title: Three-dimensional eukaryotic genomic organization is strongly correlated with codon usage expression and function.
abstract: It has been shown that the distribution of genes in eukaryotic genomes is not random; however, formerly reported relations between gene function and genomic organization were relatively weak. Previous studies have demonstrated that codon usage bias is related to all stages of gene expression and to protein function. Here we apply a novel tool for assessing functional relatedness, codon usage frequency similarity (CUFS), which measures similarity between genes in terms of codon and amino acid usage. By analyzing chromosome conformation capture data, describing the three-dimensional (3D) conformation of the DNA, we show that the functional similarity between genes captured by CUFS is directly and very strongly correlated with their 3D distance in Saccharomyces cerevisiae, Schizosaccharomyces pombe, Arabidopsis thaliana, mouse and human. This emphasizes the importance of three-dimensional genomic localization in eukaryotes and indicates that codon usage is tightly linked to genome architecture.
authors.affiliation: Department of Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel.
authors.forename: Alon
authors.initials: A
authors.lastname: Diament
authors.affiliation: Department of Computer Science, Technion-Israel Institute of Technology, Haifa 32000, Israel.
authors.forename: Ron Y
authors.initials: RY
authors.lastname: Pinter
authors.affiliation: 1] Department of Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel [2] The Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel.
authors.forename: Tamir
authors.initials: T
authors.lastname: Tuller
mesh_terms: D000818:Animals; D017360:Arabidopsis / Q000235:genetics; D003062:Codon / Q000737:chemistry* / Q000648:ultrastructure*; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure; D015870:Gene Expression; D005815:Genetic Code; D016678:Genome; D006801:Humans; D051379:Mice; D008957:Models, Genetic; D009690:Nucleic Acid Conformation; D012441:Saccharomyces cerevisiae / Q000235:genetics; D012568:Schizosaccharomyces / Q000235:genetics; D012984:Software
chemical_list: D003062:Codon; D004247:DNA