Vol 55, No 2 (2019)

The tumor suppressors are fundamental development genes with a complete penetrance. Recessive mutations in the l(2)gl suppressor in drosophila are accompanied by complex phenotypic syndromes. Realization of the l(2)gl locus functions is performed by genetic and epigenetic pathways. The Lgl gene product in complex protein complexes controls the establishment of the cell polarity in epithelial stem and nerve cells. The degree of the l(2)gl involvement in the regulation of early development, longevity, stress response, and tumor development can depend on the microRNA expression level, the presence of intracellular symbionts, and mutations of other vital genes and is affected by various impacts.

Insulators are usually defined as DNA elements with the property to defend the gene from the influence of the other regulatory elements: enhancer-blocking insulators prevent activation of the gene promoter by the enhancer, when located in between them; barrier insulators remove the so-called position-effect variegation, preventing the spread of heterochromatin. In recent years, applications of the whole-genome methods of analysis led to the accumulation of data on the function of insulator elements that go beyond the framework of canonical definitions. This review summarizes the most up-to-date data on the canonical function of insulators in the organization of chromatin architecture and gene transcription and also considers their noncanonical functions supplementing the generally accepted concepts of the role of insulators in the regulation of the genome function.

The ftz-f1 gene encodes a nuclear receptor that plays an important role in ontogenesis of Drosophila melanogaster. Transcription of this gene at the onset of metamorphosis occurs for a short period of time and is subjected to complex multistep regulation. Recently, in the distal part of the first intron of the ftz-f1 gene, we discovered a regulatory element with enhancer properties. In the present work, we continued the study of the chromatin properties in the ftz-f1 gene locus. Using the chromosome conformation capture method (3C), spatial interaction between promoter and intronic enhancer of the studied locus was detected. At the preparatory stage of gene transcription, knockdown of the SAYP subunit, which recruits the SWI/SNF complex to the ftz-f1 gene, caused considerable attenuation of this interaction. At the stage of active gene transcription, SAYP knockdown led to a considerable decrease in the level of histone H3 acetylation at position 27 on the promoter and enhancer. The data obtained indicate the important role of SWI/SNF in the formation of chromatin structure needed for adequate expression of the ftz-f1 gene and its important role in the intronic enhancer activity.

The present study investigated the genetic diversity and structure within the P. domestica species on the basis of analysis of 60 varieties by eight SSR loci. The study sample included various subspecies of domestic plum: mirabelle plums, greengages, damsons, and zwetschgen. The number of alleles per locus revealed in the study varied from 6 to 39; in total, 153 alleles were identified. The Bayesian method made it possible to identify four reconstructed panmictic populations. The contribution of reconstructed panmictic populations is specific to each group of P. domestica. According to the obtained data of the cluster analysis by UPGMA and PCoA, damsons represent the most genetically isolated subspecies of plums. On the other hand, the majority of varieties of domestic and foreign breeding do not form distinct groups in clustering, indicating the unity of the gene pool of cultivated plum forms.

The genetic diversity of Larix × lubarskii Sukaczev and its genetic relationships to other larches from the south of Primorsky krai and Far Eastern and Siberian Larix species were for the first time studied according to the analysis of the UBC460 mitochondrial origin fragment length polymorphism and nucleotide sequences of the 5'-flanking region of the atpA gene and nad4(3c–4r) region in mitochondrial DNA. Two length variants of the UBC460 fragment were detected in the L. × lubarskii population (with a predominance of the short one). This taxon is characterized by an average haplotype (0.582) and low nucleotide (0.0003) diversity. The comparative analysis of nucleotide polymorphism of two mtDNA regions in larches from the south of Primorsky krai revealed three mitotypes in L. × lubarskii; only one of them was common with L. olgensis A. Henry (locus classicus). The network of mitotype genealogical relationships indicates a common origin of L. × lubarskii and L. olgensis and their relatively recent divergence, as well as a closer relationship to L. sibirica Ledeb. than to L. gmelinii (Rupr.) Rupr.

The nucleotide sequences of the alleles of the DRB3 gene of the major histocompatibility complex (class II) of saiga antelope are described. A high degree of heterozygosity is found. The results of the analysis are consistent with the hypothesis of overdominance of heterozygotes. Phylogenetic relations of the DRB3 gene alleles of the saiga antelope and other Bovidae species do not correspond to the systematic position of Saiga tatarica. It is assumed that the polymorphism of the DRB3 gene alleles of saiga is primarily due to the variety of extracellular pathogens (bacteria, protozoa, helminths, and others) affecting its population during the evolutionary history of the species.

The largest genome-wide association studies have identified schizophrenia and intelligence associated variants in the MIR137HG locus containing genes encoding microRNA-137 and microRNA-2682. In the present study, we investigated DNA methylation in the MIR137HG intragenic CpG island (CGI) in the peripheral blood of 44 patients with schizophrenia and 50 healthy controls. The CGI included the entire MIR137 gene and the region adjacent to the 5'-end of MIR2682. The aim of the study was to examine the relationship of the CGI methylation with schizophrenia and cognitive functioning. The methylation level of 91 CpG located in the selected region was established for each participant by means of single-molecule real-time bisulfite sequencing. All subjects completed the battery of neuropsychological tests. We found that the CGI was hypomethylated in both groups, except for one site—CpG (chr1: 98 511 049), with significant interindividual variability in methylation. A higher level of methylation of this CpG was seen in male patients and was associated with a decrease in the cognitive index in the combined sample of patients and controls. Our data suggest that further investigation of mechanisms that regulate the MIR137 and MIR2682 genes expression might help to understand the molecular basis of cognitive deficits in schizophrenia.

The InDel, based on the insertion or deletion in the human genome, is an alternative genetic marker for the widely used forensic STRs identification method. In this study we aim to determine forensic parameters of autosomal 30 InDel loci in Turkish population and to analyze the genetic differences between Turkish population and previously published other population data of alleged loci. We collected 250 blood samples from non-relative healthy volunteers. Then 30 insertion-deletion loci and amelogenin were amplified according to Investigator DIPplex® Kit manual (Qiagen). The PCR products were separated and analyzed. Forensic and population parameters of the 30 InDels were estimated with Promega PowerStats Excel worksheet, p-values of Hardy–Weinberg Equilibrium and F_ST test of population differentiation were calculated with Arlequin ver. 3.5. After Bonferonni correction the DIPplex allele frequency distributions showed no significant deviation from HWE. F_ST indicated that significant statistical differences were found between our population and Korean population at 16, Somalian population at 16, Taiwanian population at 9, Finnish population at 5, Polish population at 1 InDel loci. There is no statistically significant results in between our Turkish population sample, Turkish population in Denmark, and Italian populations in North-East Italy. We present population data and forensic parameters for 30 autosomal InDels studied in Turkish population samples. This data set will be useful in paternity, kinship analysis and also in identification of the forensic case samples. We also emphesis that Turkish population data is genetically closer to the nearby European populations as expected.

INNER NO OUTER belongs to the YABBY transcription factor family and determines the abaxial identity of the outer ovule integument. In this study, complete genomic INO sequences were identified and characterized in 12 accessions of 11 tomato species (Solanum section Lycopersicon). It was shown that the identified INO genes encode proteins with the conserved zinc finger and YABBY domains. The INO sequences of all analyzed tomato species contain 243 (12.9% of the aligned length) variable sites, 43 of which are exon-specific and include 22 nonsynonymous SNPs leading to amino acid residue substitutions in zinc finger domain (10), YABBY domain (2), and interdomain regions (10). A deletion of 10 aa at the C-terminal interdomain sequence is characteristic of the S. arcanum INO.

The goat’s rue rhizobia (Neorhizobium galegae) represent a convenient model to study the evolution and speciation of symbiotic bacteria. This rhizobial species is composed of two biovars (bv. orientalis and bv. officinalis), which form N₂-fixing nodules with certain species of goat’s rue (Galega orientalis and G. officinalis). The cross-inoculation between them results in the formation of nodules unable to fix nitrogen. On the basis of the data on the whole-genome sequencing, we studied the nucleotide polymorphism of 11 N. galegae strains isolated from the North Caucasus ecosystems, where G. orientalis has higher diversity than G. officinalis. The low level of differences in the polymorphism within the group of the sym genes in comparison with the nonsymbiotic genes can be associated with the active participation of host plants in the evolution of rhizobia. The intragenic polymorphism of bv. orientalis proved to be significantly higher than that of bv. officinalis. The level of polymorphism of nonsymbiotic genes was lower than that of the symbiotic genes, which are functionally more homogeneous. The divergence of the nitrogen fixation genes (nif/fix) is more pronounced than that of the nodule formation genes (nod) in the N. galegae biovars. These facts indicate the leading role of the host-specific nitrogen fixation in the evolution of the studied rizhobial species.