title: Start/stop codon like trinucleotides extensions in primate alpha satellites.
abstract: The centromeres remain "the final frontier" in unexplored segments of genome landscape in primate genomes, characterized by 2-5 Mb arrays of evolutionary rapidly evolving alpha satellite (AS) higher order repeats (HORs). Alpha satellites as specific noncoding sequences may be also significant in light of regulatory role of noncoding sequences. Using the Global Repeat Map (GRM) algorithm we identify in NCBI assemblies of chromosome 5 the species-specific alpha satellite HORs: 13mer in human, 5mer in chimpanzee, 14mer in orangutan and 3mers in macaque. The suprachromosomal family (SF) classification of alpha satellite HORs and surrounding monomeric alpha satellites is performed and specific segmental structure was found for major alpha satellite arrays in chromosome 5 of primates. In the framework of our novel concept of start/stop Codon Like Trinucleotides (CLTs) as a "new DNA language in noncoding sequences", we find characteristics and differences of these species in CLT extensions, in particular the extensions of stop-TGA CLT. We hypothesize that these are regulators in noncoding sequences, acting at a distance, and that they can amplify or weaken the activity of start/stop codons in coding sequences in protein genesis, increasing the richness of regulatory phenomena.
authors.affiliation: Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia. rosandic@hazu.hr
authors.forename: Marija
authors.initials: M
authors.lastname: Rosandić
authors.forename: Matko
authors.initials: M
authors.lastname: Glunčić
authors.forename: Vladimir
authors.initials: V
authors.lastname: Paar
mesh_terms: D000818:Animals; D001483:Base Sequence; D033481:Chromosomes, Mammalian / Q000235:genetics; D018387:Codon, Initiator / Q000235:genetics*; D018388:Codon, Terminator / Q000235:genetics*; D016384:Consensus Sequence / Q000235:genetics; D004276:DNA, Satellite / Q000235:genetics*; D016678:Genome / Q000235:genetics; D006801:Humans; D008969:Molecular Sequence Data; D009707:Nucleosomes / Q000235:genetics; D009711:Nucleotides / Q000235:genetics; D011323:Primates / Q000235:genetics*; D019680:Trinucleotide Repeat Expansion / Q000235:genetics*
chemical_list: D018387:Codon, Initiator; D018388:Codon, Terminator; D004276:DNA, Satellite; D009707:Nucleosomes; D009711:Nucleotides