Wild type and mvp2 (maintained vegetative phase) deletion mutant T. monococcum plants incapable of flowering were compared in order to determine the effect of the deleted region of chromosome 5A on transcript profile and hormone metabolism. This region contains the vernalization1 (VRN1) gene, a major regulator of the vegetative/generative transition. Transcript profiling in the crowns of T. monococcum during the transition and the subsequent formation of flower primordia showed that 306 genes were affected by the mutation, 198 by the developmental phase and 14 by the interaction of these parameters. In addition, 546 genes were affected by two or three factors. The genes controlled by the deleted region encode transcription factors, antioxidants and enzymes of hormone, carbohydrate and amino acid metabolism. The observed changes in the expression of the gene encoding phenylalanine ammonia lyase (PAL) might indicate the effect of mvp2 mutation on the metabolism of salicylic acid, which was corroborated by the differences in 2-hydroxycinnamic acid and cinnamic acid contents in both of the leaves and crowns, and in the concentrations of salicylic acid and benzoic acid in crowns during the vegetative/generative transition. The amount and ratio of active cytokinins and their derivatives (ribosides, glucosides and phosphates) were affected by developmental changes as well as by mvp2 mutation, too.

• MeSH
• Biosynthetic Pathways genetics   MeSH
• Cytokinins metabolism   MeSH
• Gene Deletion MeSH
• Genotype MeSH
• Gene Regulatory Networks MeSH
• Salicylic Acid metabolism   MeSH
• RNA, Messenger genetics   metabolism   MeSH
• Mutation genetics   MeSH
• Triticum genetics   growth & development   MeSH
• Gene Expression Regulation, Plant MeSH
• Reproducibility of Results MeSH
• Plant Proteins genetics   metabolism   MeSH
• Oligonucleotide Array Sequence Analysis MeSH
• Cluster Analysis MeSH
• Transcriptome genetics   MeSH
• Gene Expression Regulation, Developmental MeSH
• Publication type
• Journal Article MeSH

• MeSH
• Epigenesis, Genetic * MeSH
• RNA genetics   metabolism   MeSH
• Transcriptome * MeSH
• Publication type
• Journal Article MeSH

The hop plant (Humulus lupulus L.) produces several valuable secondary metabolites, such as prenylflavonoid, bitter acids, and essential oils. These compounds are biosynthesized in glandular trichomes (lupulin glands) endowed with pharmacological properties and widely implicated in the beer brewing industry. The present study is an attempt to generate exhaustive information of transcriptome dynamics and gene regulatory mechanisms involved in biosynthesis and regulation of these compounds, developmental changes including trichome development at three development stages, namely leaf, bract, and mature lupulin glands. Using high-throughput RNA-Seq technology, a total of 61.13, 50.01, and 20.18 Mb clean reads in the leaf, bract, and lupulin gland libraries, respectively, were obtained and assembled into 43,550 unigenes. The putative functions were assigned to 30,996 transcripts (71.17%) based on basic local alignment search tool similarity searches against public sequence databases, including GO, KEGG, NR, and COG families, which indicated that genes are principally involved in fundamental cellular and molecular functions, and biosynthesis of secondary metabolites. The expression levels of all unigenes were analyzed in leaf, bract, and lupulin glands tissues of hop. The expression profile of transcript encoding enzymes of BCAA metabolism, MEP, and shikimate pathway was most up-regulated in lupulin glands compared with leaves and bracts. Similarly, the expression levels of the transcription factors and structural genes that directly encode enzymes involved in xanthohumol, bitter acids, and terpenoids biosynthesis pathway were found to be significantly enhanced in lupulin glands, suggesting that production of these metabolites increases after the leaf development. In addition, numerous genes involved in primary metabolism, lipid metabolism, photosynthesis, generation of precursor metabolites/energy, protein modification, transporter activity, and cell wall component biogenesis were differentially regulated in three developmental stages, suggesting their involvement in the dynamics of the lupulin gland development. The identification of differentially regulated trichome-related genes provided a new foundation for molecular research on trichome development and differentiation in hop. In conclusion, the reported results provide directions for future functional genomics studies for genetic engineering or molecular breeding for augmentation of secondary metabolite content in hop.

• MeSH
• Flavonoids biosynthesis   chemistry   metabolism   MeSH
• Gene Ontology MeSH
• Humulus chemistry   metabolism   MeSH
• Plant Leaves genetics   metabolism   MeSH
• Propiophenones chemistry   metabolism   MeSH
• Gene Expression Regulation, Plant MeSH
• Plant Proteins genetics   metabolism   MeSH
• RNA-Seq MeSH
• Terpenes chemistry   metabolism   MeSH
• Transcription Factors metabolism   MeSH
• Transcriptome genetics   MeSH
• Trichomes genetics   metabolism   ultrastructure   MeSH
• Publication type
• Journal Article MeSH

Insecticide resistance is an increasingly global problem that hampers pest control. We sought the mechanism responsible for survival following pyrethroid treatment and the factors connected to paralysis/death of the pollen beetle Meligethes aeneus through a proteome-level analysis using nanoLC coupled with Orbitrap Fusion™ Tribrid™ mass spectrometry. A tolerant field population of beetles was treated with deltamethrin, and the ensuing proteome changes were observed in the survivors (resistant), dead (paralyzed) and control-treated beetles. The protein database consisted of the translated transcriptome, and the resulting changes were manually annotated via BLASTP. We identified a number of high-abundance changes in which there were several dominant proteins, e.g., the electron carrier cytochrome b5, ribosomal proteins 60S RPL28, 40S RPS23 and RPS26, eIF4E-transporter, anoxia up-regulated protein, 2 isoforms of vitellogenin and pathogenesis-related protein 5. Deltamethrin detoxification was influenced by different cytochromes P450, which were likely boosted by increased cytochrome b5, but glutathione-S-transferase ε and UDP-glucuronosyltransferases also contributed. Moreover, we observed changes in proteins related to RNA interference, RNA binding and epigenetic modifications. The high changes in ribosomal proteins and associated factors suggest specific control of translation. Overall, we showed modulation of expression processes by epigenetic markers, alternative splicing and translation. Future functional studies will benefit. BIOLOGICAL SIGNIFICANCE: Insects develop pesticide resistance, which has become one of the key issues in plant protection. This growing resistance increases the demand for pesticide applications and the development of new substances. Knowledge in the field regarding the resistance mechanism and its responses to pesticide treatment provides us the opportunity to propose a solution for this issue. Although the pollen beetle Meligethes aeneus was effectively controlled with pyrethroids for many years, there have been reports of increasing resistance. We show protein changes including production of isoforms in response to deltamethrin at the protein level. These results illustrate the insect's survival state as a resistant beetle and in its paralyzed state (evaluated as dead) relative to resistant individuals.

• MeSH
• Coleoptera drug effects   genetics   metabolism   MeSH
• Databases, Genetic * MeSH
• Insect Proteins genetics   metabolism   MeSH
• Insecticides toxicity   MeSH
• Nitriles toxicity   MeSH
• Proteomics methods   MeSH
• Pollen metabolism   MeSH
• Pyrethrins toxicity   MeSH
• Insecticide Resistance genetics   MeSH
• Transcriptome * MeSH
• Animals MeSH
• Check Tag
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH

Viroids are small non-capsidated, single-stranded, covalently-closed circular noncoding RNA replicons of 239-401 nucleotides that exploit host factors for their replication, and some cause disease in several economically important crop plants, while others appear to be benign. The proposed mechanisms of viroid pathogenesis include direct interaction of the genomic viroid RNA with host factors and post-transcriptional or transcriptional gene silencing via viroid-derived small RNAs (vd-sRNAs) generated by the host defensive machinery. Humulus lupulus (hop) plants are hosts to several viroids among which Hop latent viroid (HLVd) and Citrus bark cracking viroid (CBCVd) are attractive model systems for the study of viroid-host interactions due to the symptomless infection of the former and severe symptoms induced by the latter in this indicator host. To better understand their interactions with hop plant, a comparative transcriptomic analysis based on RNA sequencing (RNA-seq) was performed to reveal the transcriptional alterations induced as a result of single HLVd and CBCVd infection in hop. Additionally, the effect of HLVd on the aggressiveness of CBCVd that underlies severe stunting in hop in a mixed infection was studied by transcriptomic analysis. Our analysis revealed that CBCVd infection resulted in dynamic changes in the activity of genes as compared to single HLVd infection and their mixed infection. The differentially expressed genes that are involved in defense, phytohormone signaling, photosynthesis and chloroplasts, RNA regulation, processing and binding; protein metabolism and modification; and other mechanisms were more modulated in the CBCVd infection of hop. Nevertheless, Gene Ontology (GO) classification and pathway enrichment analysis showed that the expression of genes involved in the proteolysis mechanism is more active in a mixed infection as compared to a single one, suggesting co-infecting viroids may result in interference with host factors more prominently. Collectively, our results provide a deep transcriptome of hop and insight into complex single HLVd, CBCVd, and their coinfection in hop-plant interactions.

• MeSH
• Humulus genetics   virology   MeSH
• Plant Diseases genetics   virology   MeSH
• Transcriptome * MeSH
• Viroids pathogenicity   MeSH
• Publication type
• Journal Article MeSH

Current progress in the field of next-generation transcriptome sequencing have contributed significantly to the study of various malignancies including glioblastoma multiforme (GBM). Differential sequencing of transcriptomes of patients and non-tumor controls has a potential to reveal novel transcripts with significant role in GBM. One such candidate group of molecules are long non-coding RNAs (lncRNAs) which have been proved to be involved in processes such as carcinogenesis, epigenetic modifications and resistance to various therapeutic approaches. To maximize the value of transcriptome sequencing, a proper protocol for library preparation from tissue-derived RNA needs to be found which would produce high quality transcriptome sequencing data and increase the number of detected lncRNAs. It is important to mention that success of library preparation is determined by the quality of input RNA, which is in case of real-life tissue specimens very often altered in comparison to high quality RNA commonly used by manufacturers for development of library preparation chemistry. In the present study, we used GBM and non-tumor brain tissue specimens and compared three different commercial library preparation kits, namely NEXTflex Rapid Directional qRNA-Seq Kit (Bioo Scientific), SENSE Total RNA-Seq Library Prep Kit (Lexogen) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB). Libraries generated using SENSE kit were characterized by the most normal distribution of normalized average GC content, the least amount of over-represented sequences and the percentage of ribosomal RNA reads (0.3-1.5%) and highest numbers of uniquely mapped reads and reads aligning to coding regions. However, NEBNext kit performed better having relatively low duplication rates, even transcript coverage and the highest number of hits in Ensembl database for every biotype of our interest including lncRNAs. Our results indicate that out of three approaches the NEBNext library preparation kit was most suitable for the study of lncRNAs via transcriptome sequencing. This was further confirmed by highly consistent data reached in an independent validation on an expanded cohort.

• MeSH
• Gene Library MeSH
• Glioblastoma genetics   MeSH
• Humans MeSH
• Brain Neoplasms genetics   MeSH
• Reagent Kits, Diagnostic MeSH
• Gene Expression Regulation, Neoplastic MeSH
• RNA, Long Noncoding genetics   MeSH
• Sequence Analysis, RNA MeSH
• Gene Expression Profiling methods   MeSH
• High-Throughput Nucleotide Sequencing methods   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Comparative Study MeSH

Eukaryotic mRNAs are modified by several chemical marks which have significant impacts on mRNA biology, gene expression, and cellular metabolism as well as on the survival and development of the whole organism. The most abundant and well-studied mRNA base modifications are m6A and ADAR RNA editing. Recent studies have also identified additional mRNA marks such as m6Am, m5C, m1A and Ψ and studied their roles. Each type of modification is deposited by a specific writer, many types of modification are recognized and interpreted by several different readers and some types of modifications can be removed by eraser enzymes. Several works have addressed the functional relationships between some of the modifications. In this review we provide an overview on the current status of research on the different types of mRNA modifications and about the crosstalk between different marks and its functional consequences.

• MeSH
• Epigenesis, Genetic * MeSH
• Epigenomics methods   MeSH
• Humans MeSH
• RNA, Messenger genetics   metabolism   MeSH
• RNA Processing, Post-Transcriptional * MeSH
• Transcriptome * MeSH
• Animals MeSH
• Check Tag
• Humans MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Review MeSH

In eukaryotes, genes produce a variety of distinct RNA isoforms, each with potentially unique protein products, coding potential or regulatory signals such as poly(A) tail and nucleotide modifications. Assessing the kinetics of RNA isoform metabolism, such as transcription and decay rates, is essential for unraveling gene regulation. However, it is currently impeded by lack of methods that can differentiate between individual isoforms. Here, we introduce RNAkinet, a deep convolutional and recurrent neural network, to detect nascent RNA molecules following metabolic labeling with the nucleoside analog 5-ethynyl uridine and long-read, direct RNA sequencing with nanopores. RNAkinet processes electrical signals from nanopore sequencing directly and distinguishes nascent from pre-existing RNA molecules. Our results show that RNAkinet prediction performance generalizes in various cell types and organisms and can be used to quantify RNA isoform half-lives. RNAkinet is expected to enable the identification of the kinetic parameters of RNA isoforms and to facilitate studies of RNA metabolism and the regulatory elements that influence it.

• Publication type
• Journal Article MeSH

BACKGROUND & AIMS: N-linked glycosylation of proteins is critical for proper protein folding and trafficking to the plasma membrane. Drug transporters are one class of proteins that have reduced function when glycosylation is impaired. N-linked glycosylation of plasma proteins has also been investigated as a biomarker for several liver diseases, including non-alcoholic fatty liver disease (NAFLD). The purpose of this study was to assess the transcriptomic expression of genes involved in protein processing and glycosylation, and to determine the glycosylation status of key drug transporters during human NAFLD progression. METHODS: Human liver samples diagnosed as healthy, steatosis, and non-alcoholic steatohepatitis (NASH) were analysed for gene expression of glycosylation-related genes and for protein glycosylation using immunoblot. RESULTS: Genes involved in protein processing in the ER and biosynthesis of N-glycans were significantly enriched for down-regulation in NAFLD progression. Included in the down regulated N-glycan biosynthesis category were genes involved in the oligosaccharyltransferase complex, N-glycan quality control, N-glycan precursor biosynthesis, N-glycan trimming to the core, and N-glycan extension from the core. N-glycan degradation genes were unaltered in the progression to NASH. Immunoblot analysis of the uptake transporters organic anion transporting polypeptide-1B1 (OATP1B1), OATP1B3, OATP2B1, and Sodium/Taurocholate Co-transporting Polypeptide (NTCP) and the efflux transporter multidrug resistance-associated protein 2 (MRP2) demonstrated a significant loss of glycosylation following the progression to NASH. CONCLUSIONS: These data suggest that the loss of glycosylation of key uptake and efflux transporters in humans NASH may influence transporter function and contribute to altered drug disposition observed in NASH.

• MeSH
• Biological Transport MeSH
• Endoplasmic Reticulum metabolism   MeSH
• Glycosylation MeSH
• Liver metabolism   MeSH
• Humans MeSH
• Membrane Transport Proteins genetics   metabolism   MeSH
• Non-alcoholic Fatty Liver Disease diagnosis   genetics   metabolism   MeSH
• Protein Processing, Post-Translational * MeSH
• Gene Expression Profiling MeSH
• Case-Control Studies MeSH
• Transcriptome MeSH
• Blotting, Western MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, N.I.H., Extramural MeSH

The ovarian granulosa cells (GCs) that form the structure of follicle undergo substantial modification during the various stages of human folliculogenesis. These modifications include morphological changes, accompanied by differential expression of genes, encoding proteins which are mainly involved in cell growth, proliferation and differentiation. Recent data bring a new insight into the aspects of GCs' stem-like specificity and plasticity, enabling their prolonged proliferation and differentiation into other cell types. This manuscript focuses attention on emerging alterations during GC cell cycle - a series of biochemical and biophysical changes within the cell. Human GCs were collected from follicles of women set to undergo intracytoplasmic sperm injection procedure, as a part of remnant follicular fluid. The cells were primarily cultured for 30 days. Throughout this time, we observed the prominent change in cell morphology from epithelial-like to fibroblast-like, suggesting differentiation to other cell types. Additionally, at days 1, 7, 15 and 30, the RNA was isolated for molecular assays. Using Affymetrix® Human Genome U219 Array, we found 2579 human transcripts that were differentially expressed in GCs. From these genes, we extracted 582 Gene Ontology Biological Process (GO BP) Terms and 45 KEGG pathways, among which we investigated transcripts belonging to four GO BPs associated with cell proliferation: "cell cycle phase transition", "G1/S phase transition", G2/M phase transition" and "cell cycle checkpoint". Microarray results were validated by RT-qPCR. Increased expression of all the genes studied indicated that increase in GC proliferation during long-term in vitro culture is orchestrated by the up-regulation of genes related to cell cycle control. Furthermore, observed changes in cell morphology may be regulated by a presented set of genes, leading to the induction of pathways specific for stemness plasticity and transdifferentiation in vitro.

• MeSH
• Cell Cycle * MeSH
• Granulosa Cells cytology   MeSH
• Humans MeSH
• Ovarian Follicle cytology   MeSH
• Transcriptome * MeSH
• Check Tag
• Humans MeSH
• Female MeSH
• Publication type
• Journal Article MeSH