Tandemly repeated DNA families in the mouse genome

Abstract

BackgroundFunctional and morphological studies of tandem DNA repeats, that combine high portion of most genomes, are mostly limited due to the incomplete characterization of these genome elements. We report here a genome wide analysis of the large tandem repeats (TR) found in the mouse genome assemblies.ResultsUsing a bioinformatics approach, we identified large TR with array size more than 3 kb in two mouse whole genome shotgun (WGS) assemblies. Large TR were classified based on sequence similarity, chromosome position, monomer length, array variability, and GC content; we identified four superfamilies, eight families, and 62 subfamilies - including 60 not previously described. 1) The superfamily of centromeric minor satellite is only found in the unassembled part of the reference genome. 2) The pericentromeric major satellite is the most abundant superfamily and reveals high order repeat structure. 3) Transposable elements related superfamily contains two families. 4) The superfamily of heterogeneous tandem repeats includes four families. One family is found only in the WGS, while two families represent tandem repeats with either single or multi locus location. Despite multi locus location, TRPC-21A-MM is placed into a separated family due to its abundance, strictly pericentromeric location, and resemblance to big human satellites.To confirm our data, we next performed in situ hybridization with three repeats from distinct families. TRPC-21A-MM probe hybridized to chromosomes 3 and 17, multi locus TR-22A-MM probe hybridized to ten chromosomes, and single locus TR-54B-MM probe hybridized with the long loops that emerge from chromosome ends. In addition to in silico predicted several extra-chromosomes were positive for TR by in situ analysis, potentially indicating inaccurate genome assembly of the heterochromatic genome regions.ConclusionsChromosome-specific TR had been predicted for mouse but no reliable cytogenetic probes were available before. We report new analysis that identified in silico and confirmed in situ 3/17 chromosome-specific probe TRPC-21-MM. Thus, the new classification had proven to be useful tool for continuation of genome study, while annotated TR can be the valuable source of cytogenetic probes for chromosome recognition.

A novel satellite DNA sequence in the Peromyscus genome (PMSat): Evolution via copy number fluctuation

“…Moreover, the experimental evidence regarding the functional features of satellite DNA sequences suggest that they are not selectively neutral, supporting "unexpected" nucleotide conservation, which could be a more extensive event than first thought. However, the functional nature of tandem repeats in any genome remains enigmatic because limited tools are available for dissecting and elucidating the functions of repeated DNA, and the assemblies do not cover even the beginning of the regions of constitutive heterochromatin (Komissarov et al, 2011). The sequences of those regions can only be found in whole-genome shotgun contigs, as in Peromyscus maniculatus bairdii, BioProject: 53563, as analyzed in the present study.…”

“…However, the landscape of satDNAs can be modified and may differ among species without necessarily changing the monomeric sequence. In recent years, diverse studies have reported the existence of satellite DNA sequences preserved among evolutionarily distant species, indicating possible functional roles (Li and Kirby, 2003;Mravinac et al, 2005;Komissarov et al, 2011). Transcripts from satellite-containing regions have been identified in multiple organisms (Stimpson and Sullivan, 2010), and proteins that interact with those transcripts have been described (Hall et al, 2012).…”

A Signature of Genomic Instability Resulting from Deficient Replication Licensing

“…Major satellite (MaSat) and minor satellite (MiSat) sequences [29] were concatenated into a single sequence and along with the 45S rRNA gene sequence [30] appended into the mm9 reference sequence to build the new reference sequence for mapping.…”

The Robertsonian phenomenon in the house mouse: mutation, meiosis and speciation

“…All three SatDNAs are AT-rich (64 %, MajSat; 67 %, MinSat; 63-65 %, TLCSat) and show sequence uniformity; monomer variation is about 5.6 % for the MinSat (Kipling et al 1994) and less than 5.0 % for the MajSat (Vissel and Choo 1989), although for the latter, a recent bioinformatic analysis did not confirm such high sequence conservation, perhaps a reflection of chromosome specificity (Komissarov et al 2011). Among the three SatDNA families, TLCSat sequences are the least uniform (82 %), perhaps because of its possible spacer role between telomeres and centromeres, a role for which sequence identity may be less critical (Kalitsis et al 2006).…”