ArticleGenomics, proteomics & bioinformatics2010
Sequence signatures of nucleosome positioning in Caenorhabditis elegans.
Article in Genomics, proteomics & bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 13 citations in OpenAlex.
- HDGS-Net: nucleosome occupancy prediction based on a hybrid dilated gated separable convolutional neural network.BMC genomics · 2026Article
- NucMap: a database of genome-wide nucleosome positioning map across species.Nucleic acids research · 2019Article
- Ribogenomics: the science and knowledge of RNA.Genomics, proteomics & bioinformatics · 2014Article
- Nucleosome loss leads to global transcriptional up-regulation and genomic instability during yeast aging.Genes & development · 2014Article
- An analysis and prediction of nucleosome positioning based on information content.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2013Article
- Does the genetic code have a eukaryotic origin?Genomics, proteomics & bioinformatics · 2013Article
- The pendulum model for genome compositional dynamics: from the four nucleotides to the twenty amino acids.Genomics, proteomics & bioinformatics · 2012Article
- Predicting nucleosome binding motif set and analyzing their distributions around functional sites of human genes.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2012Article
- Challenges to the common dogma.Genomics, proteomics & bioinformatics · 2012Article
- Preferential nucleosome occupancy at high values of DNA helical rise.DNA research : an international journal for rapid publication of reports on genes and genomes · 2012Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.