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Introduction Gene duplications giving rise to multigene superfamilies are one of the ways that members of the plant kingdom have evolved to adapt to and survive persistent biotic and abiotic [...], Pirins are nuclear bicupin proteins, encoded by genes that are one of several gene families that comprise the cupin super-family in plants. Pirin genes have been implicated in stress response pathways studied in Arabidopsis and At-Pirinl has been shown to interact with the heterotrimeric G-protein alpha subunit (GPA1). The aim of this study was to identify the members of the Pirin gene family in Triticum aestivum, to correct their annotations in the whole genome, and gain an insight into their tissue-specific expression as well as their response to abiotic and biotic stresses. The Pirin gene family in T. aestivum is comprised of 18 genes that represent six paralogous gene copies, each having an A, B, and D homeolog. Expression analysis of the Pirin genes in T. aestivum Illumina RNA-seq libraries, which included sampling from differing tissue types as well as abiotic and biotic stresses, indicates that the members of the Pirin gene family have specialized expression and play a role in stress responses. Pirin gene families are also identified in other monocots including Aegilops tauschii, Hordeum vulgare, Brachypodium distachyon, Oryza sativa, Zea mays, Sorghum bicolor, and the dicot Arabidopsis thaliana. Key words: Cupin superfamily, bicupins, pirins, Pirin gene family, Triticum Les pirines sont des protéines bicupines nucléaires, codées par des gènes qui appartiennent à l'une de plusieurs familles de gènes que compte la superfamille des cupines chez les plantes. Les gènes Pirin ont été impliqués dans les voies de réponse aux stress chez l'Arabidopsis et il a été montré que l'At-Pirin1 interagit avec la sous-unité alpha de la protéine G hétérotrimérique (GPA1). Le but de cette étude était d'identifier les membres de la famille de gènes Pirin chez le Triticum aestivum, de corriger leur annotation dans le génome entier et de mieux conprendre leur expression tissulaire ainsi que sur leur réponse aux stress abiotiques et biotiques. La famille de gènes Pirin chez le T. aestivum comprend 18 gènes, ce qui correspond à six copies paralogues, chacune ayant un homéologue au sein des génomes A, B et D. L analyse de l expression des gènes Pirin au sein de librairies RNA-seq Illumina du T. aestivum, lesquelles étaient préparées à partir de différents tissus de même qu' en conditions de stress abiotiques et biotiques, ont indiqué que les membres de cette famille présentent une expression spécialisée et qu ils jouent un rôle dans la réponse aux stress. Les familles de gènes Pirin sont également identifiées chez d ' autres monocoytlédones dont l'Aegilops tauschii,! Hordeum vulgare,le Brachypodium distachyon,l ' Oryza sativa,le Zea mays,le Sorghum bicolor et la dicotylédone Arabidopsis thaliana. Mots-clés : superfamille des cupines, bicupines, pirines, famille de gènes Pirin, Triticum

Author(s): Thomas Powles [sup.1] , Zoe June Assaf [sup.2] , Nicole Davarpanah [sup.2] , Romain Banchereau [sup.2] , Bernadett E. Szabados [sup.3] , Kobe C. Yuen [sup.2] , Petros Grivas [...], Minimally invasive approaches to detect residual disease after surgery are needed to identify patients with cancer who are at risk for metastatic relapse. Circulating tumour DNA (ctDNA) holds promise as a biomarker for molecular residual disease and relapse.sup.1. We evaluated outcomes in 581 patients who had undergone surgery and were evaluable for ctDNA from a randomized phase III trial of adjuvant atezolizumab versus observation in operable urothelial cancer. This trial did not reach its efficacy end point in the intention-to-treat population. Here we show that ctDNA testing at the start of therapy (cycle 1 day 1) identified 214 (37%) patients who were positive for ctDNA and who had poor prognosis (observation arm hazard ratio = 6.3 (95% confidence interval: 4.45-8.92); P < 0.0001). Notably, patients who were positive for ctDNA had improved disease-free survival and overall survival in the atezolizumab arm versus the observation arm (disease-free survival hazard ratio = 0.58 (95% confidence interval: 0.43-0.79); P = 0.0024, overall survival hazard ratio = 0.59 (95% confidence interval: 0.41-0.86)). No difference in disease-free survival or overall survival between treatment arms was noted for patients who were negative for ctDNA. The rate of ctDNA clearance at week 6 was higher in the atezolizumab arm (18%) than in the observation arm (4%) (P = 0.0204). Transcriptomic analysis of tumours from patients who were positive for ctDNA revealed higher expression levels of cell-cycle and keratin genes. For patients who were positive for ctDNA and who were treated with atezolizumab, non-relapse was associated with immune response signatures and basal-squamous gene features, whereas relapse was associated with angiogenesis and fibroblast TGF[beta] signatures. These data suggest that adjuvant atezolizumab may be associated with improved outcomes compared with observation in patients who are positive for ctDNA and who are at a high risk of relapse. These findings, if validated in other settings, would shift approaches to postoperative cancer care. The authors report on prospective exploratory analyses of circulating tumour DNA in an urothelial carcinoma immunotherapy clinical trial.

Author(s): John T. Lovell [sup.1] , Alice H. MacQueen [sup.2] , Sujan Mamidi [sup.1] , Jason Bonnette [sup.2] , Jerry Jenkins [sup.1] , Joseph D. Napier [sup.2] , Avinash Sreedasyam [...], Long-term climate change and periodic environmental extremes threaten food and fuel security.sup.1 and global crop productivity.sup.2-4. Although molecular and adaptive breeding strategies can buffer the effects of climatic stress and improve crop resilience.sup.5, these approaches require sufficient knowledge of the genes that underlie productivity and adaptation.sup.6--knowledge that has been limited to a small number of well-studied model systems. Here we present the assembly and annotation of the large and complex genome of the polyploid bioenergy crop switchgrass (Panicum virgatum). Analysis of biomass and survival among 732 resequenced genotypes, which were grown across 10 common gardens that span 1,800 km of latitude, jointly revealed extensive genomic evidence of climate adaptation. Climate-gene-biomass associations were abundant but varied considerably among deeply diverged gene pools. Furthermore, we found that gene flow accelerated climate adaptation during the postglacial colonization of northern habitats through introgression of alleles from a pre-adapted northern gene pool. The polyploid nature of switchgrass also enhanced adaptive potential through the fractionation of gene function, as there was an increased level of heritable genetic diversity on the nondominant subgenome. In addition to investigating patterns of climate adaptation, the genome resources and gene-trait associations developed here provide breeders with the necessary tools to increase switchgrass yield for the sustainable production of bioenergy. The genome of the biofuel crop switchgrass (Panicum virgatum) reveals climate-gene-biomass associations that underlie adaptation in nature and will facilitate improvements of the yield of this crop for bioenergy production.

Author(s): Murukarthick Jayakodi [sup.1] , Sudharsan Padmarasu [sup.1] , Georg Haberer [sup.2] , Venkata Suresh Bonthala [sup.2] , Heidrun Gundlach [sup.2] , Cécile Monat [sup.1] , Thomas Lux [sup.2] , [...], Genetic diversity is key to crop improvement. Owing to pervasive genomic structural variation, a single reference genome assembly cannot capture the full complement of sequence diversity of a crop species (known as the &apos;pan-genome&apos;.sup.1). Multiple high-quality sequence assemblies are an indispensable component of a pan-genome infrastructure. Barley (Hordeum vulgare L.) is an important cereal crop with a long history of cultivation that is adapted to a wide range of agro-climatic conditions.sup.2. Here we report the construction of chromosome-scale sequence assemblies for the genotypes of 20 varieties of barley--comprising landraces, cultivars and a wild barley--that were selected as representatives of global barley diversity. We catalogued genomic presence/absence variants and explored the use of structural variants for quantitative genetic analysis through whole-genome shotgun sequencing of 300 gene bank accessions. We discovered abundant large inversion polymorphisms and analysed in detail two inversions that are frequently found in current elite barley germplasm; one is probably the product of mutation breeding and the other is tightly linked to a locus that is involved in the expansion of geographical range. This first-generation barley pan-genome makes previously hidden genetic variation accessible to genetic studies and breeding. Chromosome-scale sequence assemblies of 20 diverse varieties of barley are used to construct a first-generation pan-genome, revealing previously hidden genetic variation that can be used by studies aimed at crop improvement

Author(s): Sander Lambo [sup.1] [sup.2] [sup.3] , Susanne N. Gröbner [sup.1] [sup.2] [sup.3] , Tobias Rausch [sup.4] , Sebastian M. Waszak [sup.4] , Christin Schmidt [sup.1] [sup.2] [sup.3] , Aparna [...], Embryonal tumours with multilayered rosettes (ETMRs) are aggressive paediatric embryonal brain tumours with a universally poor prognosis.sup.1. Here we collected 193 primary ETMRs and 23 matched relapse samples to investigate the genomic landscape of this distinct tumour type. We found that patients with tumours in which the proposed driver C19MC.sup.2-4 was not amplified frequently had germline mutations in DICER1 or other microRNA-related aberrations such as somatic amplification of miR-17-92 (also known as MIR17HG). Whole-genome sequencing revealed that tumours had an overall low recurrence of single-nucleotide variants (SNVs), but showed prevalent genomic instability caused by widespread occurrence of R-loop structures. We show that R-loop-associated chromosomal instability can be induced by the loss of DICER1 function. Comparison of primary tumours and matched relapse samples showed a strong conservation of structural variants, but low conservation of SNVs. Moreover, many newly acquired SNVs are associated with a mutational signature related to cisplatin treatment. Finally, we show that targeting R-loops with topoisomerase and PARP inhibitors might be an effective treatment strategy for this deadly disease. Analyses of primary and relapse samples of embryonal tumours with multilayered rosettes provide insights into the molecular mechanisms that underlie the development and opportunities for the treatment of this deadly disease.

Introduction Citrus species are subtropical fruit trees that have been cultivated for at least 4000 years. Citrus is native to south Asia and spread worldwide following ancient land and sea [...], Seedlessness is a highly desirable trait in citrus varieties. Sterility is the key determination for seedlessness formation. However, the molecular basis for female sterility in seedless mandarin remains unclear. Thus, a seedless Ponkan mandarin (Citrus reticulata Blanco &apos;Lipeng No.2&apos;), considered the bud mutation of normal seedy Ponkan, was collected to identify candidate genes involved in seedless variation. Suppression subtractive hybridization (SSH) screened 1091 uniESTs related to seedy and seedless Ponkan (727 singlets and 364 contigs), which mainly governed catalytic activity, transferase activity, and oxygen binding. By using RNA-Seq technology, 106 differentially expressed genes (DEGs) were captured, of which 74 were up-regulated and 32 were down-regulated. Gene Ontology and pathway analysis showed that six DEGs were enriched in the biosynthesis of secondary metabolite, whereas five DEGs were enriched in the signaling of plant hormones. The combined results of SSH and RNA-Seq indicated the importance of amino acid metabolism in seedless Ponkan. Our findings revealed that the mechanism of seedless Ponkan generation may be related to gene regulation, signal cascade, and hormone levels. This study provided a solid foundation for functional gene identification in seedless Ponkan and a good reference for relevant research on molecular mechanisms of female sterility in Ponkan mandarin. Key words: Ponkan, female sterility, seedlessness, SSH, RNA-Seq. L&apos;absence de pépins est un caractère hautement désiré chez les variétés d&apos;agrumes. La stérilité est le déterminant majeur de l&apos;absence de pépins. Cependant, les bases moléculaires de la stérilité femelle chez la mandarine sans pépins demeurent méconnues. La variété Ponkan sans pépins (Citrus reticulata Blanco &apos;Lipeng No. 2&apos;) est considérée comme étant une mutation spontanée de la variété Ponkan normalement dotée de pépins. Celle-ci a été employée pour identifier des gènes candidats impliqués dans l&apos;absence de pépins. Une hybridation suppressive soustractive (SSH) a permis d&apos;identifier 1091 uniEST associés à la présence/absence de pépins chez Ponkan (727 singletons et 364 contigs), lesquels étaient principalement impliqués dans des activités catalytiques, des activités transférases ou dans la liaison de l&apos;oxygène. À l&apos;aide d&apos;une approche RNA-Seq, 106 gènes exprimés différemment (DEG) ont été capturés dont 74 étaient exprimés à la hausse et 32 à la baisse. Des analyses d&apos;ontologie génique et des sentiers ont révélé que six DEG étaient enrichis dans la synthèse de métabolites secondaires tandis que cinq l&apos;étaient au sein de la signalisation hormonale. Les résultats combinés des analyses SSH et RNA-Seq indiquent que le métabolisme des acides aminés est important chez le Ponkan sans pépins. Ces résultats révèlent que les mécanismes menant à l&apos;absence de pépins seraient liés à la régulation génique, à la signalisation et aux niveaux d&apos;hormones. Cette étude fournit une assise solide pour l&apos;identification de gènes fonctionnellement impliqués dans l&apos;absence de pépins chez Ponkan et une bonne référence pour des travaux pertinents sur les mécanismes moléculaires de la stérilité femelle chez la mandarine Ponkan. [Traduit par la Rédaction] Mots-clés: Ponkan, stérilité femelle, absence de pépins, SSH, RNA-Seq.

Protein synthesis is a fundamental process for all cells, but its precise regulatory roles in development, stem cells and cancer are not well understood. We recently identified post-transcriptional methylation of [...], Whether protein synthesis and cellular stress response pathways interact to control stem cell function is currently unknown. Here we show that mouse skin stem cells synthesize less protein than their immediate progenitors in vivo, even when forced to proliferate. Our analyses reveal that activation of stress response pathways drives both a global reduction of protein synthesis and altered translational programmes that together promote stem cell functions and tumorigenesis. Mechanistically, we show that inhibition of post-transcriptional cytosine-5 methylation locks tumour- initiating cells in this distinct translational inhibition programme. Paradoxically, this inhibition renders stem cells hypersensitive to cytotoxic stress, as tumour regeneration after treatment with 5-fluorouracil is blocked. Thus, stem cells must revoke translation inhibition pathways to regenerate a tissue or tumour.

Adequate insulin secretion from pancreatic beta cells is necessary to maintain blood glucose levels within a physiological range. During the development of T2D, insulin secretion becomes insufficient to normalize blood [...], Pancreatic beta cell death is a hallmark of type 1 (T1D) and type 2 (T2D) diabetes, but the molecular mechanisms underlying this aspect of diabetic pathology are poorly understood. Here we report that expression of the microRNA (miR)-200 family is strongly induced in islets of diabetic mice and that beta cell-specific overexpression of miR-200 in mice is sufficient to induce beta cell apoptosis and lethal T2D. Conversely, mir-200 ablation in mice reduces beta cell apoptosis and ameliorates T2D. We show that miR-200 negatively regulates a conserved anti-apoptotic and stress-resistance network that includes the essential beta cell chaperone Dnajc3 (also known as p58IPK) and the caspase inhibitor Xiap. We also observed that mir-200 dosage positively controls activation of the tumor suppressor Trp53 and thereby creates a pro-apoptotic gene-expression signature found in islets of diabetic mice. Consequently, miR-200-induced T2D is suppressed by interfering with the signaling of Trp53 and Bax, a proapoptotic member of the B cell lymphoma 2 protein family. Our results reveal a crucial role for the miR-200 family in beta cell survival and the pathophysiology of diabetes.

Author(s): Chong Sun [sup.1] , Liqin Wang [sup.1] , Sidong Huang [sup.1] [sup.2] , Guus J. J. E. Heynen [sup.1] , Anirudh Prahallad [sup.1] , Caroline Robert [sup.3] , John [...], Patients with melanomas carrying an activating BRAF mutation respond to treatment with BRAF inhibitors although resistance to the inhibitor usually emerges; this resistance is shown to arise through increased expression of receptor tyrosine kinases such as EGFR; however, these changes decrease cell fitness and during a break from inhibitor treatment these cells are selected against, revealing that some patients who acquire EGFR expression may benefit from inhibitor re-treatment after a drug holiday. &apos;Drug holiday&apos; boosts anti-melanoma therapy Melanomas carrying a mutant BRAF gene generally respond to treatment with BRAF inhibitors, but in the majority of cases resistant cancer clones emerge. It has been shown that such resistant clones can nevertheless exhibit reduced fitness when the drug is removed. This paper demonstrates a molecular mechanism underlying this observation. Rene Bernards and colleagues show that a signalling cascade leading from suppression of SOX10 to increased expression of the EGFR (epidermal growth factor receptor) gene confers resistance to BRAF inhibitors and at the same time reduces melanoma cell proliferation and induces senescence in the absence of inhibitors. With preliminary evidence that this pathway is induced in patients who have developed resistance, the authors suggest that temporary withdrawal of BRAF inhibitors -- a drug holiday -- would reverse induced EGFR expression and thus may re-sensitize melanoma cells to BRAF inhibition when treatment is reinstated. Treatment of BRAF(V600E) mutant melanoma by small molecule drugs that target the BRAF or MEK kinases can be effective, but resistance develops invariably.sup.1,2. In contrast, colon cancers that harbour the same BRAF(V600E) mutation are intrinsically resistant to BRAF inhibitors, due to feedback activation of the epidermal growth factor receptor (EGFR).sup.3,4. Here we show that 6 out of 16 melanoma tumours analysed acquired EGFR expression after the development of resistance to BRAF or MEK inhibitors. Using a chromatin-regulator-focused short hairpin RNA (shRNA) library, we find that suppression of sex determining region Y-box 10 (SOX10) in melanoma causes activation of TGF-[beta] signalling, thus leading to upregulation of EGFR and platelet-derived growth factor receptor-[beta] (PDGFRB), which confer resistance to BRAF and MEK inhibitors. Expression of EGFR in melanoma or treatment with TGF-[beta] results in a slow-growth phenotype with cells displaying hallmarks of oncogene-induced senescence. However, EGFR expression or exposure to TGF-[beta] becomes beneficial for proliferation in the presence of BRAF or MEK inhibitors. In a heterogeneous population of melanoma cells having varying levels of SOX10 suppression, cells with low SOX10 and consequently high EGFR expression are rapidly enriched in the presence of drug, but this is reversed when the drug treatment is discontinued. We find evidence for SOX10 loss and/or activation of TGF-[beta] signalling in 4 of the 6 EGFR-positive drug-resistant melanoma patient samples. Our findings provide a rationale for why some BRAF or MEK inhibitor-resistant melanoma patients may regain sensitivity to these drugs after a &apos;drug holiday&apos; and identify patients with EGFR-positive melanoma as a group that may benefit from re-treatment after a drug holiday.

In animals, maternal gene products drive early development in a transcriptionally silent embryo, and are responsible for ZGA. ZGA occurs during the MZT, when developmental control transfers to the embryonic [...], After fertilization, maternal factors direct development and trigger zygotic genome activation (ZGA) at the maternal-to-zygotic transition (MZT). In zebrafish, ZGA is required for gastrulation and clearance of maternal messenger RNAs, which is in part regulated by the conserved microRNA miR-430. However, the factors that activate the zygotic program in vertebrates are unknown. Here we show that Nanog, Pou5f1 (also called Oct4) and SoxB1 regulate zygotic gene activation in zebrafish. We identified several hundred genes directly activated by maternal factors, constituting the first wave of zygotic transcription. Ribosome profiling revealed that nanog, sox19b and pou5f1 are the most highly translated transcription factors pre-MZT. Combined loss of these factors resulted in developmental arrest before gastrulation and a failure to activate > 75% of zygotic genes, including miR-430. Our results demonstrate that maternal Nanog, Pou5f1 and SoxB1 are required to initiate the zygotic developmental program and induce clearance of the maternal program by activating miR-430 expression.