Reduced levels of methyltransferase DNMT2 sensitize human fibroblasts to oxidative stress and DNA damage that is accompanied by changes in proliferation-related miRNA expression.

Methyltransferase DNMT2 is suggested to be involved in the regulation of numerous processes, however its biological significance and underlying molecular mechanisms remain elusive. In the present study, we have used WI-38 and BJ human fibroblasts as an in vitro model system to investigate the effects of siRNA-based DNMT2 silencing. DNMT2-depleted cells were found to be sensitive to oxidative stress conditions as judged by increased production of reactive oxygen species and susceptible to DNA damage that resulted in the inhibition of cell proliferation. DNMT2 silencing promoted upregulation of proliferation-related and tumor suppressor miRNAs, namely miR-28-3p, miR-34a-3p, miR-30b-5p, miR-29b-3p, miR-200c-3p, miR-28-5p, miR-379-5p, miR-382-5p, miR-194-5p, miR-193b-3p and miR-409-3p. Moreover, DNMT2 silencing induced cellular senescence and DNMT2 levels were elevated in replicatively senescent cells. Taken together, we found that DNMT2 may take part in the regulation of cell proliferation and longevity in human fibroblasts and speculate that the manipulation of DNMT2 levels that limits cell proliferation may be potentially useful anticancer strategy.

Curcumin induces oxidation-dependent cell cycle arrest mediated by SIRT7 inhibition of rDNA transcription in human aortic smooth muscle cells.

It is widely accepted that abnormal accumulation of vascular smooth muscle cells (VSMCs) may promote atherosclerosis and post-angioplasty restenosis. The use of some plant polyphenols with potent antiproliferative activities may be considered as a therapeutic intervention to diminish/prevent the development of cardiovascular pathologies. In the present study, VSMC response to curcumin treatment was evaluated. 5 µM curcumin elicited a cytostatic effect, which was accompanied by protein carbonylation, oxidative DNA damage and changes in the nucleolar activity (the size and number of nucleoli, nucleolar protein levels and their localization). The levels of p53 and p21 were elevated. However, this was independent of DNA DSBs. Curcumin caused inhibition of rDNA transcription, which could be due to SIRT7 downregulation, site-specific methylation of RNA18S5 gene promoter or both. Curcumin-induced DNA methyltransferase 2 (DNMT2) upregulation was also shown. DNMT2-mediated RNA methylation could promote RNA stabilization upon curcumin treatment. In conclusion, a nucleolus-focused cytostatic action of curcumin at a low micromolar concentration range, which could be feasibly achieved through dietary means, was established in VSMCs and we propose a novel mechanism underlying this action. We believe that our results may contribute to better understanding of the biological and pharmacological effects of curcumin on the human cardiovascular system.

The application of genome-wide SNP genotyping methods in studies on livestock genomes.

Animal genomics is currently undergoing dynamic development, which is driven by the flourishing of high-throughput genome analysis methods. Recently, a large number of animals has been genotyped with the use of whole-genome genotyping assays in the course of genomic selection programmes. The results of such genotyping can also be used for studies on different aspects of livestock genome functioning and diversity. In this article, we review the recent literature concentrating on various aspects of animal genomics, including studies on linkage disequilibrium, runs of homozygosity, selection signatures, copy number variation and genetic differentiation of animal populations. Our work is aimed at providing insight into certain achievements of animal genomics and to arouse interest in basic research on the complexity and structure of the genomes of livestock.

General assessment of copy number variation in normal and tumor tissues of the domestic dog (Canis lupus familiaris).

In recent years, characterization of a copy number variation (CNV) of the genomic DNA has provided evidence for the relationship of this type of genetic variation with the occurrence of a broad spectrum of diseases, including cancer lesions. Copy number variants (CNVs) also occur in the genomes of healthy individuals as a result of abnormal recombination processes in germ cells and have a hereditary character contributing to the natural genetic diversity. Recent image analysis methods and advanced computational techniques allow for identification of CNVs using SNPs genotyping microarrays based on the analysis of signal intensity observed for markers located in the specific genomic regions. In this study we used CanineHD BeadChip assay (Illumina) to identify both natural and cancer-induced CNVs in the genomes of different dog breeds and in different cancer types occurring in this species. The obtained results showed that structural aberrations are a common phenomenon arising during a tumor progression and are more complex and widespread in tumors of mesenchymal tissue origin than in epithelial tissue originating tumors. The tumor derived CNVs, in comparison to healthy samples, were characterized by larger sizes of regions, higher number of amplifications, and in some cases encompassed genes with potential effect on tumor progression.

The evaluation of bovine SNP50 beadchip assay performance in Polish red cattle breed.

According to increasing interest in the use of high density SNP (single nucleotide polymorphism) genotyping assays for genome-wide genetic studies in farm animals, there is a need to assess the usefulness of currently available genomic tools for application in different breeds. The performance of the assays may differ between the breeds because of discrepancies in allele frequencies of the polymorphisms or differences in linkage disequilibrium patterns. In this study we attempted to test the performance of the Bovine SNP50 v2 genotyping assay (Illumina) for population genetic and other applications in the Polish Red cattle breed. We found that 37,977 of the 53,438 autosomal markers included in the assay give high quality genomic information and can be used for different applications concerning this breed. The remaining markers were denoted as "of limited use" or redundant because of their weak performance, deviation from Hardy-Weinberg equilibrium, low minor allele frequency, high linkage disequilibrium with other neighboring markers or location on sex chromosomes.

The evaluation of the usefulness of pedigree verification-dedicated SNPs for breed assignment in three polish cattle populations.

The breed assignment in cattle is one of the issues of molecular genetics which needs further testing and development. Although several statistical approaches have been developed to enable such application, the obtained results strongly depend on specific populations differentiation and power of markers discrimination or their informativeness. Currently, all breeding animals are being tested for parentage with the use of panel of 12 microsatellite markers, which in near future probably will be replaced by about 100 single nucleotide polymorphisms (SNPs). Despite the fact that SNPs are mainly bi-allelic, the multilocus genotypes can reach the level of polymorphism of a panel of microsatellite markers. In this study we attempted to determine the breed of origin of 741 cattle by using 120 SNPs dedicated for parentage testing and included in the BovineSNP50 BeadChip genotyping assay (Illumina). The applied Bayesian and frequency-based methods allowed such differentiation, however, the reliability of the results was not completely satisfying, suggesting that the studied markers are not the best tool for breed assignment.