The pRb-E2F pathway is involved in mediating diverse cell fates, and oncogenic disruption of the pathway is regarded as a hallmark of cancer. Recent studies highlighted the pRb-E2F axis as a regulator of a large gene network which includes RNA splicing and transcription targets. Here, we have performed a deep genome-wide analysis of differentially expressed genes (DEGs) and alternatively spliced (AS) RNA targets which highlighted broadly non-overlapping networks of genes that are independently regulated by the pRb-E2F pathway. Individual pathway components, including E2F1, pRb, and PRMT5, either as single or combined knockouts, were found to influence DEG and AS networks but to different extents. An analysis of the E2F1 interactome revealed SRSF2 and HNRNPC as candidate proteins that were able to functionally assist E2F1 in mediating AS events. Moreover, E2F1 AS activity was evident as cells progress through the cell cycle and during the DNA damage response, and apparent in tumour models. Our results highlight gene networks where transcription and splicing are linked and coordinated by the pRb-E2F pathway, and further establish the widespread influence that pRb, E2F1, and PRMT5 have on regulating biological diversity through RNA splicing control.

PRMT5 is expressed at high levels in many cancers, where it regulates diverse cellular pathways that contribute to oncogenesis. Here, we have defined a new role for PRMT5 in regulating and coordinating the interplay between the innate and adaptive immune response. This occurs, in part, through the influence of PRMT5 and E2F1 on RNA splicing and the presence of retained introns (RIs). We found that RIs have a propensity to form double-stranded RNAs that contribute to the innate response. Furthermore, many RIs contain non-canonical open-reading frames (ncORFs), which can be translated and then processed into small peptides that assemble with the MHC class I complex. Significantly, RI-derived peptides are highly immunogenic and, as a murine cancer vaccine, carrying a string of antigenic RI peptides, delayed tumour growth and enhanced survival. RIs are present in human tumour cells, and we identified T lymphocytes in human cancer patients, with antigen specificity for RI-derived peptides, that killed human tumour cells in vitro. Regulating intron retention thus offers a new therapeutic approach to enhance tumour immunogenicity. PRMT5-regulated intron retention generates non-canonical MHC class I antigens that drive anti-tumour immunity and can be exploited for cancer vaccine development. PRMT5-regulated intron retention generates non-canonical MHC class I antigens that drive anti-tumour immunity and can be exploited for cancer vaccine development.

This study analyzed genetic data using DNA isolated from museum specimens of polar bears in the collection of the Zoological Institute of the Russian Academy of Sciences. The unique data obtained in this study made it possible to characterize the population structure of polar bears in the past and to lay the foundation for further research. Methods of DNA isolation used in archaeogenetics and paleogenetics were applied to historical materials. These methods provided a sufficient quantity and quality of DNA suitable for high-throughput sequencing. The analysis of genetic variants made it possible to reveal the population structure of spatial and temporal polar bear populations in the Russian Arctic regions and its changes associated with the economic activities that unfolded in the first third of the 20th century.

One important direction in cancer prevention is the development of novel strategies that can be used in treatment by affecting the mechanisms of the regulatory pathways and genomic elements involved in malignant transformation. The strategy proposed in this study is to initiate cell death mechanisms in response to the depletion of the energy resources within a cancer cell due to the uncontrolled spread of mobile genetic elements throughout its genome. The calculation results obtained using a preliminary mathematical model that simulates the cellular bioenergetic balance, taking the energy consumption for retrotransposition of the mobile elements such as LINE-1 and SINE into account, show that this scenario is plausible. Intracellular resources undergo a critical redistribution when affecting the genomic defense mechanisms and the LINE-1 transcription rate. This leads to a sharp increase in energy consumption for retrotransposon transcription that causes a significant decrease in the pool of free ATP in the cell.

Retrotransposons exhibit increased activity in cancer cells. One possible approach to anticancer therapy is to use this activity to influence the energy balance in cells. Abnormal distribution of retrotransposons in the genome requires additional energy consumption, which can lead to a significant decrease in the total amount of free ATP molecules in the cell. A decrease in ATP levels below a certain threshold can in turn trigger a cell death program. To investigate the possibility of such a scenario, we developed a mathematical model of the cellular energy balance that describes the dynamics of energy consumption by the main cellular processes, including costs of retrotransposon activity. The model considers changes in the concentrations of ATP, active retrotransposons (LINE-1 and SINE) in the human genome, as well as mRNAs and proteins that are expression products of retrotransposon and constitutive genes. We estimated the parameter values in the model based on literature data and numerical optimization. We found a single stable stationary solution, characterized by low retrotransposon activity, and used it as the reference steady state for further analysis. Parametric sensitivity analysis revealed the parameters whose changes had the greatest impact on cellular ATP levels. The LINE-1 deactivation rate constant and the maximum LINE-1 transcription rate were the most sensitive among the transposon-related parameters. Perturbation of these parameters led to a decrease in the number of free ATP to 30% of the reference value and below. Transcription of retrotransposons under perturbed parameters became comparable to the translation of constitutive genes in terms of energy costs. The presented results indicate that cancer cell death can be initiated by increasing the load on the energy balance due to the activation of transposons.

Chickpea is the second most important legume crop, which is used as a food by people in different parts of the world due to its high nutritive value. Omics technologies have revolutionized the characterization of chickpea genetic diversity by considering single-nucleotide polymorphisms, while structural variants and transposons have been overlooked. The specific contribution of transposons to the phenotypic diversification of crop species is still poorly documented, therefore its characterization is important. We focused on landraces collected before the “green revolution”, as they are a valuable source of species diversity and can be used to broaden the genetic base of modern cultivars. Analyzing 190 chickpea genomes, we found 42,324 new transposon insertion sites from 83 families and showed that such sites are highly polymorphic. Most insertions were caused by mobilization of retrotransposons (67 % of insertions); among DNA transposons, the highest number of insertions was found for the superfamilies MuDR, PIF, hAT, CMC, and TcMar. We also demonstrated an uneven distribution of insertion sites along chromosomes. Analysis of the localization of transposon insertion sites relative to genes and their structural elements has shown that the largest number of insertions in all transposon superfamilies falls on introns and the smallest, on exons. We also showed that transposon insertion sites, which until recently have been overlooked by population genomics, are an important factor that diversifies phenotypes and can be used in GWAS as markers replacing SNPs. Comparative analysis of landraces collected in different geographic regions showed that the Ethiopian accessions have many unique transposon insertion sites. Our results highlight the unique role of transposon mobilization in chickpea diversification and have important implications for breeding improved chickpea varieties adapted to global climate change.

High-throughput sequencing of ancient DNA from Fatyanovo and Abashevo cultures (7 and 3 men, respectively) has led to new hypotheses about their origin and contacts. According to published archaeological evidence, i. e., due to striking similarities between the grave goods discovered in the Middle Volga Abashevo burial complexes and those found in the bell-shaped beaker culture, it is believed that the Fatyanovo people may have descended from the Corded Ware Culture. The present study demonstrates, for the first time, the remarkable similarity between the Fatyanovo people, as represented by the Volosovo-Danilovsky and Nikultsino burial grounds in the Yaroslavl region, and three distinct cultural groups: a) the Corded Culture People, primarily from Bohemia and Germany, b) the Bell-Beaker cultures, found in the same region as well as in France and the Netherlands, and c) the bearers of the Unetice culture. Furthermore, the Abashevite from the Pepkino mound (burial id 18) is genetically similar to several Fatyanovo individuals from the Volosovo-Danilovsky and Nikultsino burial grounds. Finally, the new set of AMS-radiocarbon dates has helped to narrow down the chronological gap between the Fatyanovo and Abashevo people’s expansion towards the Upper and Middle Volga regions, thereby indicating a direct contact between these two groups. Therefore, we can hypothesize that the highly mobile and dispersed lifestyle intrinsic to cattle-breeders may have led to the reclamation of vast territories in the east while still maintaining close ties with their ancestral lands. In conclusion, our findings demonstrate that the Fatyanovo and Abashevo people likely originate from the same genetic background and are integral parts of the Corded Culture world, rather than “lost children” as previously assumed.

The focus of our study is the burials of two young men who died in distant lands (Middle Volga region and Southern Urals). Whole genome sequencing revealed a remarkable genetic similarity between the individuals and their potential decent from common ancestors. Men from the excavations of the Pepkino mound (burial No. 8, bronze caster) and buried No. 3 at the settlement of Maloyuldashevo 1 (sacrificed individual) were the owners of haplogroup R1b (Z2103) with a common paternal ancestor. The search of genome fragments identical by origin (IBD method — Identity-By-Descent) showed patterns inherited from a common ancestor without recombination. In a pairwise comparison of Pepkino caster with other samples, the probability of the occurrence of at least one IBD fragment in the genomes was more than 0.9 for both the Maloyldashevo sample, as well for a female (sample POST_131) from Southern Bavaria with close AMS date. Using the PCA method, we identified the owner of a similar genotype in a burial of the Sintashta culture (Kamennyi Ambar 5 burial ground, mound 2, burial 16), for which a mixed origin was previously established with the participation of West Siberian hunter-gatherers and steppe dwellers of the Bronze Age. In addition, among other genetic outliers of the same necropolis, there were men with haplogroup of the Y chromosome R1b, which brings them closer to the individuals we studied from the Pepkino mound and Maloyuldashevo settlement. Thus, the distribution of a mobile group has been shown, which was incorporated into different cultural traditions.

Genomic structural variations (SVs) are among the main sources of genetic diversity. Structural variants as mutagens may significantly affect human health, causing hereditary diseases and cancers. Existing methods analyze high-throughput sequencing data to find structural variants. Despite substantial progress in their development, the methods still fail to detect structural variations with an accuracy sufficient for their use in diagnosis. Analysis of the sequencing coverage signal (i.e., the number of aligned sequencing reads for every point of a genome) holds the new potential for designing approaches to structural variation detection and can be used as time-series analysis. A method to detect repetitive patterns in the coverage signal was developed based on the time series-assessing algorithms KNN (K-nearest neighbor) and SAX (Symbolic Aggregation Approximation). Using the rich dataset encompassing the full genomes of 911 individuals with different ethnic backgrounds from the Human Genome Diversity Project, generalized patterns of the coverage signal were constructed for regions in the vicinity of breakpoints corresponding to various structural variant types. The patterns were used to develop a software package for fast detection of anomalies in the coverage signal.

Protein arginine methyltransferase 5 (PRMT5) is over‐expressed in a wide variety of cancers and is implicated as having a key oncogenic role, achieved in part through its control of the master transcription regulator E2F1. We investigated the relevance of PRMT5 and E2F1 in neuroblastoma (NB) and found that elevated expression of PRMT5 and E2F1 occurs in poor prognosis high‐risk disease and correlates with an amplified Myelocytomatosis viral‐related oncogene, neuroblastoma‐derived (MYCN) gene. Our results show that MYCN drives the expression of splicing factor genes that, together with PRMT5 and E2F1, lead to a deregulated alternative RNA splicing programme that impedes apoptosis. Pharmacological inhibition of PRMT5 or inactivation of E2F1 restores normal splicing and renders NB cells sensitive to apoptosis. Our findings suggest that a sustained cancer‐relevant alternative RNA splicing programme desensitises NB cells to apoptosis, and identify PRMT5 as a potential therapeutic target for high‐risk disease.

Background Bisulfite sequencing detects and quantifies DNA methylation patterns, contributing to our understanding of gene expression regulation, genome stability maintenance, conservation of epigenetic mechanisms across divergent taxa, epigenetic inheritance and, eventually, phenotypic variation. Graphical representation of methylation data is crucial in exploring epigenetic regulation on a genome-wide scale in both plants and animals. This is especially relevant for non-model organisms with poorly annotated genomes and/or organisms where genome sequences are not yet assembled on chromosome level. Despite being a technology of choice to profile DNA methylation for many years now there are surprisingly few lightweight and robust standalone tools available for efficient graphical analysis of data in non-model systems. This significantly limits evolutionary studies and agrigenomics research. BSXplorer is a tool specifically developed to fill this gap and assist researchers in explorative data analysis and in visualising and interpreting bisulfite sequencing data more easily. Results BSXplorer provides in-depth graphical analysis of sequencing data encompassing (a) profiling of methylation levels in metagenes or in user-defined regions using line plots and heatmaps, generation of summary statistics charts, (b) enabling comparative analyses of methylation patterns across experimental samples, methylation contexts and species, and (c) identification of modules sharing similar methylation signatures at functional genomic elements. The tool processes methylation data quickly and offers API and CLI capabilities, along with the ability to create high-quality figures suitable for publication. Conclusions BSXplorer facilitates efficient methylation data mining, contrasting and visualization, making it an easy-to-use package that is highly useful for epigenetic research.

To assess the genomic diversity of Fusarium oxysporum f. sp. lini strains and compile a comprehensive gene repertoire, we constructed a pangenome using 13 isolates from four different clonal lineages, each exhibiting distinct levels of virulence. Syntenic analyses of two selected genomes revealed significant chromosomal rearrangements unique to each genome. A comprehensive examination of both core and accessory pangenome content and diversity points at an open genome state. Additionally, Gene Ontology (GO) enrichment analysis indicated that non-core pangenome genes are associated with pathogen recognition and immune signaling. Furthermore, the Folini pansecterome, encompassing secreted proteins critical for fungal pathogenicity, primarily consists of three functional classes: effector proteins, CAZYmes, and proteases. These three classes account for approximately 3.5% of the pangenome. Each functional class within the pansecterome was meticulously annotated and characterized with respect to pangenome category distribution, PFAM domain frequency, and strain virulence assessment. This analysis revealed that highly virulent isolates have specific types of PFAM domains that are exclusive to them. Upon examining the repertoire of SIX genes known for virulence in other formae speciales, it was found that all isolates had a similar gene content except for two, which lacked SIX genes entirely.

Classical methods for identification of genetic variants associated with certain macroscopic phenotypic traits are, as a rule, limited to analysis of single nucleotide polymorphisms. Copy number variations and more general structural variants may provide a plethora of useful information due to the magnitude of the changes they induce. However, their use in genome-wide association studies is seriously limited mostly due to the uncertainties in their discovery by computational algorithms from genomic data (i.e., failure to resolve an event with nucleotide resolution). Nevertheless, in certain cases, such analysis is possible and may yield valuable results. Our recent work revealed genetic variants (single nucleotide polymorphisms) possibly related to phenotypic traits determining fiber quality in flax. Here, we decided to extend the analyses to structural variants, namely copy number variations. Importantly, we use a novel high-coverage dataset allowing accurate prediction of copy number variations. Altogether, a list of 41 candidate genes associated with five quantitative phenotypic traits was compiled. Furthermore, the genome stability metric developed earlier facilitated stratification of copy number variant loci with regard to their stability. On the whole, our analysis suggests that the genomic regions less resilient to external and internal stresses are more susceptible to changes associated with the studied phenotypic traits.

Modern genome technologies and a widespread use of omics data have revolutionized healthcare and brought unprecedented opportunities to apply genetics to medicine to maximize patient benefit. Genomic medicine provides innovative approaches to rapid and reliable early disease diagnostics, patients stratification to assess and monitor the effectiveness of therapy and, finally, population-scale screening for predisposition to certain diseases. In view of this, many countries took steps to adopt of genomics in clinical practice, thus transforming national healthcare systems. Here we discuss main applications of genomic data in clinical practice, its contribution to personalised medicine and associated emerging challenges, as well as key considerations for the successful integration of genomic technologies into healthcare systems. Besides that, we showcase several national genomic medicine programmes, particularly the UK one, providing a detailed review of approaches to transformation of the national healthcare system as implemented by Genomics England initiative. Finally, we discuss possible avenues for the development of genomic medicine system in Russia.

Recent advances in high-throughput sequencing have enabled the development of a novel approach to the evaluation of genome stability and integrity. The depth of the coverage signal at a particular genome location may point to DNA integrity loss in the region. In this work, the previously developed metric of local genomic integrity, which estimates the uniformity of the coverage signal, has been transformed to a quantitative trait, and genetic variants associated with coverage signal uniformity in the flax genome have been sought. Quantitative Trait Loci (xQTLs; where x is the designation of an arbitrary quantitative parameter associated with a particular genome region, for example, the levels of gene expression, the degree of coverage by ribosomes, etc.) have been analyzed to identify genomic regions that most likely contribute to the loss of genomic integrity and may be involved in the maintenance of genome stability. The analysis invokes information on the whole-genome sequence assembly of 100 flax samples and enables the identification of genes presumably implicated in maintenance of genomic integrity in flax and, possibly, in plants in general. It also reveals novel processes associated with the maintenance of genomic integrity.

SWaveform, a newly created open genome-wide resource for read depth signal in the vicinity of structural variant (SV) breakpoints, aims to boost development of computational tools and algorithms for discovery of genomic rearrangement events from sequencing data. SVs are a dominant force shaping genomes and substantially contributing to genetic diversity. Still, there are challenges in reliable and efficient genotyping of SVs from whole genome sequencing data, thus delaying translation into clinical applications and wasting valuable resources. SWaveform includes a database containing ~7 M of read depth profiles at SV breakpoints extracted from 911 sequencing samples generated by the Human Genome Diversity Project, generalised patterns of the signal at breakpoints, an interface for navigation and download, as well as a toolbox for local deployment with user’s data. The dataset can be of immense value to bioinformatics and engineering communities as it empowers smooth application of intelligent signal processing and machine learning techniques for discovery of genomic rearrangement events and thus opens the floodgates for development of innovative algorithms and software.

Chickpea (Cicer arietinum L.) is a major grain legume and a good source of plant-based protein. However, comprehensive knowledge of flowering time control in Cicer is lacking. In this study, we acquire high-throughput transcriptome sequencing data and analyze changes in gene expression during floral transition in the early flowering cultivar ICCV 96029, later flowering C. arietinum accessions, and two wild species, C. reticulatum and C. echinospermum. We identify Cicer orthologs of A. thaliana flowering time genes and analyze differential expression of 278 genes between four species/accessions, three tissue types, and two conditions. Our results show that the differences in gene expression between ICCV 96029 and other cultivated chickpea accessions are vernalization-dependent. In addition, we highlight the role of FTa3, an ortholog of FLOWERING LOCUS T in Arabidopsis, in the vernalization response of cultivated chickpea. A common set of differentially expressed genes was found for all comparisons between wild species and cultivars. The direction of expression change for different copies of the FT-INTERACTING PROTEIN 1 gene was variable in different comparisons, which suggests complex mechanisms of FT protein transport. Our study makes a contribution to the understanding of flowering time control in Cicer, and can provide genetic strategies to further improve this important agronomic trait.

This study addresses a fundamental question of the origins and migration patterns of paleopopulations of the Fatyanovo and the Middle Volga Abashevo archaeological cultures. It is for the first time that we report a paleogenetic analysis of 14 Abashevo individuals (Pepkino and Starshy Nikitinsky sites). Besides, we analysed ancient DNA samples of 25 Fatyanovo individuals. Specifically, we performed analyses of STR marker and haplogroups of the Y chromosome, which revealed the distinct R1a (Z93) haplogroup in Fatyanovo samples. It indicates the influence of the founder effect and gene drift, confirming the hypothesis of their migrant origin. In contrast, the Abashevo culture samples are heterogenous, as we discovered 2 groups with different origins on the paternal line. To be more specific, three men from Pepkino mound are haplogroup R1b (Z2103) carriers, while seven other individuals have haplogroup R1a (Z93>Z94). In addition, close relatives with identical STR haplotypes of the Y-chromosome were identified in both Fatyanovo and Abashevo groups. The comparative analyses of autosomal markers from 19 samples and previously published data uncovered similarities between Abashevo men from Pepkino mound (the haplogroup R1a (Z93>Z94)) with the Fatyanovo people, as well as with some representatives of the Unetice culture. These results are suggestive of the genetic continuity in the Russian Plain. Yet, less recent ancestors of Abashevo group interred in Pepkino mound could have migrated from the same region as the Fatyanovo predesessors.

Whole genome sequencing data allow access not only to information about genetic variation, but also provide an opportunity to evaluate the overall genome stability. Sequencing coverage signal considered as the number of fragments aligned to a given region within the genome can be used as a trustworthy source of data both on discovery of genomic rearrangements and the current state of whole genome sequencing as well as on accuracy of structural variant predictions by computational algorithms. The latter is of utmost importance, since various tools for finding gene rearrangements often produce conflicting results concerning gene rearrangement events. However, until recently, validation of predicted variants presented a significant challenge, mainly due to the lack of information sources allowing researchers to work directly with coverage signals and to visualize the signals with high precision. The present study proposes Sequence COverage ProfilEs (SCOPE), a prototype toolset that includes databases, web interface, and a series of programs for the processing of sequencing data, as well as for visualization and storage of signal coverage profiles. The computing platform and the interface are equipped with open-source software, support local host deployment, and allow users to process and analyze their own sequencing data.