Identification of the higher order repeats from T.castaneum to Human and Neanderthal genome using computational Global Repeat Map method

Higher order repeats (HORs) function in species genomes is still mainly unknown. HOR could be classified as regular (head-to-tail within tandem pattern) and complex, where for regular ones is known that they are a result of recent evolutionary processes in primates. We use our Global Repeat Map method (http://genom.hazu.hr/tools.html) for identification of tandem repeats and HORs. Main characteristic of this method is creation of global repeat map of the investigated DNA sequence by direct mapping of it into frequency domain using complete Kstring ensemble [1]. We identified in T.castaneum complex and, surprisingly, regular HORs, not identified previously in insects (only large tandem repeats and complex HOR with different size of primary repeat units were found). Moreover, in human and Neanderthal genome, we identified accelerated HOR structures [2] which are located in NBPF family gene. In addition, we confirm that there are no accelerated HOR structures in NBPF family gene of other primates genomes. NBPF family gene is relevant for human brain expansion and mutation in them, as well as number of variations, lead to neurological disease development (schizophrenia, autism, microcephaly and macrocephaly).[1] Gluncic M, Paar V. 2012. Direct mapping of symbolic DNA sequence into frequency domain in global repeat map algorithm. Nucleic Acids Res. 41:e17.[2] Paar V, Gluncic M, Rosandic M, Basar I, Vlahovic I. 2011b. Intragene higher order repeats in neuroblastoma breakpoint family genes distinguish humans from chimpanzees. Mol. Biol. Evol. 28:1877-1892.