ЕКСПОРТНИЙ ПОТЕНЦІАЛ АГРАРНОГО СЕКТОРУ УКРАЇНИ В УМОВАХ КОНКУРЕНТНОГО СЕРЕДОВИЩА

The purpose of the paper is to investigate the level of competitiveness of agricultural and food products and to identify the possible areas of export development on the basis of scientific works and the existing system of national strategy of the agricultural sector development. The concept of «export potential of the agricultural sector” and its relation to the competitiveness of agricultural enterprises was revealed. The dynamics and the geography of Ukrainian export of agro-food products was investigated. The data of the State Statistics Committee of Ukraine for 2005—2016, Internet resources, and own observations served as the basis for the research. For the purposes of the research such groups of the most important product types were selected: cereals, namely: winter wheat, winter barley, corn; vegetable oil (sunflower, rapeseed, soybean), strawberry, sunflower and soya, etc., and as well as those that at the present stage are advocated and, thus, may significantly raise export potential in the long term (meat, poultry, dairy products, etc.). Change in the orientation of agro-export is associated with several factors: firstly, difficult political relationships with the Russian Federation resulted in a significant reduction in the volumes of exports to this country; secondly, the increase in exports to EU countries in connection to the signing of association agreement with the EU; thirdly, the continued growth of exports to the countries of Asia and Africa.It is the «competitiveness» that identifies the opportunities for the products supply on external markets, and this is a potential set of types of agro-food products, which domestic agricultural enterprises are able to export, that identifies the potential of the agricultural sector. Ukrainian producers have the advantage over the competitors in terms of the quality and products prices which is confirmed by the fact that domestic products are exported to more than 90 countries of the world. The use of the model of potential growth of export potential of the Ukrainian agro-products will able to fully provide growers with information about potential markets for products, to ensure the proper support for the promotion of products on foreign markets.Раскрыто понятие «экспортный потенциал аграрного сектора» и его взаимосвязь с «конкурентоспособностью сельскохозяйственных предприятий». Исследованы динамика и география экспорта агропродовольственной продукции в Украине. Использование предложенной модели потенциального роста экспортного потенциала украинской агропродовольственной продукции позволит полностью обеспечить аграриев информацией о возможных рынков сбыта продукции, обеспечить надлежащую поддержку при продвижении продукции на зарубежные рынки.Ціллю дослідження є дослідження на базі наукових доробків і чинної системи вітчизняної стратегії розвитку аграрного сектору економіки рівень розвитку конкурентоспроможності вітчизняної аграрної та продовольчої продукції і визначення можливих напрямів експортного розвитку. Розкрито поняття «експортний потенціал аграрного сектору» і його взаємозв’язок з «конкурентоспроможністю сільськогосподарських підприємств». Досліджено динаміку і географію експорту агропродовольчої продукції в Україні. Основою дослідження слугували дані Державного комітету статистики України за 2005—2016 роки, дані Інтернет-ресурсів і власні спостереження авторів. Для цілей роботи відібрано групи найбільш значущих видів продукції [озима пшениця, озимий ячмінь, кукурудза; рослинна олія (соняшникова, ріпакова, соєва), полуниця, насіння соняшнику та боби сої тощо] і тих, які на сучасному етапі виступають бюджетоформувальними та таких, що можуть суттєво наростити експортний потенціал у перспективі (м’ясо, птиця, молочні продукти тощо). Зміна орієнтирів експорту агропродовольчої продукції пов’язана з декількома основними чинниками: по-перше, важкі політичні стосунки з Російською Федерацією призвели до суттєвого скорочення обсягів продукції в цю країну; по-друге, збільшення експорту до країн ЄС у зв’язку з укладенням Угоди про асоціацію з ЄС; по-третє, подальше зростання експорту в країни Азії та Африки. Саме «конкурентоспроможність» визначає можливості постачання продуктів на зовнішні ринки і включає потенційний набір типів агропродовольчих товарів, які вітчизняні сільськогосподарські підприємства можуть експортувати, що визначає потенціал аграрного сектору. Українські виробники мають перевагу перед конкурентами щодо якості та цін виробів, що підтверджується тим фактом, що вітчизняна продукція експортується в більш ніж 90 країн світу. Використання запропонованої моделі потенційного зростання експортного потенціалу української агропродовольчої продукції дасть можливість повністю забезпечити аграріїв інформацією щодо можливих ринків збуту продукції, забезпечити належну підтримку при просуванні продукції на зарубіжні ринки

Does co-transcriptional regulation of alternative splicing mediate plant stress responses?

Plants display exquisite control over gene expression to elicit appropriate responses under normal and stress conditions. Alternative splicing (AS) of pre-mRNAs, a process that generates two or more transcripts from multi-exon genes, adds another layer of regulation to fine-tune condition-specific gene expression in animals and plants. However, exactly how plants control splice isoform ratios and the timing of this regulation in response to environmental signals remains elusive. In mammals, recent evidence indicate that epigenetic and epitranscriptome changes, such as DNA methylation, chromatin modifications and RNA methylation, regulate RNA polymerase II processivity, co-transcriptional splicing, and stability and translation efficiency of splice isoforms. In plants, the role of epigenetic modifications in regulating transcription rate and mRNA abundance under stress is beginning to emerge. However, the mechanisms by which epigenetic and epitranscriptomic modifications regulate AS and translation efficiency require further research. Dynamic changes in the chromatin landscape in response to stress may provide a scaffold around which gene expression, AS and translation are orchestrated. Finally, we discuss CRISPR/Cas-based strategies for engineering chromatin architecture to manipulate AS patterns (or splice isoforms levels) to obtain insight into the epigenetic regulation of AS

Differential nucleosome occupancy modulates alternative splicing in Arabidopsis thaliana

• Alternative splicing (AS) is a major gene regulatory mechanism in plants. Recent evidence supports co-transcriptional splicing in plants, hence the chromatin state can impact AS. However, how dynamic changes in the chromatin state such as nucleosome occupancy influence the cold-induced AS remains poorly understood. • Here, we generated transcriptome (RNA-Seq) and nucleosome positioning (MNase-Seq) data for Arabidopsis thaliana to understand how nucleosome positioning modulates cold-induced AS. • Our results show that characteristic nucleosome occupancy levels are strongly associated with the type and abundance of various AS events under normal and cold temperature conditions in Arabidopsis. Intriguingly, exitrons, alternatively spliced internal regions of protein-coding exons, exhibit distinctive nucleosome positioning pattern compared to other alternatively spliced regions. Likewise, nucleosome patterns differ between exitrons and retained introns pointing to their distinct regulation. • Collectively, our data show that characteristic changes in nucleosome positioning modulate AS in plants in response to cold

Reciprocal regulation of glycine-rich RNA-binding proteins via an interlocked feedback loop coupling alternative splicing to nonsense-mediated decay in Arabidopsis

The Arabidopsis RNA-binding protein AtGRP8 undergoes negative autoregulation at the post-transcriptional level. An elevated AtGRP8 protein level promotes the use of a cryptic 5′ splice site to generate an alternatively spliced transcript, as_AtGRP8, retaining the 5′ half of the intron with a premature termination codon. In mutants defective in nonsense-mediated decay (NMD) abundance of as_AtGRP8 but not its pre-mRNA is elevated, indicating that as_AtGRP8 is a direct NMD target, thus limiting the production of functional AtGRP8 protein. In addition to its own pre-mRNA, AtGRP8 negatively regulates the AtGRP7 transcript through promoting the formation of the equivalent alternatively spliced as_AtGRP7 transcript, leading to a decrease in AtGRP7 abundance. Recombinant AtGRP8 binds to its own and the AtGRP7 pre-mRNA, suggesting that this interaction is relevant for the splicing decision in vivo. AtGRP7 itself is part of a negative autoregulatory circuit that influences circadian oscillations of its own and the AtGRP8 transcript through alternative splicing linked to NMD. Thus, we identify an interlocked feedback loop through which two RNA-binding proteins autoregulate and reciprocally crossregulate by coupling unproductive splicing to NMD. A high degree of evolutionary sequence conservation in the introns retained in as_AtGRP8 or as_AtGRP7 points to an important function of these sequences

Regulation of Plant Developmental Processes by a Novel Splicing Factor

Serine/arginine-rich (SR) proteins play important roles in constitutive and alternative splicing and other aspects of mRNA metabolism. We have previously isolated a unique plant SR protein (SR45) with atypical domain organization. However, the biological and molecular functions of this novel SR protein are not known. Here, we report biological and molecular functions of this protein. Using an in vitro splicing complementation assay, we showed that SR45 functions as an essential splicing factor. Furthermore, the alternative splicing pattern of transcripts of several other SR genes was altered in a mutant, sr45-1, suggesting that the observed phenotypic abnormalities in sr45-1 are likely due to altered levels of SR protein isoforms, which in turn modulate splicing of other pre-mRNAs. sr45-1 exhibited developmental abnormalities, including delayed flowering, narrow leaves and altered number of petals and stamens. The late flowering phenotype was observed under both long days and short days and was rescued by vernalization. FLC, a key flowering repressor, is up-regulated in sr45-1 demonstrating that SR45 influences the autonomous flowering pathway. Changes in the alternative splicing of SR genes and the phenotypic defects in the mutant were rescued by SR45 cDNA, further confirming that the observed defects in the mutant are due to the lack of SR45. These results indicate that SR45 is a novel plant-specific splicing factor that plays a crucial role in regulating developmental processes

Alternative splicing of barley clock genes in response to low temperature:evidence for alternative splicing conservation

Alternative splicing (AS) is a regulated mechanism that generates multiple transcripts from individual genes. It is widespread in eukaryotic genomes and provides an effective way to control gene expression. At low temperatures, AS regulates Arabidopsis clock genes through dynamic changes in the levels of productive mRNAs. We examined AS in barley clock genes to assess whether temperature-dependent AS responses also occur in a monocotyledonous crop species. We identify changes in AS of various barley core clock genes including the barley orthologues of Arabidopsis AtLHY and AtPRR7 which showed the most pronounced AS changes in response to low temperature. The AS events modulate the levels of functional and translatable mRNAs, and potentially protein levels, upon transition to cold. There is some conservation of AS events and/or splicing behaviour of clock genes between Arabidopsis and barley. In addition, novel temperature-dependent AS of the core clock gene HvPPD-H1 (a major determinant of photoperiod response and AtPRR7 orthologue) is conserved in monocots. HvPPD-H1 showed a rapid, temperature-sensitive isoform switch which resulted in changes in abundance of AS variants encoding different protein isoforms. This novel layer of low temperature control of clock gene expression, observed in two very different species, will help our understanding of plant adaptation to different environments and ultimately offer a new range of targets for plant improvement

The fitness cost of mis-splicing is the main determinant of alternative splicing patterns

Background Most eukaryotic genes are subject to alternative splicing (AS), which may contribute to the production of protein variants or to the regulation of gene expression via nonsense-mediated messenger RNA (mRNA) decay (NMD). However, a fraction of splice variants might correspond to spurious transcripts and the question of the relative proportion of splicing errors to functional splice variants remains highly debated. Results We propose a test to quantify the fraction of AS events corresponding to errors. This test is based on the fact that the fitness cost of splicing errors increases with the number of introns in a gene and with expression level. We analyzed the transcriptome of the intron-rich eukaryote Paramecium tetraurelia. We show that in both normal and in NMD-deficient cells, AS rates strongly decrease with increasing expression level and with increasing number of introns. This relationship is observed for AS events that are detectable by NMD as well as for those that are not, which invalidates the hypothesis of a link with the regulation of gene expression. Our results show that in genes with a median expression level, 92–98% of observed splice variants correspond to errors. We observed the same patterns in human transcriptomes and we further show that AS rates correlate with the fitness cost of splicing errors. Conclusions These observations indicate that genes under weaker selective pressure accumulate more maladaptive substitutions and are more prone to splicing errors. Thus, to a large extent, patterns of gene expression variants simply reflect the balance between selection, mutation, and drift

Comparative Analysis of Serine/Arginine-Rich Proteins across 27 Eukaryotes: Insights into Sub-Family Classification and Extent of Alternative Splicing

Alternative splicing (AS) of pre-mRNA is a fundamental molecular process that generates diversity in the transcriptome and proteome of eukaryotic organisms. SR proteins, a family of splicing regulators with one or two RNA recognition motifs (RRMs) at the N-terminus and an arg/ser-rich domain at the C-terminus, function in both constitutive and alternative splicing. We identified SR proteins in 27 eukaryotic species, which include plants, animals, fungi and “basal” eukaryotes that lie outside of these lineages. Using RNA recognition motifs (RRMs) as a phylogenetic marker, we classified 272 SR genes into robust sub-families. The SR gene family can be split into five major groupings, which can be further separated into 11 distinct sub-families. Most flowering plants have double or nearly double the number of SR genes found in vertebrates. The majority of plant SR genes are under purifying selection. Moreover, in all paralogous SR genes in Arabidopsis, rice, soybean and maize, one of the two paralogs is preferentially expressed throughout plant development. We also assessed the extent of AS in SR genes based on a splice graph approach (http://combi.cs.colostate.edu/as/gmap_SRgenes). AS of SR genes is a widespread phenomenon throughout multiple lineages, with alternative 3′ or 5′ splicing events being the most prominent type of event. However, plant-enriched sub-families have 57%–88% of their SR genes experiencing some type of AS compared to the 40%–54% seen in other sub-families. The SR gene family is pervasive throughout multiple eukaryotic lineages, conserved in sequence and domain organization, but differs in gene number across lineages with an abundance of SR genes in flowering plants. The higher number of alternatively spliced SR genes in plants emphasizes the importance of AS in generating splice variants in these organisms