GlaI digestion of mouse γ-satellite DNA: study of primary structure and ACGT sites methylation

Abdurashitov, M. A.; Chernukhin, V. A.; Gonchar, D. A.; Degtyarev, S. Kh.

doi:10.1186/1471-2164-10-322

Cited by 8 publications

(9 citation statements)

References 7 publications

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“…The most clear and compact cloud is formed by MaSat arrays though it is not as uniform as might have been expected from the experimental studies [24,25]. MiSat cloud is in proximity to the MaSat but forms a distinct group.…”

Section: Resultsmentioning

confidence: 93%

“…In case of same coordinates an array with a longer unit size was removed. Both in MGSC (~3%) and Celera (~5%) WGS the amount of non-redundant TR is less than the experimentally determined amount of the MaSat alone (~8%) [ 24 ], indicating that even in WGS data sets TR remain underrepresented (Table 1 ). Since the mouse genome is enriched with micro- and minisatellites [ 21 ], we tried to get rid of them with a filter that excluded any array less than 3 kb.…”

Section: Resultsmentioning

confidence: 99%

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Tandemly repeated DNA families in the mouse genome

et al. 2011

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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.

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Section: Resultsmentioning

confidence: 93%

Section: Resultsmentioning

confidence: 99%

Tandemly repeated DNA families in the mouse genome

et al. 2011

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“…Mouse satellites annotated as GSAT_MM in RepeatMasker (γ-satellite) have been verified experimentally to exist in high copy number in these centromeres (but not in humans), and to contain highly conserved and highly methylated CpG sites. 27 …”

Section: Discussionmentioning

confidence: 99%

Detection of differential DNA methylation in repetitive DNA of mice and humans perinatally exposed to bisphenol A

et al. 2016

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Developmental exposure to bisphenol A (BPA) has been shown to induce changes in DNA methylation in both mouse and human genic regions; however, the response in repetitive elements and transposons has not been explored. Here we present novel methodology to combine genomic DNA enrichment with RepeatMasker analysis on next-generation sequencing data to determine the effect of perinatal BPA exposure on repetitive DNA at the class, family, subfamily, and individual insertion level in both mouse and human samples. Mice were treated during gestation and lactation to BPA in chow at 0, 50, or 50,000 ng/g levels and total BPA was measured in stratified human fetal liver tissue samples as low (non-detect to 0.83 ng/g), medium (3.5 to 5.79 ng/g), or high (35.44 to 96.76 ng/g). Transposon methylation changes were evident in human classes, families, and subfamilies, with the medium group exhibiting hypomethylation compared to both high and low BPA groups. Mouse repeat classes, families, and subfamilies did not respond to BPA with significantly detectable differential DNA methylation. In human samples, 1251 individual transposon loci were detected as differentially methylated by BPA exposure, but only 19 were detected in mice. Of note, this approach recapitulated the discovery of a previously known mouse environmentally labile metastable epiallele, CabpIAP. Thus, by querying repetitive DNA in both mouse and humans, we report the first known transposons in humans that respond to perinatal BPA exposure.

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“…In order to check if there are differences in methylation level, we have searched the sites for another methylation-specific enzyme: GalI (Abdurashitov, Chernukhin, Gonchar, & Degtyarev, 2009). GalI, in spite of BsiI, is able to operate a symmetric cut of 5-methylcytosine facing each other on two strands.…”

Section: Resultsmentioning

confidence: 99%

Prediction of potential barcoding sites on ITS1 by wavelet transform

Maggi

Ruggiero

Arrigo

2015

Journal of Biomolecular Structure and Dynamics

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For sustainable development, biodiversity conservation and life-quality improvement must be simultaneously considered. Molecular techniques have greatly impacted biotechnology. These methods have, in particular, improved the capability to investigate the fine differences among organisms and, as a consequence, to better investigate the effects on environmental factors on them. We propose an approach to support the optimal selection of molecular probes for barcoding application in many biotechnological fields. The aim of our work is specificity maximization. To this purpose, we have integrated a filter system based on wavelet transforms with biological knowledge about the sequence proneness to mutation and post-translational modification. Specifically, we have tested the proposed method on ITS1 sequences that are a region of the rRNA locus. Our analysis has shown the presence of other local relative stable conformations in addition to known cleavage site. Their characteristics differ within the group of mammals selected for our analysis. These variations could be used to design new species-specific barcoding probes or other quick molecular screening tools.

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GlaI digestion of mouse γ-satellite DNA: study of primary structure and ACGT sites methylation

Cited by 8 publications

References 7 publications

Tandemly repeated DNA families in the mouse genome

Tandemly repeated DNA families in the mouse genome

Detection of differential DNA methylation in repetitive DNA of mice and humans perinatally exposed to bisphenol A

Prediction of potential barcoding sites on ITS1 by wavelet transform

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