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

Glunčić, Matko and Rosandić, Marija and Jelovina, Denis and Dekanić, Krešimir and Vlahović, Ines and Paar, Vladimir (2012) Global Repeat Map Method for Higher Order Repeat Alpha Satellites in Human and Chimpanzee Genomes (Build 37.2 Assembly). Croatica Chemica Acta, 85 (3). pp. 327-351. ISSN 0011-1643

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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.

Item Type: Article
Keywords: alpha satellites higher order repeats; human chromosome 4; chimpanzee chromosome 4; GRM; trinucleotide extensions
Date: 2012
Subjects: BIOMEDICINE AND HEALTH CARE > Basic Medical Sciences > Human Genetics, Genomics and Proteomics
Divisions: Faculty of Science > Department of Physics
Project code: 119-0982464-1253
Publisher: Hrvatsko kemijsko društvo
Depositing User: Gordana Stubičan Ladešić
Date Deposited: 23 Apr 2014 18:22
Last Modified: 23 Feb 2016 16:46
URI: http://digre.pmf.unizg.hr/id/eprint/930

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