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Conserved DNA motifs, including the CENP-B box-like, are involved in satellite DNA array rearrangements

Meštrović, Nevenka; Pavlek, Martina; Car, Ana; Castagnone-Sereno, Philippe; Abad, Pierre; Plohl, Miroslav (2013) Conserved DNA motifs, including the CENP-B box-like, are involved in satellite DNA array rearrangements. PLoS ONE, 8 (6). e67328/1-e67328/10. ISSN 1932-6203

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Abstract

Satellite DNAs (satDNAs), despite rapid evolution that continuously remodel the genomic landscape, occupy functionally essential centromeric regions. Difficult to be explored due to their repetitive nature and divergence, satDNAs are still hardly accessible frontiers of eukaryotic genomes and knowledge concerning functional significance of satellite DNAs is rather limited. In this work, we provide a comprehensive analysis of six satDNAs in the library of recently separated root-knot nematodes Meloidogyne chitwoodi and M. fallax. We disclosed two different conserved regions common for analyzed satDNAs. One appeared to be highly similar to the CENP-B box of human alpha satDNA, which emerged, in sequence alignment, as a conserved segment common for six divergent satDNAs shared by closely related genomes. Observed results emphasize it as the most prominent example of the CENP-B box-like motif out of mammals. The proposed feature of the CENP-B box-like motif is to act as a promoter in the hypothesized cut-and-paste transposition-related mechanism. This observation could represent a novel role of the CENP-B box, in addition to the known function in centromere protein binding. We propose that the second conserved sequence motif detected in explored satDNAs is involved in illegitimate recombination. In parallel to alpha satDNAs, we found organization of satDNA arrays in nematodes comparable to that found in human and primates, in the form of simple and complex higher order repeats (HORs). In contrast to human satDNA organization, characterized by phylogenetically distinct HOR and monomeric forms, organizational patterns observed in nematodes are consistent with frequent and continuous shuffling of sequences between HORs and monomeric arrays. Our results suggest the role of conserved domains in mechanisms that cause rapid shuffling of sequences among divergent satDNAs, on the level of short-segment tracts. In context of satDNA evolution, our finding provides, for the first time, an experimentally verified link between conserved domains and satDNA rearrangement events.

Item Type: Article
Uncontrolled Keywords: satellite DNAs, conserved motifs; CENPB box; evolution
Subjects: NATURAL SCIENCES > Biology
Divisions: Division of Molecular Biology
Projects:
Project titleProject leaderProject codeProject type
Evolucija, osobitosti i funkcionalne interakcije sekvenci satelitnih DNA[3986] Miroslav Plohl098-0982913-2756MZOS
Depositing User: Nevenka Meštrović Radan
Date Deposited: 06 Jul 2015 12:36
Last Modified: 06 Jul 2015 12:36
URI: http://fulir.irb.hr/id/eprint/2022
DOI: 10.1371/journal.pone.0067328

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