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Cotton (Gossypum L.) is the most important fiber crop worldwide. Here, transcriptome analysis was conducted on developing fibers of a G. mustelinum introgression line, IL9, and its recurrent parent, PD94042, at 17 and 21 days post-anthesis (dpa). Differentially expressed genes (DEGs) of PD94042 and IL9 were identified. Gene Ontology (GO) enrichment analysis showed that the annotated DEGs were rich in two main biological processes and two main molecular functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis likewise showed that the annotated DEGs were mainly enriched in metabolic pathways and biosynthesis of secondary metabolites. In total, 52 DEGs were selected as candidate genes based on comparison of the DEGs and GO function annotation information. Quantitative real-time PCR (RT-qPCR) analysis results for 12 randomly selected DEGs were consistent with transcriptome analysis. SNP identification based on G. mustelinum chromatin segment introgression showed that 394 SNPs were identified in 268 DEGs, and two genes with known functions were identified within fiber strength quantitative trait loci (QTL) regions or near the confidence intervals. We identified 52 key genes potentially related to high fiber strength in a G. mustelinum introgression line and provided significant insights into the study of cotton fiber quality improvement. Key words: Gossypium mustelinum, fiber strength, key genes, transcriptome analysis. Le cotonnier (Gossypium L.) est la plus importante plante a fibres dans le monde. Dans ce travail, une analyse transcriptomique a ete realisee sur des fibres en developpement chez une lignee d'introgression du G. mustelinum, IL9, et son parent recurrent, PD94042, a 17 et 21 jours apres l'anthese. Les genes presentant une expression differente (DEG) entre PD94042 et IL9 ont ete identifies. Uneanalysedel'enrichissement sur la base de l'ontologie genique (GO) a montre que les DEG annotes etaient surrepresentes au sein de deux processus biologiques principaux et de deux classes de fonctions moleculaires. Une analyse des sentiers KEGG a egalement montre que les DEG annotes etaient principalement enrichis pour les sentiers metaboliques et biosynthetiques de metabolites secondaires. Au total, 52 DEG ont ete retenus comme genes candidats sur la base de leur expression et de leur annotation fonctionnelle GO. Les resultats d'analyses par PCR quantitatif en temps reel (RT-qPCR) pour 12 candidats choisis au hasard ont revele une bonne concordance avec l'analyse transcriptomique. L'identification de SNP bases sur l'introgression de chromatine du G. mustelinum a montre que 394 SNP ont ete identifies au sein de 268 DEG, et que deux genes de fonction connue ont ete identifies au sein (ou a l'interieur de l'intervalle de confiance) de QTL pour la resistance de la fibre. Les auteurs ont identifie 52 genes cles potentiellement responsables de la resistance de la fibre au sein d'une lignee d'introgression du G. mustelinum et cela apporte un eclairage important dans l'etude de la qualite de la fibreet deson amelioration. [Traduit par la Redaction] Mots-cles : Gossypium mustelinum,resistancede la fibre, genes cles, analyse du transcriptom., Introduction Cotton (Gossypium L.) is one of the most important industrial crops, supplying both food and fiber to human society (Sunilkumar et al. 2006). Upland cotton from G. hirsutum and [...]

Spinach (Spinacia oleracea L.) is commonly considered a dioecious plant with heterogametic (XY) and homogametic (XX) sex chromosomes. The characteristic is also utilized for the production of spinach hybrid seeds. However, the molecular mechanisms of sex determination in spinach are still unclear because of a lack of genomic and transcriptomic information. In this study, RNA sequencing (RNA-seq) was performed in male and female inflorescences to provide insight into the molecular basis of sex determination in spinach. Comparative transcriptome analyses showed that 2278 differentially expressed genes (DEGs) were identified between male and female inflorescences. A high correlation between the RNA-Seq and qRT-PCR validation for DEGs was observed. Among these, 182 DEGs were annotated to transcription factors including the MYB family protein, bHLH family, and MADS family, suggesting these factors might play a vital role in sex determination. Moreover, 26 DEGs related to flower development, including nine ABCE class genes, were detected. Expression analyses of hormone pathways showed that brassinosteroids may be key hormones related to sex determination in spinach. Overall, this study provides a large amount of DEGs related to sexual expression and lays a foundation for unraveling the regulatory mechanism of sex determination in spinach. Key words: spinach, dioecious, RNA-seq, floral sex determination, flower development. L'epinard (Spinacea oleraca L.) est generalement considere comme une plante dioique avec des chromosomes sexuels heterogametiques (XY) et homogametiques (XX). Cette caracteristique est egalement exploitee pour la production de semences hybrides chez l'epinard. Cependant, les mecanismes moleculaires de la determination du sexe demeurent nebuleux en raison de l'absence de donnees genomiques et transcriptomiques. Dans ce travail, une analyse RNA-seq a ete realisee sur les inflorescences males et femelles pour jeter un eclairage sur les assises moleculaires de la determination du sexe chez l'epinard. Des comparaisons des transcriptomes ont permis d'identifier 2278 genes exprimes de maniere differentielle (DEG) entre les inflorescences males et femelles. Une forte correlation a ete observee entre les donnees RNA-seq et des donnees de validation obtenues par qRT-PCR. Parmi les DEG, 182 sont annotes comme codant pour des facteurs de transcription dont certains sont de type MYB, bHLH et MADS, ce qui suggere que ces facteurs pourraient jouer des roles vitaux dans la determination du sexe. De plus, 26 DEG etaient associes au developpement floral, dont neuf genes de la classe ABCE. Des analyses de l'expression de sentiers hormonaux ont montre que les brassinosteroides seraient des hormones cles dans la determination du sexe chez l'epinard. Globalement, cette etude fournit un grand nombre de DEG presentant une expression differenciee selon le sexe et constitue une assise pour mieux comprendre les mecanismes regulant la determination du sexe chez l'epinard. [Traduit par la Redaction] Mots-cles: epinards, dioique, RNA-seq, determination du sexe des fleurs, developpement floral., Introduction The sexual system is remarkably complex in angiosperms. Monoecy and hermaphroditism are prevalent in angiosperms, while only a few species have evolved dioecy (Renner 2014). Hermaphroditic flowers have four [...]

Water stress associated with drought-like conditions is a major factor limiting plant growth and impacts productivity of natural plant communities and agricultural crops. Molecular responses of plants to water stress have been studied most extensively in model species and crops, few of which have evolved natural drought tolerance. In the current study, we examined physiological and transcriptomic responses at multiple timepoints during increasing water stress and following initial recovery from stress in a drought-tolerant C3 species, Festuca ovina. Results demonstrated non-linear transcriptomic changes during increasing stress, but largely linear declines in physiological measurements during this same period. Transcription factors represented approximately 12.7% of all differentially expressed genes. In total, 117 F. ovina homologs of previously identified and molecularly characterized drought-responsive plant genes were identified. This information will be valuable for further investigations of the molecular mechanisms involved in drought tolerance in [C.sub.3] plants. Key words: Festuca ovina, RNA-seq, water stress, transcription factor, drought tolerant. Le stress hydrique associe a des conditions de secheresse est un facteur important limitant la croissance des plantes et affectant la productivite au sein de communautes vegetales naturelles et chez les especes cultivees. Les reponses moleculaires des plantes au stress hydrique ont ete etudiees le plus chez des especes modeles et des especes cultivees, dont certaines ont acquis une tolerance naturelle a la secheresse. Dans le present travail, les auteurs examinent les reponses physiologiques et transcriptomiques a differents stades temporels suite a l'imposition d'un stress hydrique croissant et apres retablissement post-stress chez une espece C3 tolerante a la secheresse, Festuca ovina. Les resultats ont montre une evolution non-lineaire des reponses transcriptomiques en reponse a l'accroissement du stress, alors que les declins physiologiques etaient largement lineaires au cours des memes periodes. Les facteurs de transcription constituaient environ 12,7 % des genes montrant une expression differentielle. Chez F. ovina, les auteurs ont identifie 117 homologues de genes precedemment connus au plan moleculaire pour reagir a la secheresse. Cette information sera utile pour des futurs travaux des mecanismes moleculaires impliques dans la tolerance a la secheresse chez les plantes [C.sub.3]. [Traduit par la Redaction] Mots-cles : Festuca ovina, RNA-seq, stress hydrique, facteur de transcription, tolerance a la secheresse., Introduction Drought is a major environmental stress for plants and negatively affects growth and reproduction. Drought events cause yield loss in crop systems (Brevedan and Egli 2003; van Asten et [...]

The plant Nothapodytes nimmoniana is an important source of camptothecin (CPT), an anticancer compound widely used in the treatment of colorectal, lung, and ovarian cancers. CPT is biosynthesized by the combination of the seco-iridoid and indole pathways in plants. The majority of the biosynthetic steps and associated genes still remain unknown. Certain reactions in the seco-iridoid pathway are catalyzed by cytochrome P450 enzymes. Hence, identifying transcriptionally active cytochrome P450 genes becomes essential in the elucidation of the CPT biosynthetic pathway. Here, we report the identification of 94 cytochrome P450s from the assembled transcriptomic data from leaf and root tissues of N. nimmoniana. The identified cytochrome P450 genes were full length and possessed all four conserved characteristic signature motifs of cytochrome P450 genes. Phylogenetic analysis of the protein sequences revealed their evolution and diversification and further categorized them into A-type (52.12%) and non-A-type (47.87%) cytochrome P450s. These 94 sequences represent 38 families and 63 subfamilies of cytochrome P450s. We also compared the transcriptional activity of identified cytochrome P450s with the expression of their homologs in the CPT-producing plant Ophiorrhiza pumila. Based on expression profiles and quantitative PCR validation, we propose NnCYP8lCBl and NnCYP89RL as candidate cytochrome P450 genes involved in camptothecin biosynthesis in N. nimmoniana. Key words: cytochrome P450, Nothapodytes nimmoniana, phylogeny, camptothecin, transcriptome-wide gene discovery. La plante Nothapodytes nimmoniana est une source importante de la camptothecine (CPT), un compose anticancereux largement utilise dans le traitement du cancer colorectal, des poumons et des ovaires. La CPT est synthetisee conjointement par les sentiers des seco-iridoides et de l'indole chez les plantes. La plupart des etapes et des genes associes demeurent inconnus a ce jour. Certaines reactions dans le sentier des seco-iridoides sont catalysees par des cytochromes P450. Ainsi, l'identification des genes codant pour des cytochromes P450 qui sont activement transcrits offre une voie powur elucider la voie de synthese de la CPT. Dans ce travail, les auteurs rapportent l'identification de 94 cytochromes P450 a partir d'un transcriptome assemble pour les feuilles et les racines du N. nimmoniana.Les cytochromes P450 identifiees etaient completes et possedaient les quatre motifs conserves qui sont une signature caracteristique des genes codant pour des cytochromes P450. Une analyse phylogenetique des sequences proteiques a apporte un eclairage sur leur evolution et diversification et a permis de les classifier en deux types, le type A (52,12 %) et le type non-A (47,87 %). Ces 94 sequences comptent des representants de 38 familles et 63 sous-familles de cytochromes P450. Les auteurs ont egalement compare l'activite transcriptionnelle des cytochromes P450 identifiees avec l'expression de leurs homologues chez Ophiorrhiza pumila, une autre plante qui produit de la CPT. Sur la base des profils d'expression et de la validation par PCR quantitative, les auteurs proposent que NnCYP8lCBl et NnCYP89Sl constituent des genes candidats codant pour des cytochromes P450 impliquees dans la synthese de la CPT chez le N. nimmoniana. Mots-cles : cytochrome P450, Nothapodytes nimmoniana, phylogenie, camptothecine, identification de genes par une approche pan-transcriptomique., Introduction Cancer is the second leading cause of death globally, with nearly 1 in 6 deaths due to cancer (https://www.who.int/news-room/fact-sheets/detail/cancer). Plant-derived anticancer compounds such as vinca alkaloids, podo-phyllotoxins, taxanes, and [...]

In cold water coastal regions, the marine dinoflagellate Alexandrium catenella (Group I) is associated with paralytic shellfish poisoning. Here, we characterized the transcriptome of A. catenella isolated from Korean coastal waters during spring. RNA sequencing generated 15.5 Gb nucleotides that were assembled into 103,362 unique transcripts (unigenes). Upon comparison with known proteins, 53,547 (51.81%) unigenes were successfully annotated in public databases, among which, 28,463 and 35,447 unigenes were assigned to gene ontology categories and evolutionary genealogy of genes with enhanced non-supervised orthologous groups, respectively. Notably, we identified numerous toxin- and cold response-related genes in this species. The conserved dinoflagellate spliced leader (dinoSL) was detected in many unigenes, thereby indicating the occurrence of trans-splicing mRNA processing. Moreover, the identification of second or third dinoSL relicts in a few genes indicate that they have been recycled in the past between the genome and mRNA and are potential sources of genome expansion in this species., Author(s): Hui Wang [sup.1] , Hansol Kim [sup.1] , Jang-Seu Ki [sup.1] Author Affiliations: (1) grid.263136.3, 0000 0004 0533 2389, Department of Biotechnology, Sangmyung University, , 03016, Seoul, South Korea [...]

The neuronal mechanisms that establish 24-hour rhythms in feeding and metabolism remain incompletely understood. In this issue of the JCI, Adlanmerini and colleagues explored the relationship between temporal and homeostatic control of energy balance by focusing on mice that lacked the genes encoding the clock repressor elements REV-ERB[alpha] and -[beta], specifically in the tuberal hypothalamus. Notably, the clock transcription cycle mediated intraneuronal response to the adipostatic hormone leptin. These results show that REV-ERB[alpha] and -[beta] in the hypothalamus are necessary for maintaining leptin responsiveness and metabolic homeostasis and lay the foundation to explore how transcriptional changes may link energy-sensing cell types with day/night rhythms. Such information may lead to therapeutics that alleviate the adverse effects of chronic shift work., Clock genes In the early 1970s, Ron Konopka and Seymour Benzer proved that genes control behavior in Drosophila melanogaster by isolating progeny of mutagenized flies that exhibited alteration in 24-hour [...]

The DNA replication and transcription machineries share a common DNA template and thus can collide with each other co-directionally or head-on (1,2). Replication-transcription collisions can cause replication fork arrest, premature transcription termination, DNA breaks, and recombination intermediates threatening genome integrity (1-10). Collisions may also trigger mutations, which are major contributors to genetic disease and evolution (5,7,11). However, the nature and mechanisms of collision-induced mutagenesis remain poorly understood. Here we reveal the genetic consequences of replication-transcription collisions in actively dividing bacteria to be two classes of mutations: duplications/deletions and base substitutions in promoters. Both signatures are highly deleterious but are distinct from the previously well-characterized base substitutions in the coding sequence. Duplications/deletions are probably caused by replication stalling events that are triggered by collisions; their distribution patterns are consistent with where the fork first encounters a transcription complex upon entering a transcription unit. Promoter substitutions result mostly from head-on collisions and frequently occur at a nucleotide that is conserved in promoters recognized by the major a factor in bacteria. This substitution is generated via adenine deamination on the template strand in the promoter open complex, as a consequence of head-on replication perturbing transcription initiation. We conclude that replication-transcription collisions induce distinct mutation signatures by antagonizing replication and transcription, not only in coding sequences but also in gene regulatory elements., Mutations cause genetic diseases and drive evolution by altering either the gene-coding sequence or the noncoding elements that control gene expression. A variety of mechanisms underlie mutagenesis: DNA replication errors, [...]

Single-cell RNA sequencing (scRNA-seq) has highlighted the important role of intercellular heterogeneity in phenotype variability in both health and disease.sup.1. However, current scRNA-seq approaches provide only a snapshot of gene expression and convey little information on the true temporal dynamics and stochastic nature of transcription. A further key limitation of scRNA-seq analysis is that the RNA profile of each individual cell can be analysed only once. Here we introduce single-cell, thiol-(SH)-linked alkylation of RNA for metabolic labelling sequencing (scSLAM-seq), which integrates metabolic RNA labelling.sup.2, biochemical nucleoside conversion.sup.3 and scRNA-seq to record transcriptional activity directly by differentiating between new and old RNA for thousands of genes per single cell. We use scSLAM-seq to study the onset of infection with lytic cytomegalovirus in single mouse fibroblasts. The cell-cycle state and dose of infection deduced from old RNA enable dose-response analysis based on new RNA. scSLAM-seq thereby both visualizes and explains differences in transcriptional activity at the single-cell level. Furthermore, it depicts 'on-off' switches and transcriptional burst kinetics in host gene expression with extensive gene-specific differences that correlate with promoter-intrinsic features (TBP-TATA-box interactions and DNA methylation). Thus, gene-specific, and not cell-specific, features explain the heterogeneity in transcriptomes between individual cells and the transcriptional response to perturbations. A technique known as scSLAM-seq that combines single-cell RNA sequencing with metabolic RNA labelling and nucleoside conversion is used to study the onset of cytomegalovirus infection in single mouse fibroblasts., Author(s): Florian Erhard [sup.1] , Marisa A. P. Baptista [sup.1] , Tobias Krammer [sup.2] , Thomas Hennig [sup.1] , Marius Lange [sup.3] [sup.4] , Panagiota Arampatzi [sup.5] , Christopher S. [...]

T helper 17 ([T.sub.H]17) lymphocytes protect mucosal barriers from infections, but also contribute to multiple chronic inflammatory diseases. Their differentiation is controlled by RORγt, a ligand-regulated nuclear receptor. Here we identify the RNA helicase DEAD-box protein 5 (DDX5) as a RORγt partner that coordinates transcription of selective [T.sub.H]17 genes, and is required for [T.sub.H]17-mediated inflammatory pathologies. Surprisingly, the ability of DDX5 to interact with RORγt and coactivate its targets depends on intrinsic RNA helicase activity and binding of a conserved nuclear long noncoding RNA (lncRNA), Rmrp, which is mutated in patients with cartilage-hair hypoplasia. A targeted Rmrp gene mutation in mice, corresponding to a gene mutation in cartilage-hair hypoplasia patients, altered lncRNA chromatin occupancy, and reduced the DDX5-RORγt interaction and RORγt target gene transcription. Elucidation of the link between Rmrp and the DDX5-RORγt complex reveals a role for RNA helicases and lncRNAs in tissue-specific transcriptional regulation, and provides new opportunities for therapeutic intervention in [T.sub.H]17-dependent diseases., [T.sub.H]17 cells are [CD4.sup.+] lymphocytes that help to protect mucosal epithelial barriers against bacterial and fungal infections (1), and are also important in multiple autoimmune diseases (2-7). The [T.sub.H]17 cell [...]

DEAD-box RNA helicase DDX21 is involved in both the transcription and RNA processing of ribosomal genes in human cells, sensing the transcriptional status of both RNA polymerase I and RNA polymerase II and associating with non-coding RNAs involved in ribonucleoprotein formation, possibly allowing for coordinated regulation of protein synthesis. Role of DDX21 in ribosome biogenesis RNA helicases remodel RNA secondary structure and ribonucleoprotein (RNP) complexes during various steps of RNA metabolism. Here, Joanna Wysocka and colleagues find that a DEAD-box RNA helicase, DDX21, is involved in both the transcription and RNA processing of ribosomal genes in human cells. DDX21 senses the transcriptional status of RNA polymerases I and II, and associates with non-coding RNAs involved in RNP formation. These broad interactions in different nuclear compartments are specific for ribosomal biogenesis and may allow coordinated regulation of protein synthesis. DEAD-box RNA helicases are vital for the regulation of various aspects of the RNA life cycle.sup.1, but the molecular underpinnings of their involvement, particularly in mammalian cells, remain poorly understood. Here we show that the DEAD-box RNA helicase DDX21 can sense the transcriptional status of both RNA polymerase (Pol) I and II to control multiple steps of ribosome biogenesis in human cells. We demonstrate that DDX21 widely associates with Pol I- and Pol II-transcribed genes and with diverse species of RNA, most prominently with non-coding RNAs involved in the formation of ribonucleoprotein complexes, including ribosomal RNA, small nucleolar RNAs (snoRNAs) and 7SK RNA. Although broad, these molecular interactions, both at the chromatin and RNA level, exhibit remarkable specificity for the regulation of ribosomal genes. In the nucleolus, DDX21 occupies the transcribed rDNA locus, directly contacts both rRNA and snoRNAs, and promotes rRNA transcription, processing and modification. In the nucleoplasm, DDX21 binds 7SK RNA and, as a component of the 7SK small nuclear ribonucleoprotein (snRNP) complex, is recruited to the promoters of Pol II-transcribed genes encoding ribosomal proteins and snoRNAs. Promoter-bound DDX21 facilitates the release of the positive transcription elongation factor b (P-TEFb) from the 7SK snRNP in a manner that is dependent on its helicase activity, thereby promoting transcription of its target genes. Our results uncover the multifaceted role of DDX21 in multiple steps of ribosome biogenesis, and provide evidence implicating a mammalian RNA helicase in RNA modification and Pol II elongation control., Author(s): Eliezer Calo [sup.1] , Ryan A. Flynn [sup.2] , Lance Martin [sup.2] , Robert C. Spitale [sup.2] , Howard Y. Chang [sup.2] , Joanna Wysocka [sup.1] [sup.3] Author Affiliations: [...]