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Croatica Chemica Acta, Vol. 85 No. 3, 2012.

Original scientific paper

https://doi.org/10.5562/cca1987

Global Repeat Map Method for Higher Order Repeat Alpha Satellites in Human and Chimpanzee Genomes (Build 37.2 Assembly)

Matko Glunčić ; Faculty of Science, University of Zagreb, Zagreb, Croatia
Marija Rosandić ; Faculty of Science, University of Zagreb, Zagreb, Croatia
Denis Jelovina ; Faculty of Science, University of Zagreb, Zagreb, Croatia
Krešimir Dekanić ; Faculty of Science, University of Zagreb, Zagreb, Croatia
Ines Vlahović ; Faculty of Science, University of Zagreb, Zagreb, Croatia
Vladimir Paar ; Faculty of Science, University of Zagreb, Zagreb, Croatia

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Abstract

Alpha satellites are tandemly repeated sequences found in all human centromeres. In addition to the functional and structural role within centromere they are also a suitable model for evolutionary stud-ies, because of being subject to concerted evolution. The Global Repeat Map (GRM) algorithm is a convenient computational tool to determine consensus repeat units and their exact size within a given genomic sequence, both of monomeric and higher-order (HOR) type. Using GRM, we identify in Build 37.2 assembly fifteen different alpha satellite HORs, three of them novel, not reported previously. In the next step we compute suprachromosomal family classification and CENP-B box / pJ distributions for these HORs. All human alpha satellite sequences originate from one pra-ancestral alpha satellite monomer. For the first time we perform GRM analysis and compare human and chimpanzee alpha satellite HORs for chromosomes 4 and give an evidence that the human and chimpanzee alpha satellites originate from a common ancestor that predated the human-chimpanzee separation. We also compare the codon-like trinucleotide (CLT) extensions of human and chimpanzee chromosome 4. Our results are consistent with the expectation that the alpha satellite HORs in human and chimpanzee have been created after the human-chimpanzee separation. (doi: 10.5562/cca1987)

Keywords

alpha satellites higher order repeats; human chromosome 4; chimpanzee chromosome 4; GRM; trinucleotide extensions

Hrčak ID:

92410

URI

https://hrcak.srce.hr/92410

Publication date:

31.10.2012.

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