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Strong nucleosomes of mouse genome including recovered centromeric sequences

Salih, BF and Teif, VB and Tripathi, V and Trifonov, EN (2015) 'Strong nucleosomes of mouse genome including recovered centromeric sequences.' Journal of Biomolecular Structure and Dynamics, 33 (6). 1164 - 1175. ISSN 0739-1102

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Abstract

© 2014 Taylor and Francis. Recently discovered strong nucleosomes (SNs) characterized by visibly periodical DNA sequences have been found to concentrate in centromeres of Arabidopsis thaliana and in transient meiotic centromeres of Caenorhabditis elegans. To find out whether such affiliation of SNs to centromeres is a more general phenomenon, we studied SNs of the Mus musculus. The publicly available genome sequences of mouse, as well as of practically all other eukaryotes do not include the centromere regions which are difficult to assemble because of a large amount of repeat sequences in the centromeres and pericentromeric regions. We recovered those missing sequences using the data from MNase-seq experiments in mouse embryonic stem cells, where the sequence of DNA inside nucleosomes, including missing regions, was determined by 100-bp paired-end sequencing. Those nucleosome sequences, which are not matching to the published genome sequence, would largely belong to the centromeres. By evaluating SN densities in centromeres and in non-centromeric regions, we conclude that mouse SNs concentrate in the centromeres of telocentric mouse chromosomes, with ~3.9 times excess compared to their density in the rest of the genome. The remaining non-centromeric SNs are harbored mainly by introns and intergenic regions, by retro-transposons, in particular. The centromeric involvement of the SNs opens new horizons for the chromosome and centromere structure studies.

Item Type: Article
Subjects: Q Science > Q Science (General)
Divisions: Faculty of Science and Health > Biological Sciences, School of
Depositing User: Vladimir Teif
Date Deposited: 22 Oct 2015 09:53
Last Modified: 30 Jan 2019 16:19
URI: http://repository.essex.ac.uk/id/eprint/15256

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