Power-law Behavior of the Alternative Splicing of Exons in Human Transcriptome

Aims: To establish the common rules of exon combinatorics during RNA splicing. Study Design: Inferring a plausible statistical model of exon combinatorics from the annotated models of human genes during RNA splicing. Place and Duration of Study: Department of Genetics (Belarusian State University), Proteome and Genome Research Unit (Luxembourg Institute of Health), Department of Genetics (Lomonosov Moscow State University) and Moscow Center of Experimental Embryology and Reproductive Biotechnologies, between January 2017 and July 2019. Methodology: We used human mRNA and EST sequences from GenBank (1093522 unique records in total) and linear models of the human genes from Ensembl (58051 genes), AceView (72384 genes), ECgene (57172 genes), NCBI RefSeq (54262 genes), UCSC Genome Browser (58037 genes) and VEGA (54950 genes) to calculate a combinatorial index of human exons. We inferred the most plausible statistical model describing the distribution of combinatorial index of human exons using Clauset’s mathematical formalism. Predictors of the combinatorial index values and functional outcomes of the predefined behavior of exons during splicing were also determined. Results: Power-law is the most plausible statistical model describing the combinatorics of exons during RNA splicing. The combinatorial index of human exons is defined by more than 90% by the 138 features that have different importance. The most important of these features are the abundance of exon in transcripts, the strength of splice sites, the rank of exon in transcripts and the type of exon. Analysis of the marginal effects shows that different values of the same feature have unequal influence on the combinatorial index of human exons. Power-law behavior of exons during RNA splicing pre-determines structural diversity of transcripts, low sensitivity of splicing process to random perturbations and its high vulnerability to manipulation with highly combinative exons. Conclusion: Exons widely involved in alternative splicing are a part of the common power-law phenomenon in human cells. The power-law behavior of exons during RNA splicing gives the unique characteristics to human genes.

A Novel Test System for Genotyping rs43703016 Single-nucleotide Substitutions in the Bovine CSN3 Gene

Aims: Caseins are among the main milk proteins that determine many of its properties. Bovine kappa-casein (CSN3) is associated with the qualitative composition of milk, as well as with the quality of cheese obtained from this milk. The rs43703016 single-nucleotide substitution (g.88532332A>C; Asp148Ala) in exon 4 of the bovine CSN3 gene plays an important role in the production of quality hard cheeses. Various methods for the DNA testing of this substitution have been developed in the last three decades. Emergent DNA technologies provide an opportunity to modernize methods of genotyping single-nucleotide polymorphisms. Results: We have developed and verified a method to differentiate A/C alleles of the rs43703016 substitution in the bovine CSN3 gene by real-time PCR using allele-specific fluorescent probes. Conclusion: Our new method allows fast genotyping of animals, and may be used for selection of cows carrying the CC genotype, which determines good cheese-making properties of milk.

Frequencies of Genotypes and Alleles of the K232A Substitution in the DGAT1 Gene in Four Cattle Breeds of Russian Selection

The enzyme DGAT1 is involved in the synthesis of triglycerides. The most well-known polymorphic variant of the DGAT1 gene is substitution of lysine with alanine at position 232 of the protein (K232A). The 232K allele is associated with increased enzyme activity and a higher content and yield of fat in milk. There is less data on the frequencies of alleles of this replacement in different breeds in literature. In our research work, we analyzed the frequencies of genotypes and alleles of the K232A substitution in the DGAT1 gene in 4 breeds of Russian selection: Black-and-white Holsteinized, Kalmyk, Ayshire and Angus. We demonstrated that the K allele is minor in the populations of the analyzed cattle breeds.

The Search for a Receptor for Cell Infection by Bovine Leukemia Virus: Data Mining and Signaling Pathways Analysis

The bovine leukaemia virus (BLV) is widely spread all over the world. Currently, treatment of leukaemia-infected animals is not carried out. Not all virus carriers become ill with leukaemia. The existing genetic resistance to the disease is due to the presence of alleles of resistance of the main histocompatibility complex. However, another mechanism of resistance is possible, which is associated with the penetration of the virus into the cell. The work aimed to analyse the currently available data on possible receptors of the virus. Four potential molecules were found. The results suggest that the potential BLV receptor is a CD209 protein.

The Polymorphism of Regulatory Region of NOS3 Gene (rs2070744, Genotype CC) Protect Patients from Chronic Migraine.

Aims: There is evidence that endothelial nitric oxide synthase has a role in migraine pathophysiology. In our research, the role of SNP rs2070744 (c.-813C>T) in promoter region of NOS3 gene in the episodic and chronic forms of migraine is considered. Place and Duration of Study: University Headache Clinic between June 2012 and November 2014 and Department of Genetics, Faculty of Biology of Lomonosov Moscow State University between October 2013 and March 2016. Methodology: The study included 138 patients with migraine (44 with chronic and 96 with episodic migraine). The control group included 348 unexamined subjects. Genotypes were determined using real-time PCR with allelic discrimination test. Statistical processing was performed using Fisher test and Pearson's chi-squared test. Results: Our study evaluated the link of CC genotype of rs2070744 with migraine (Fisher’s p=0.026) and episodic migraine (Fisher’s p=0.022). Conclusion: Genotype CC of SNP rs2070744 in the regulatory region of NOS3 gene is more specific for episodic migraine and may prevents the chronification of migraine.