.5-nt periodicity, the sequence signature of DNA double helix, may not be sufficient for cross-nucleosome positioning but provides essential guiding rails to facilitate positioning. We further dissected nucleosome-protected sequences and identified a strong positive purine (AG) gradient from the 5′-end to the 3′-end, and also learnt that the nucleosome-enriched regions are GC-rich as compared to the nucleosome-free sequences as purine content is positively correlated with GC content. Sequence characterization allowed us to develop a hidden Markov model (HMM) algorithm for decoding nucleosome positioning computationally, and based on a set of training data from the fifth chromosome of C. elegans, our algorithm predicted 60%-70% of the well-positioned nucleosomes, which is 15%-20% higher than random positioning. We concluded that nucleosomes are not randomly positioned on DNA sequences and yet bind to different genome regions with variable stability, well-positioned nucleosomes leave sequence signatures on DNA, and statistical positioning of nucleosomes across genome can be decoded computationally based on these sequence signatures. |
Year | DOI | Venue |
|---|---|---|
2010 | 10.1016/S1672-0229(10)60010-1 | Genomics, Proteomics & Bioinformatics |
Keywords | Field | DocType |
nucleosome positioning,sequence signature,periodicity,HMM | Genome,Chromosome,Biology,Caenorhabditis elegans,DNA,DNA sequencing,Bioinformatics,GC-content,Nucleosome,Genetics,A-DNA | Journal |
Volume | Issue | ISSN |
8 | 2 | 1672-0229 |
Citations | PageRank | References |
4 | 0.46 | 1 |
Authors | ||
14 | ||