ArticleNucleic acids research2008
A novel DNA sequence periodicity decodes nucleosome positioning.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Detection of tandem repeats in the Capsicum annuum genome.DNA research : an international journal for rapid publication of reports on genes and genomes · 2023Article
- A Computer Simulation of SARS-CoV-2 Mutation Spectra for Empirical Data Characterization and Analysis.Biomolecules · 2022Article
- The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function.PLoS computational biology · 2021Article
- Periodic power spectrum with applications in detection of latent periodicities in DNA sequences.Journal of mathematical biology · 2016Article
- Context based computational analysis and characterization of ARS consensus sequences (ACS) of Saccharomyces cerevisiae genome.Genomics data · 2016Article
- Replication dynamics in fission and budding yeasts through DNA polymerase tracking.BioEssays : news and reviews in molecular, cellular and developmental biology · 2015Article
- A species-specific nucleosomal signature defines a periodic distribution of amino acids in proteins.Open biology · 2015Article
- Trichomonas vaginalis Cysteine Proteinases: Iron Response in Gene Expression and Proteolytic Activity.BioMed research international · 2015Review
- The structure of selective dinucleotide interactions and periodicities in D melanogaster mtDNA.Biological research · 2014Article
- 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
- Does the genetic code have a eukaryotic origin?Genomics, proteomics & bioinformatics · 2013Article
- DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing.Genome research · 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
- The transcript-centric mutations in human genomes.Genomics, proteomics & bioinformatics · 2012Article
- Article
- Sequence signatures of nucleosome positioning in Caenorhabditis elegans.Genomics, proteomics & bioinformatics · 2010Article
- Genome-wide colonization of gene regulatory elements by G4 DNA motifs.Nucleic acids research · 2009Article
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8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
There have been two types of well-characterized DNA sequence periodicities; both are found to be associated with important molecular mechanisms. One is a 3-nt periodicity corresponding to codon triplets, the other is a 10.5-nt periodicity related to the structure of DNA helixes. In the process of analyzing the genome and transcriptome of Trichomonas vaginalis, we observed a 120.9-nt periodicity along DNA sequences. Different from the 3- and 10.5-nt periodicities, this novel periodicity originates near the 5'-end of transcripts, extends along the direction of transcription, and weakens gradually along transcripts. As a result, codon usage as well as amino acid composition is constrained by this periodicity. Similar periodicities were also identified in other organisms, but with variable length associated with the length of nucleosome units. We validated this association experimentally in T. vaginalis, and demonstrated that the periodicity manifests nucleotide variations between linker-DNA and wrapping-DNA along nucleosome array. We conclude that this novel DNA sequence periodicity is a signature of nucleosome organization suggesting that nucleosomes are well-positioned with regularity, especially near the 5'-end of transcripts.
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