Vol 61, No 1 (2025)

Long non-coding RNAs (lncRNAs) are a class of linear or circular RNA molecules longer than 200 nucleotides without open reading frames. Experimental studies have shown the involvement of lncRNAs in the regulation of resistance to cold, salt, and heat stress, and in fruit, root, and leaf development. However, experimental methods are labor-intensive and costly approaches and cannot yet be used for genome-wide mass studies of lncRNAs. For this purpose, bioinformatic approaches that aim at large-scale recognition of lncRNA sequences in genomes and transcriptomes have been applied. However, despite the growing number of studies devoted to the structural and functional analysis of lncRNAs, this type of molecule remains poorly understood. This is due to the many factors that need to be considered when identifying lncRNAs. The use of pan-genomes and pan-transcriptomes will improve the efficiency of the study and the total number of predicted lncRNAs compared to using the genome of a single species representative. This review focuses on describing the molecular and biological functions of lncRNAs, experimental and bioinformatic methods of identification, patterns of evolution, detection and analysis of lncRNAs at the scale of pan-genomes and pan-transcriptomes.

The paper discusses a promising herbal preparation – thymoquinone, a component of black cumin (Nigella sativa), studied in experimental animals (mice, rats) in many pathologies, characterized by a positive effect and lack of toxic effect. The drug has been studied in a wide range of doses for injection and oral administration. Thymoquinone has antimicrobial, antiviral, anti-inflammatory, and radioprotective properties. The main damaging component of ionizing radiation is oxidative stress. For this reason, radioprotectors have recently been evaluated based on the drug’s ability to reduce oxidative stress. As markers of oxidative stress, we used parameters of changes in the expression of nuclear and mitochondrial DNA genes that perform essential functions in the cell. C57Bl/6 mice were administered thymoquinone (10 mg/kg) after 30 min. irradiation was performed (6 Gy). After 6 and 24 hours, gene expression in brain and spleen cells was studied using real-time PCR. It was shown that the activity of nuclear genes increased after exposure to radiation, but was normalized if thymoquinone was administered to mice 30 minutes before irradiation. Mitochondrial genes were also modified to target the activity of control cells. The test results show that thymoquinone has protective properties and may be promising as a radioprotector.

Using microsatellite markers (SSR), the genetic polymorphism of five coenopopulations of Siberian larch (L. sibirica) growing in the Republic of Khakassia was assessed. The highest values of the average number of alleles per locus were found in coenopopulations of L. sibirica from the steppe meadows of the valley of Lake Fyrkal (3.9 ± 0.458) and forested upland slopes in the valley of Lake Agaskyr (3.9 ± 0.348). The latter cenopopulation is also characterized by the maximum value of the effective number of alleles per locus (2.302 ± 0.283) and the highest rates of observed and expected heterozygosity (H_O = 0.487 ± 0.074, H_E = 0.492 ± 0.070). Analysis of the population structure indicates a 0.8% excess of heterozygous genotypes relative to the population (F_IS = −0.008 ± 0.031) and a 3.4% deficiency of heterozygous genotypes (F_IT = 0.034 ± 0.034) relative to the species. The differentiation of the studied cenopopulations of L. sibirica by SSR markers is 4.3% (F_ST = 0.043). The smallest genetic distance (0.036) was detected between ecotopically most similar (forest) coenopopulations of L. sibirica, and the largest genetic distance (0.077), on the contrary, was identified between ecotopically contrasting (swamp and steppe) coenopopulations.

The results of a research of polymorphism of 12 micro-satellite loci in Holstein cattle from an ordinal number of regions of Russia and external countries were presented. The average number of alleles per locus was 5.43 ± 0.19, with variation in the range of 4–13 alleles, the average number of effective alleles was 3.26 ± 0.11. A list of 29 most frequent alleles has been fixed. 22 private alleles were identified, and the frequency of private alleles was 0.004–0.033. It has been demonstrated that the amount of locally alleles in domestic herds is higher than in animals of external selection. The mean level of observed heterozygosity for all loci hold at 0.681 ± 0.017 and varied in the range of 0.65–0.78 for a fixation index of –0.131 ± 0.005. Genetic length between herds of domestic selection were < 0.074. It was revealed that groups of cow herds come down into two clusters. The first cluster included animals from three areas of Russia, associated with bulls from Germany and the Netherlands, and the second cluster included individuals from other two provinces closest to the males of Canada, the USA and GB. At once, the oxen of Denmark and Finland founds themselves in a separate cluster. The basis of this work was to evaluate the allele reservoir of Holstein cattle of domestic selection and determine the genetic profile of the breed by STR markers.

The article examined samples of domestic yak and three breeds of cattle to assess the differentiating potential of the polymorphic variants Chr4:68609356G>T (JAZF1 gene), Chr14:35695388G>T (SLCO5A1 gene) and Chr19:63181970C>G (CEP112 gene). The high accuracy (99.67%), specificity (100%) and sensitivity (100%) of the proposed test model consisting of these three polymorphisms for the identification of domestic yaks and cattle were confirmed. A fast and simple identification method has been developed based on this model using competitive allele-specific PCR (KASP) technology, which can significantly reduce the time and financial costs of molecular genetic analysis, as well as reduce the risk of cross-contamination of samples.

To assess the contribution to survival of Alu-insertions in the ACE, PLAT, COL13A1, LAMA2, CDH4, SEMA6A, PKHD1L1, STK38L, HECW1, TEAD1 genes, which are candidates of aging and longevity, amid the senile physiological and pathological phenotype, was carried out the association analysis with life expectancy. Survival and mortality data were obtained for 1,382 elderly people, who were selected from the sample of Tatars residing in the Republic of Bashkortostan (total 1790 people from 18 to 109 years). Mortality risk was higher among carriers of the STK38L Alu-insertion genotype (Ya5ac2145*II, HR = 2.07, P = 0.02). Alu-insertion in the HECW1 and TEAD1 genes has demonstrated a survival protection effect (Ya5NBC182*II, HR = 0.71, P = 0.038 and Ya5ac2013*II, HR = 0.74, P = 0.035 respectively). The survival amid the persons with various clinical phenotypes was associated with the Alu polymorphism of the SEMA6A (Yb8NBC597*ID, HR = 0.54, P = 0.016 for the cerebrovascular diseases), TEAD1 (Ya5ac2013*II, HR = 0.57, P = 0.016 for the cardiovascular pathologies) and LAMA2 (Ya5-MLS19*ID, HR = 0.36, P = 0.03 for multimorbidity status) genes. Thus, the genes involved in the regulation of autophagy and apoptosis were associated with survival and longevity.

The study aimed to analyze the associations between cognitive domains impaired in schizophrenia and the rs58335419 polymorphism located within the schizophrenia GWAS-significant locus, in the gene MIR137 encoding miR-137. Schizophrenia spectrum patients (n = 787) and healthy volunteers without a family history of psychosis (n = 622) completed tests of semantic verbal fluency (VF), attention/working memory, verbal episodic memory, and executive functions. After correction for multiple testing, VF abnormalities were associated with homozygosity for the common allele (with three repeats) in male patients. Similar trends occurred in the pooled sample for attention/working memory and the general index of cognitive functioning. The four-repeat allele was not associated with variance in cognitive performance. The results obtained indicate an association between homozygosity for the common allele at rs58335419 and lower levels of cognitive functions, which is opposite to the effect of this polymorphism on the risk of developing schizophrenia.