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Global repeat map algorithm (GRM) reveals differences in alpha satellite number of tandem and higher order repeats (HORs) in human, Neanderthal and chimpanzee genomes – novel tandem repeat database

Development of novel sequencing methods (NGS) enabled investigation of DNA sequence in centromere region that, as is shown in previous studies, are replete with alpha satellite sequences, 171bp long monomer units. Those units (monomers) are found in each of human chromosomes as tandem repeats or as higher order repeat (HOR) structures. Except for their role in chromosome segregation and microtubule attachment to kinetochores, recent studies show that alpha satellite copy number variations are associated with cancer outcomes, aneuploidy, aging, differences in gene expression and evolutionary development. Using Global Repeat Map algorithm (GRM) and its extended ALPHAsub tool for finding all alpha monomers in genomic sequence, we created tandem repeat database for human, Neanderthal and chimpanzee genomes. This database has almost 3000 records (only main data table is shown on-line, http://genom.hazu.hr with information about build of inserted genomes, start position in chromosome, sequence length of array, monomer length and number of monomers for specific array. Analysis of large set of data based on alpha satellites will help us to understand their role in centromeric organization and function and enable us to make conclusions about evolution between closely related species even though technologic limitation of assembly of centromere region are still present.

human, chimpanzee and Neanderthal genomes ; DNA sequence ; tandem repeats ; Alphasub ; Global Repeat Map algorithm, alpha satellites ; database

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