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 studies, 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 / pJα 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.
Highlights
Centromeres in all eukaryotes play an essential role in many of chromosome functions, such as segregation in mitosis and meiosis, recognition and pairing of homologous chromosomes, sister chromatid attachment, and formation of kinetochore structures.[1]. They are characterized by highly repetitive DNA regions and bound kinetochore proteins, which are required for the attachment of microtubules to chromosomes during mitosis
The most pronounced peaks in this diagram correspond to the following tandem repeats in chromosome 4: alpha satellite repeats (GRM peaks at multiples of the ≈171 bp repeat unit), Global Repeat Map (GRM) peaks at 135 bp, 166 bp, and ≈310 bp which are signature of Alu sequences, GRM peak at HOR Copy No
1409 bp and GRM peaks at 2210 bp
Summary
Centromeres in all eukaryotes play an essential role in many of chromosome functions, such as segregation in mitosis and meiosis, recognition and pairing of homologous chromosomes, sister chromatid attachment, and formation of kinetochore structures.[1]. Every human centromere consists of arrays of tandemly repeated 171-bp units, known as alpha satellite DNA that can be several megabases in size;[2] among reported chromosome assemblies, the amount and type of alpha satellite varies. These massive arrays are embedded between blocks of pericentromeric heterochromatin containing highly repetitive DNA.[3,4] In situ hybridization with alpha satellite and immunolabeling using antibodies against kinetochore proteins confirms that centromeres are located in these regions.[5].
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