Academic literature on the topic 'Non transcriptional'
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Journal articles on the topic "Non transcriptional"
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Ray, J. Christian J., Jeffrey J. Tabor, and Oleg A. Igoshin. "Non-transcriptional regulatory processes shape transcriptional network dynamics." Nature Reviews Microbiology 9, no. 11 (October 11, 2011): 817–28. http://dx.doi.org/10.1038/nrmicro2667.
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Swami, Meera. "Non-cooperative transcriptional control." Nature Reviews Genetics 11, no. 4 (March 2, 2010): 240. http://dx.doi.org/10.1038/nrg2768.
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Hokello, Joseph, Adhikarimayum Lakhikumar Sharma, and Mudit Tyagi. "Efficient Non-Epigenetic Activation of HIV Latency through the T-Cell Receptor Signalosome." Viruses 12, no. 8 (August 8, 2020): 868. http://dx.doi.org/10.3390/v12080868.
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Human immunodeficiency virus type-1 (HIV-1) can either undergo a lytic pathway to cause productive systemic infections or enter a latent state in which the integrated provirus remains transcriptionally silent for decades. The ability to latently infect T-cells enables HIV-1 to establish persistent infections in resting memory CD4+ T-lymphocytes which become reactivated following the disruption or cessation of intensive drug therapy. The maintenance of viral latency occurs through epigenetic and non-epigenetic mechanisms. Epigenetic mechanisms of HIV latency regulation involve the deacetylation and methylation of histone proteins within nucleosome 1 (nuc-1) at the viral long terminal repeats (LTR) such that the inhibition of histone deacetyltransferase and histone lysine methyltransferase activities, respectively, reactivates HIV from latency. Non-epigenetic mechanisms involve the nuclear restriction of critical cellular transcription factors such as nuclear factor-kappa beta (NF-κB) or nuclear factor of activated T-cells (NFAT) which activate transcription from the viral LTR, limiting the nuclear levels of the viral transcription transactivator protein Tat and its cellular co-factor positive transcription elongation factor b (P-TEFb), which together regulate HIV transcriptional elongation. In this article, we review how T-cell receptor (TCR) activation efficiently induces NF-κB, NFAT, and activator protein 1 (AP-1) transcription factors through multiple signal pathways and how these factors efficiently regulate HIV LTR transcription through the non-epigenetic mechanism. We further discuss how elongation factor P-TEFb, induced through an extracellular signal-regulated kinase (ERK)-dependent mechanism, regulates HIV transcriptional elongation before new Tat is synthesized and the role of AP-1 in the modulation of HIV transcriptional elongation through functional synergy with NF-κB. Furthermore, we discuss how TCR signaling induces critical post-translational modifications of the cyclin-dependent kinase 9 (CDK9) subunit of P-TEFb which enhances interactions between P-TEFb and the viral Tat protein and the resultant enhancement of HIV transcriptional elongation.
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Steensels, Sandra, Jixuan Qiao, and Baran A. Ersoy. "Transcriptional Regulation in Non-Alcoholic Fatty Liver Disease." Metabolites 10, no. 7 (July 9, 2020): 283. http://dx.doi.org/10.3390/metabo10070283.
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Obesity is the primary risk factor for the pathogenesis of non-alcoholic fatty liver disease (NAFLD), the worldwide prevalence of which continues to increase dramatically. The liver plays a pivotal role in the maintenance of whole-body lipid and glucose homeostasis. This is mainly mediated by the transcriptional activation of hepatic pathways that promote glucose and lipid production or utilization in response to the nutritional state of the body. However, in the setting of chronic excessive nutrition, the dysregulation of hepatic transcriptional machinery promotes lipid accumulation, inflammation, metabolic stress, and fibrosis, which culminate in NAFLD. In this review, we provide our current understanding of the transcription factors that have been linked to the pathogenesis and progression of NAFLD. Using publicly available transcriptomic data, we outline the altered activity of transcription factors among humans with NAFLD. By expanding this analysis to common experimental mouse models of NAFLD, we outline the relevance of mouse models to the human pathophysiology at the transcriptional level.
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Ježek, Jan, Daniel G. J. Smethurst, David C. Stieg, Z. A. C. Kiss, Sara E. Hanley, Vidyaramanan Ganesan, Kai-Ti Chang, Katrina F. Cooper, and Randy Strich. "Cyclin C: The Story of a Non-Cycling Cyclin." Biology 8, no. 1 (January 4, 2019): 3. http://dx.doi.org/10.3390/biology8010003.
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The class I cyclin family is a well-studied group of structurally conserved proteins that interact with their associated cyclin-dependent kinases (Cdks) to regulate different stages of cell cycle progression depending on their oscillating expression levels. However, the role of class II cyclins, which primarily act as transcription factors and whose expression remains constant throughout the cell cycle, is less well understood. As a classic example of a transcriptional cyclin, cyclin C forms a regulatory sub-complex with its partner kinase Cdk8 and two accessory subunits Med12 and Med13 called the Cdk8-dependent kinase module (CKM). The CKM reversibly associates with the multi-subunit transcriptional coactivator complex, the Mediator, to modulate RNA polymerase II-dependent transcription. Apart from its transcriptional regulatory function, recent research has revealed a novel signaling role for cyclin C at the mitochondria. Upon oxidative stress, cyclin C leaves the nucleus and directly activates the guanosine 5’-triphosphatase (GTPase) Drp1, or Dnm1 in yeast, to induce mitochondrial fragmentation. Importantly, cyclin C-induced mitochondrial fission was found to increase sensitivity of both mammalian and yeast cells to apoptosis. Here, we review and discuss the biology of cyclin C, focusing mainly on its transcriptional and non-transcriptional roles in tumor promotion or suppression.
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O'Gorman, William, Kon Yew Kwek, Benjamin Thomas, and Alexandre Akoulitchev. "Non-coding RNA in transcription initiation." Biochemical Society Symposia 73 (January 1, 2006): 131–40. http://dx.doi.org/10.1042/bss0730131.
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Diverse classes of non-coding RNAs, including snRNAs (small nuclear RNAs), play fundamental regulatory roles in gene expression. For example, 7SK RNA and the components of the splicing apparatus U1–U6 snRNAs are implicated in the regulation of transcriptional elongation. The first evidence for the involvement of RNA in the regulation of transcriptional initiation is now emerging. TFIIH (transcription factor IIH), a general transcription initiation factor, appears to associate specifically with U1 snRNA, a core splicing component. Reconstituted transcription in vitro demonstrates an increase in the rate of formation of the first phosphodiester bond by RNA polymerase II in presence of U1 snRNA. Reconstituted re-initiation is also stimulated by U1 snRNA. These results suggest that U1 snRNA functions in the regulation of transcription by RNA polymerase II in addition to its role in RNA processing. The implications of these data extend to the development of new technologies that will allow the identification and analysis of diverse RNA species present as regulatory components in transcription-related ribonucleoprotein complexes.
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Poulat, Francis. "Non-Coding Genome, Transcription Factors, and Sex Determination." Sexual Development 15, no. 5-6 (2021): 295–307. http://dx.doi.org/10.1159/000519725.
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In vertebrates, gonadal sex determination is the process by which transcription factors drive the choice between the testicular and ovarian identity of undifferentiated somatic progenitors through activation of 2 different transcriptional programs. Studies in animal models suggest that sex determination always involves sex-specific transcription factors that activate or repress sex-specific genes. These transcription factors control their target genes by recognizing their regulatory elements in the non-coding genome and their binding motifs within their DNA sequence. In the last 20 years, the development of genomic approaches that allow identifying all the genomic targets of a transcription factor in eukaryotic cells gave the opportunity to globally understand the function of the nuclear proteins that control complex genetic programs. Here, the major transcription factors involved in male and female vertebrate sex determination and the genomic profiling data of mouse gonads that contributed to deciphering their transcriptional regulation role will be reviewed.
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Genini, Davide, Ramon Garcia-Escudero, Giuseppina M. Carbone, and Carlo V. Catapano. "Transcriptional and Non-Transcriptional Functions of PPARβ/δ in Non-Small Cell Lung Cancer." PLoS ONE 7, no. 9 (September 25, 2012): e46009. http://dx.doi.org/10.1371/journal.pone.0046009.
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Bouget, François-Yves, Marc Lefranc, Quentin Thommen, Benjamin Pfeuty, Jean-Claude Lozano, Philippe Schatt, Hugo Botebol, and Valérie Vergé. "Transcriptional versus non-transcriptional clocks: A case study in Ostreococcus." Marine Genomics 14 (April 2014): 17–22. http://dx.doi.org/10.1016/j.margen.2014.01.004.
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Chattopadhyay, Saurabh, Gayatri Subramanian, Ying Zhang, Manoj Veleeparambil, and Ganes C. Sen. "Transcriptional and non-transcriptional functions of IRF3 in host defense." Journal of Immunology 198, no. 1_Supplement (May 1, 2017): 203.3. http://dx.doi.org/10.4049/jimmunol.198.supp.203.3.
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Abstract Innate immune response is the first line of host defense against microbial infection. Interferon Regulatory Factor 3 (IRF3), a critical transcription factor, is rapidly activated during virus infection to trigger numerous antiviral genes, including the interferons. Our studies have revealed that in addition to triggering these genes, IRF3 activates direct apoptosis of virus-infected cells by a newly discovered antiviral apoptotic pathway, RIPA (Chattopadhyay et al, Immunity 2016, EMBO J, 2010). In RIPA, IRF3 is differentially modified by linear polyubiquitination of two lysine residues. Moreover, a knock-in mouse strain, without the transcriptional activity of IRF3, can still mount antiviral response by its RIPA branch. Importantly, the use of pathway-specific mutants of IRF3 revealed that both transcriptional, and RIPA, branches contribute to the overall antiviral functions of IRF3. To investigate the contribution of the transcriptional branch of IRF3, we screened a shRNA library of the human ISGs. Our screen identified a small subset of novel IRF3-dependent genes, which exhibit antiviral functions in human and mouse cells. These newly-identified ISGs are protective against a wide range of clinically relevant human viruses, e.g. RSV, HPIV3, HSV-1, HCMV. In-depth investigation revealed that these ISGs regulate cellular autophagy pathway to control virus replication. The presentation will highlight how both pathways of IRF3 mount an optimum host response against viral as well as non-viral pathogenesis.
Dissertations / Theses on the topic "Non transcriptional"
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Mayhew, Michael. "Coding regions under non-coding selection: implications for transcriptional and post-transcriptional gene regulation." Thesis, McGill University, 2008. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=21995.
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The signals that facilitate transcriptional and post-transcriptional gene expression regulation are still being understood. Comparative genomics approaches based on the premise that sequence or structure conservation implies functionality have successfully distinguished true regulatory sequences and structures from prediction noise. Protein-coding regions of genes have often been overlooked as potential regulatory sequence regions. A set of 8785 coding region sequences were previously found to be conserved significantly above a baseline protein-coding conservation level. We call these sequences coding regions under non-coding selection or CRUNCS. Analysis of the sequences, the primary contribution of this work, revealed that CRUNCS bases are more often found in coding exon edges and in middle coding exons. CRUNCS-containing genes are more significantly enriched for regulation of transcription and translation, protein ubiquitination, and mRNA processing. CRUNCS are significantly enriched for RNA secondary structure elements. We also uncovered statistical evidence linking CRUNCS to gene splicing regulation.Les méthodes de génomique comparatives qui sont tirées de la prémisse que la conservation de la séquence ou de la structure implique la conservation de la fonctionnalité, sont parvenues à identifier de vrais signaux régulateurs. Les régions codantes ont souvent été négligées comme des régions potentiellement régulatrices. Un ensemble de 8785 séquences de ces régions plus conservées que prévues a été précédement identifié. L'analyse de ces séquences appelées CRUNCS a révélé que les acides nucléiques des CRUNCS sont plus nombreux aux extrémités des exons et dans les exons centraux. Les gènes contenants des CRUNCS sont enrichis des catégories fonctionnelles comprenant : la régulation de la transcription et la traduction, l'ubiquitination des protéines et le traitement des ARNm. Les CRUNCS sont enrichis d'éléments de structure secondaire de l'ARN. Nous avons aussi découvert des preuves statistiques démontrant que les CRUNCS jouent un rôle dans la régulation de l'épissage des gènes.
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Serra, Barros Ana Cristina. "Transcriptional regulation by non-coding RNAs in Saccharomyces cerevisiae." Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:e523d0ee-bb3a-4217-aeba-9e6e398fc86a.
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Genome-wide studies in Saccharomyces cerevisiae have revealed that the majority of the genome is transcribed on both strands, producing both coding and non-coding RNAs (ncRNAs). Initially, these ncRNAs were regarded as spurious transcripts but some have since been shown to have important roles as transcriptional regulators. Very little is understood about how ncRNAs are initiated, terminated and processed or how this influences their function. To address these questions, the expression, stability, and subcellular localization of the ncRNAs at the endogenous GAL locus was analysed. This revealed a complex interleaved transcript map, challenging the conventional view of a transcription unit (TU) flanked by 5’ sequences or promoters (P) that initiate transcription and 3’ regions, known as terminators (T), which control events such as transcript cleavage, polyadenylation, export and transcription termination. By creating conventional (PGAL-T) or unconventional (PGAL-P) hybrid TUs at the GAL locus, in which a promoter or terminator is positioned downstream of a galactose-inducible promoter, this work shows that both promoters and terminators are able to initiate antisense transcription to yield stable antisense transcripts. The data suggest that terminators contribute to efficient but variable expression from the promoter. An unconventional P-P TU, lacking a terminator, is transcribed on both strands but the sense transcript remains at low levels, through the repressive action of antisense transcription, and is retained in the nucleus. In contrast, the conventional P-T bi-directional TUs are plastic, with the Rrp6 component of the nuclear exosome and TATA-like sequences in the 3’ UTR determining whether the predominant transcript is antisense or sense. By relieving the repressive action of antisense transcription, this allows high levels of sense transcript to accumulate in the cytoplasm, contributing to gene expression, supporting a novel mode of gene regulation involving components of RNA quality control pathways acting through the 3’ region of genes.
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Snead, Aaron Nathan. "Exploring the non-transcriptional activity of thyroid hormone derivatives." Diss., Search in ProQuest Dissertations & Theses. UC Only, 2008. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3339205.
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Camilleri, Emily Therese. "The Transcriptional Role of FOXP1 in Non-Hodgkin's Lymphoma." Thesis, Griffith University, 2013. http://hdl.handle.net/10072/367974.
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Non-Hodgkin's lymphoma (NHL) is a family of lymphoid malignances that are the 6th leading cause of death in Australia. B cell lymhomas account for approximately 90% of all NHL cases, and the common subtypes Diffuse Large B cell Lymphoma (DLBCL) and Follicular Lymphoma (FL) together make uo 60% of all cases. DLBCL and FL are both germinal centre derived B cell lymphomas, however these malignancies represent opposite ends of the clinical scale, being aggressive compared to indolent disease respectively. Early detection of lymphoma is highly advantageous for aggressive subtypes like DLBCL, where without treatment patient survival can be less than 2 years. Currently, there are very few genes that are found to be associated with the risk of NHL. One gene that has been implicated in NHL development and progression is , but as yet few other genes have been identified. This thesis is aimed at characterising this gene but also identifying other genes involved in NHL. The identification of genes that predispose individuals to the development of NHL may firstly provide a diagnostic tool, and also provide insight into the molecular pathogenesis of this disease. Additionally, molecular characterisation of these genes may also aid in the development of pharmacogenomic therapies.Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
Schoolo of Medical Science
Griffith Health
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Bogu, Gireesh K. 1984. "Understanding the transcriptional landscape of non-coding genome in mammals." Doctoral thesis, Universitat Pompeu Fabra, 2017. http://hdl.handle.net/10803/572043.
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Widespread transcription in mammals revealed unexpected discovery of non-coding
elements like long noncoding RNAs (lncRNAs) and repetitive elements. First,
lncRNAs were previously identified in limited number of tissues or cell lines in mouse
and the discovery of lncRNAs was still pending in many other tissues in mouse. To
address this, we applied a computational pipeline that discovered 2,803 highconfidence
novel lncRNAs by mapping and de novo assembling billions of RNA-Seq
reads in eight tissues and a primary cell line in mouse. Further, we integrated this
catalog of lncRNAs with chromatin state maps and found many regulatory lncRNAs
(promoter-associated and enhancer-associated lncRNAs). Second, more than half of
the human genome contains repetitive elements. However, it is not clear how they
are expressed across all mammalian tissues. To address this, as a part of Genotype-
Tissue Expression (GTEx) project, we profiled repetitive elements using 8,551 poly-A
RNA-Seq datasets from 53 tissues across 550 individuals and found various repeat
families transcribed across multiple human tissues in a tissue-specific manner. In
summary, to understand the transcriptional landscape of non-coding genome, we
mainly analyzed RNA-Seq datasets across many tissues in mammals and show that
the non-coding elements like lncRNA and repetitive elements are not only
transcribed but also tissue-specific. Together, this thesis work defines a unique
collection of non-coding elements that are transcribed and tissue-specific in
mammalian tissues.Una gran parte del genoma de mamiefores se expresa en forma de ARNs y se conoce hoy en dia que una gran parte de estos transcritos son no codificantes llamados lncRNAs y que contienen elementos repetitivos. En ratones, estos han sido identificados recientemente en un número limitado de tejidos y líneas celulares. Esta tesis presenta un trabajo exhaustivo de estudio de lnRNAs en ratón en ocho tejidos y una línea celular. En este trabajo se descubrieron 2803 nuevos lncRNAs a los cuáles se les asignó una función reguladora (asociados a promotores o activadores “enhancers”) en el genoma usando datos del estado de la cromatina. Asimismo, más de la mitad del genoma humano contiene elementos repetitivos. Desafortunadamente no se conoce el patrón de expresión de estos elementos repetitivos en los tejidos mamíferos. Como miembros del proyecto GTEx (GenotypeviTissue Expression), analizamos la expresión de estos elementos repetitivos en 8,551 muestras de polyA RNA-Seq en 53 tejidos de 550 individuos. Encontramos que muchas familias de elementos repetitivos son expresadas en tejidos específicos en varios individuos, y representan una característica peculiar de la identidad de cada tejido en humanos.
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POLI, VALENTINA. "A non-transcriptional role of NFAT in regulating platelets functions." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2019. http://hdl.handle.net/10281/241337.
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Le piastrine ricoprono un ruolo fondamentale nei processi di emostasi, ma, recentemente, è stato dimostrato che hanno anche un ruolo nel modulare la risposta infiammatoria, interagendo con le cellule del sistema immunitario in modo diretto e indiretto. Nonostante le piastrine siano delle cellule anucleate, esse contengono fattori trascrizionali (TF) che modulano la loro attivatione attraverso attività non-trascrizionali. In particolare, è stato dimostrato che le piastrine contengono NF-κB, un TF che controlla importanti funzioni delle cellule immunitarie durante i processi infiammatori, e che NF-κB regola l’attivazione delle piastrine.
In questo lavoro, abbiamo investigato la possibilità che altri TF oltre a NF-κB possano avere un ruolo regolatorio durante l’attivazione piastrinica. Abbiamo osservato che le piastrine contengono un altro importante TF tipicamente espresso dalle cellule immunitarie: il fattore nucleare delle cellule T attivate (NFAT). In particolare, abbiamo osservato che, a seguito dell’attivazione del recettore PAR4, la via calcineurina/NFATc2 viene attivata e regola varie funzioni piastriniche. Questa via viene attivata sia nelle piastrine murine sia umane e la sua inibizione determina un aumento dell’aggregazione piastrinica, dell’attivazione dell’integrina, del rilascio di granule e dell’adesione su fibrinogeno. Attraverso modelli murini in vivo, abbiamo dimostrato che l’attivazione di NFATc2 nelle piastrine modula l’emostasi e la trombosi. Inoltre, l’attivazione di NFATc2 nelle piastrine regola l’interazione tra piastrine e neutrofili, influenzando la severità dello sviluppo di sepsi batterica. I nostril esperimenti in vitro supportano la capacità di NFATc2 di agire a valle del recettore PAR4 attraverso un meccanismo che coinvolge il recettore dell’ADP e l’outside-in signaling dell’integrina α2bβ3.
Infine, abbiamo osservato che l’inibizione della via calcineurina/NFATc2 è in grado di compensare in parte i difetti di attivazione piastrinica in due rare patologie, la sindrome di Hermansky-Pudlack e la trombastenia di Glanzmann. I nostri dati suggeriscono che la via calcineurina/NFATc2 può essere bersaglio per lo sviluppo di approcci terapeutici innovativi per il trattamento di difetti piastrinici con prognosi infausta.
Il nostro lavoro mostra per la prima volta che l’attivatione della via calcineurina/NFATc2 nelle piastrine ha un ruolo non-trascrizionale e è un regolatore negativo delle risposte piastriniche. Ulteriori studi sono necessari per caratterizzare il meccanismo di azione attraverso il quale NFATc2 agisce nel modulare l’attivazione piastrinica e per capire se NFATc2 possa avere un ruolo non-trascrizionale anche in cellule nucleate.Platelets play a critical role in hemostasis but, more recently, it was demonstrated that they also modulate the inflammatory response by establishing direct and indirect interactions with immune cells. Although platelets are anucleated cells, they contain functional transcription factors (TFs) that modulate their activation via non-transcriptional functions. In particular, it has been shown that platelets contain NF-κB, a TF that controls important functions of immune cells during the inflammatory process, and that NF-κB regulates platelet activation. We investigated the possibility that other TFs different from NF-κB might play regulatory roles during platelet activation. We found that platelets contain another TF typically expressed by immune cells: nuclear factor of activated T cells (NFAT). In particular, we found that upon PAR4 ligation, the calcineurin/NFATc2 pathway is activated and regulates platelet functions. This pathway is activated both in murine and human platelets, and its inhibition results in enhancement of platelet aggregation, integrin activation, granules release and spreading on fibrinogen. By using murine in vivo models, we demonstrated that NFATc2 activation in platelets modulates hemostasis and thrombosis. Moreover, platelet NFATc2 activation regulates the interaction between platelets and neutrophils and impacts the severity of bacterial sepsis development. Our in vitro experiments support the capacity of NFATc2 to act downstream of PAR4 via a mechanism that involves both the ADP receptor and the outside-in integrin α2bβ3 pathway. Finally, we found that inhibition of the calcineurin/NFATc2 pathway partially rescues platelet activation defects in two rare human platelet pathologies, the Hermansky-Pudlak syndrome and the Glanzmann thrombasthenia. Our data suggest that the calcineurin/NFATc2 pathway can be targeted to develop innovative therapeutic approaches to treat platelet defects with poor prognosis. Our work reveals for the first time that the activation of the calcineurin/NFATc2 pathway in platelets has a non-transcriptional role and it is a key negative regulator of platelet responses. Further studies are needed to characterize the mechanism of action through which NFATc2 exerts its non-transcriptional function in modulating platelets activation and to understand if NFATc2 could have a non-transcriptional role also in nucleated cells.
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Evans, C. M. "Non-coding RNA and transcriptional regulation in CD4 T cell lineages." Thesis, University College London (University of London), 2015. http://discovery.ucl.ac.uk/1466165/.
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CD4 T cell lineage choice epitomises the ability of the immune system to become tailored to a specific threat and provides a framework for understanding the mechanisms behind cell specification. The differentiation of T effectors from naïve cells gives rise to pro-inflammatory lineages including T helper 1 (Th1) and Th2 and anti-inflammatory regulatory T cells (Treg). An additional lineage of Treg also exits the thymus in parallel to naïve T cells and together these Treg are required for prevention of autoimmunity. These T cell lineages are distinct in terms of their cytokine production and functional effects but also through their differences in gene expression and its regulation, which are orchestrated by the presence of lineage-specifying transcription factors specific for each lineage. In addition, post-translational modification of histones also provide insights into this transcriptional regulation and more recently the pervasive and tissue-specific transcription of multiple classes of RNA species without protein coding capacity, non-coding RNA (ncRNA), has been found to play a role in cell differentiation and function. In this thesis I identify several ncRNAs with differential expression different T cell lineages. This includes ncRNAs upregulated Treg compared to T responders. The characterisation of these, including their expression in the autoimmune context of systemic lupus erythematosus (SLE), is presented and their possible biological functions are examined. The relevance of histone modifications for influencing Treg identity in SLE is also investigated. An additional class of ncRNAs that originate from gene enhancer regions, eRNA, is also investigated in the context of Th1 versus Th2 lineage choice. This enhancer transcription is increased genome-wide in Th1 cells at enhancers with high density T-bet binding in, termed ‘super-enhancers’. The functional relevance of these eRNAs, including at the super-enhancer upstream of the Th1 signature cytokine gene, IFNG, is also investigated in knockdown experiments.
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Murfitt, Kenneth John. "Post-transcriptional regulation of miRNA activity and expression in C. elegans." Thesis, University of Cambridge, 2014. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.648749.
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Chery, Alicia. "Rôle de la transcription pervasive antisens chez Saccharomyces cerevisiae dans la régulation de l'expression des gènes." Thesis, Paris 6, 2017. http://www.theses.fr/2017PA066191/document.
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L'expression des gènes est finement régulée dans la cellule et soumise à de multiples contrôles-qualité. Cette régulation intervient à différents niveaux, de façon à garantir une synthèse efficace des produits fonctionnels de l'expression génique, et pour assurer une adaptation à un changement environnemental. Notamment, les régulations transcriptionnelles sont cruciales pour contrôler la cinétique et le niveau d'expression des gènes. La transcription pervasive est une transcription généralisée non-codante et instable qui fut révélée chez la levure Saccharomyces cerevisiae. Bien que son potentiel régulateur ait été démontré de façon ponctuelle, la question de sa fonctionnalité globale restait ouverte. Lors de ma thèse, j'ai pu montrer l'existence de phénomènes multiples d'interférence transcriptionnelle liés à la transcription pervasive, pour co-réguler un ensemble de gènes entre la phase exponentielle et la quiescence. En effet, la transcription non-codante en antisens des gènes concernés conduit à leur répression, dans des conditions où ils ne doivent pas être exprimés. Le mécanisme de répression fait intervenir des modifications de la chromatine. La levure bourgeonnante, dépourvue de la machinerie d'ARN interférence, présente donc un système fin de régulation de l'expression génique utilisant la transcription pervasiveIn the cell, gene expression is finely tuned and is submitted to different quality-controls. Gene are regulated at different expression levels in order to guarantee a proper synthesis of functional products, and to ensure an optimal adaptation to environmental changes. In particular, transcriptional regulations are critical for gene expression level and kinetics.Pervasive transcription, defined as a generalized non-coding and unstable transcription, was discovered in the yeast Saccharomyces cerevisiae. Although its regulatory potential was punctually shown, the question of its global functionality still remained. During my PhD, I could show the existence of numerous transcriptional interference mechanisms involved in the co-regulation of a group of genes between exponential phase and quiescence. Indeed, non-coding transcription in antisense to genes promoter leads to its repression in conditions where they have to be switched off. The repression mechanism is allowed by chromatin modifications.Hence, budding yeast that lacks RNA interference machinery has developed a fine regulation system using pervasive transcription
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Jones, Amy Madeline. "Post-transcriptional regulation of rpoS and HemA in salmonella." Morgantown, W. Va. : [West Virginia University Libraries], 2009. http://hdl.handle.net/10450/10826.
Full textBooks on the topic "Non transcriptional"
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S, Cho-Chung Yoon, Gewirtz A. M, Stein Cy A, and New York Academy of Sciences., eds. Therapeutic oligonucleotides: Transcriptional and translational strategies for silencing gene expression. New York: New York Academy of Sciences, 2005.
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George, MacDonald. Lilith ; Lilith A: Transcription of the original manuscript of Lilith. Whitethorn, Calif: Johannesen, 1994.
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Weng, Zhongfu. Dictionnaire pratique chinois-franc̜ais: Avec transcriptions pinyin et zhuyin : caractères simplifiés et non-simplifiés. Paris: Librairie You Feng, 2000.
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Salmiņa, Valda. Armēņu īpašvārdu atveide latviešu valodā. Rīga: LU Latviešu valodas institūts, 2009.
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Institut fondamental d'Afrique noire Cheikh Anta Diop, ed. La langue noon: Alphabet, orthographe, contes, devinettes, proverbs suivis du décret relatif à la transcription du noon. Dakar: Institut fondamental d'Afrique noire Cheikh Anta Diop, IFAN/UCAD, 2010.
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Stevens, Meredith Leigh. Global repression of non-heat shock gene transcription by activation of heat shock factor in Drosophila. Ottawa: National Library of Canada, 1999.
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Morrison, Andrew John. Heat shock transcription factors and the hsp70 induction response in neural and non-neural tissues of the hyperthermic rat during postnatal development. Ottawa: National Library of Canada, 2000.
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Cavana, Giovanni Nicolò. Lettere ad Angelico Aprosio (1665-1675). Edited by Luca Tosin. Florence: Firenze University Press, 2013. http://dx.doi.org/10.36253/978-88-6655-236-9.
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The critical edition of the correspondence (1665-1675), today housed at the University of Genoa library, between the Genoan patrician Nicolò Cavana and the bibliophile Fra' Angelico Aprosio di Ventimiglia includes an introduction and transcription of the letters, with both bibliographical and (where possible) explanatory notes on some now outdated terms. In consideration of the private nature of the 286 letters, reading them gives an interesting and informal view of seventeenth-century life, as well as much information on the variegated world of the Baroque book culture providing a constant backdrop to the relationship of collaboration and friendship between the two figures.
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Pancani, Eleonora, ed. Ruggero Jacobbi alla radio. Florence: Firenze University Press, 2008. http://dx.doi.org/10.36253/978-88-8453-664-8.
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Recent years have seen the publication of a great deal of the work of Ruggero Jacobbi, a legendary figure of Italian twentieth-century culture, thanks to a praiseworthy retrieval of unpublished material conserved in the «A. Bonsanti» contemporary archive of the Gabinetto «G.P. Vieusseux». However, despite so many new pages of poetry and translation, what was still lacking was the writer's voice. The voice which, thanks to the painstaking work of Eleonora Pancani, we can now read (if not hear), as with characteristic dexterity it intermingles verses and music, literature and theatre, politics and entertainment. Ruggero Jacobbi alla radio presents the transcription of several radio programmes of the 70s featuring the genial culture of this multi-faceted intellectual. Jacobbi entertains his audience, discorsing on literary history, the figurative arts and opera, quoting poetry, discussing plays, mingling observations on Goldoni, Pirandello, Bontempelli, Savinio, Pessoa and García Lorca in an engaging anecdotal style that involves the cinema, the theatre and literature, while the great figures of tradition and recent history are interwoven with reminiscences of private life.
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1930-, Sluyser M., ed. Zinc-finger proteins in oncogenesis: DNA-binding and gene regulation. New York, N.Y: New York Academy of Sciences, 1993.
Find full textBook chapters on the topic "Non transcriptional"
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Pandey, Radha Raman, and Chandrasekhar Kanduri. "Transcriptional and Posttranscriptional Programming by Long Noncoding RNAs." In Long Non-Coding RNAs, 1–27. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-642-16502-3_1.
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Ebhardt, H. Alexander. "Post-Transcriptional Modifications of Plant Small RNAs." In Non Coding RNAs in Plants, 59–66. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-19454-2_4.
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Noy, Noa. "Non-classical Transcriptional Activity of Retinoic Acid." In Subcellular Biochemistry, 179–99. Dordrecht: Springer Netherlands, 2016. http://dx.doi.org/10.1007/978-94-024-0945-1_7.
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Bazzini, Ariel A., and Sebastian Asurmendi. "Effects of Virus Infection on Transcriptional Activity of miR164a in Plants." In Non Coding RNAs in Plants, 359–73. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-19454-2_22.
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Aranega, Amelia E., and Diego Franco. "Post-transcriptional Regulation by Proteins and Non-coding RNAs." In Congenital Heart Diseases: The Broken Heart, 153–71. Vienna: Springer Vienna, 2016. http://dx.doi.org/10.1007/978-3-7091-1883-2_13.
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Frank, Till D., Miguel A. S. Cavadas, Lan K. Nguyen, and Alex Cheong. "Non-linear Dynamics in Transcriptional Regulation: Biological Logic Gates." In SEMA SIMAI Springer Series, 43–62. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-33054-9_3.
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Bhan, Arunoday, and Subhrangsu S. Mandal. "Estradiol-Induced Transcriptional Regulation of Long Non-Coding RNA, HOTAIR." In Methods in Molecular Biology, 395–412. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-3127-9_31.
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Mink, Sigrun, Liubov Shatkina, Andrea Nestl, and Andrew C. B. Cato. "Membrane Localization and Rapid Non-Transcriptional Action of the Androgen Receptor." In The Identities of Membrane Steroid Receptors, 111–17. Boston, MA: Springer US, 2003. http://dx.doi.org/10.1007/978-1-4615-0339-2_13.
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Passoth, Volkmar, Bärbel Hahn-Hägerdal, and Ulrich Klinner. "Investigation of Transcriptional Regulation of the Fermentative ADH in Pichia stipitis Using an EGFP Reporter Gene." In Non-Conventional Yeasts in Genetics, Biochemistry and Biotechnology, 241–44. Berlin, Heidelberg: Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-642-55758-3_38.
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Bazan, N. G., G. Allan, and V. L. Marcheselli. "An inhibitor of injury-induced COX-2 transcriptional activation elicits neuroprotection in a brain damage model." In Improved Non-Steroid Anti-Inflammatory Drugs: COX-2 Enzyme Inhibitors, 145–66. Dordrecht: Springer Netherlands, 1996. http://dx.doi.org/10.1007/978-94-010-9029-2_9.
Full textConference papers on the topic "Non transcriptional"
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Meng, Jia, Jianqiu Zhang, Yidong Chen, and Yufei Huang. "Bayesian non-negative factor analysis for reconstructing transcriptional regulatory network." In 2011 IEEE Statistical Signal Processing Workshop (SSP). IEEE, 2011. http://dx.doi.org/10.1109/ssp.2011.5967704.
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Rynne, Jennifer, Manuela Plate, Rachel Chambers, Peter Howarth, and Rocio T. Martinez-Nunez. "Post-transcriptional dysregulation as a novel mechanism underlying non-responsive severe asthma." In Abstracts from the 17th ERS Lung Science Conference: ‘Mechanisms of Acute Exacerbation of Respiratory Disease’. European Respiratory Society, 2019. http://dx.doi.org/10.1183/23120541.lungscienceconference-2019.pp208.
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Schaal, Courtney M., Smitha Pillai, Jackie L. Johnson, and Srikumar Chellappan. "Abstract 1803: Transcriptional regulation of nicotinic acetylcholine receptors (nAChRs) by E2F family transcription factors in non-small cell lung cancer." In Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC. American Association for Cancer Research, 2013. http://dx.doi.org/10.1158/1538-7445.am2013-1803.
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Rynne, Jennifer, Manuela Plate, Rachel Chambers, Peter Howarth, and Rocio T. Martinez-Nunez. "LSC - 2019 - Post-transcriptional dysregulation as a novel mechanism underlying non-responsive severe asthma." In ERS International Congress 2019 abstracts. European Respiratory Society, 2019. http://dx.doi.org/10.1183/13993003.congress-2019.pa2369.
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Razi, Abolfazl, Nilanjana Banerjee, Nevenka Dimitrova, and Vinay Varadan. "Non-linear Bayesian framework to determine the transcriptional effects of cancer-associated genomic aberrations." In 2015 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC). IEEE, 2015. http://dx.doi.org/10.1109/embc.2015.7319885.
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Bertrams, W., K. Griss, M. Han, K. Seidel, A. Klemmer, A. Sittka-Stark, S. Hippenstiel, et al. "Transcriptional Analysis identifies long non-coding RNAs as potential biomarkers in pneumonia and COPD exacerbation." In 61. Kongress der Deutschen Gesellschaft für Pneumologie und Beatmungsmedizin e.V. Georg Thieme Verlag KG, 2020. http://dx.doi.org/10.1055/s-0039-3403105.
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Lu, Tzu-Pin, Pei-Chun Chen, Jang-Ming Lee, Chung-Ping Hsu, Shin-Kuang Chen, Mong-Hsun Tsai, Chuhsing K. Hsiao, Eric Y. Chuang, and Liang-Chuan Lai. "Abstract 2944: Genome-wide transcriptional modulation screening in non-smoking female lung cancer in Taiwan." In Proceedings: AACR 101st Annual Meeting 2010‐‐ Apr 17‐21, 2010; Washington, DC. American Association for Cancer Research, 2010. http://dx.doi.org/10.1158/1538-7445.am10-2944.
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Ozes, Ali R., Dave Miller, Cong Guo, Anurag Bhattrai, Yunlong Liu, and Kenneth P. Nephew. "Abstract 5189: The transcriptional regulation of the long non-coding RNA HOTAIR in ovarian cancer." In Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC. American Association for Cancer Research, 2013. http://dx.doi.org/10.1158/1538-7445.am2013-5189.
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Kabbout, Mohamed, Melinda M. Garcia, Junya Fujimoto, Chi-Wan Chow, Denise Woods, Patricia Koch, Amin Momin, et al. "Abstract 2177: Tumor suppressor effects of ETS2 transcriptional factor in human non-small cell lung cancer." In Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL. American Association for Cancer Research, 2012. http://dx.doi.org/10.1158/1538-7445.am2012-2177.
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Tanwer, Pooja, and Daman Saluja. "P623 Post-transcriptional regulation of genes by non-coding RNA inneisseria gonorrhoeae, an obligate human pathogen." In Abstracts for the STI & HIV World Congress (Joint Meeting of the 23rd ISSTDR and 20th IUSTI), July 14–17, 2019, Vancouver, Canada. BMJ Publishing Group Ltd, 2019. http://dx.doi.org/10.1136/sextrans-2019-sti.691.
Full textReports on the topic "Non transcriptional"
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Rafaeli, Ada, and Russell Jurenka. Molecular Characterization of PBAN G-protein Coupled Receptors in Moth Pest Species: Design of Antagonists. United States Department of Agriculture, December 2012. http://dx.doi.org/10.32747/2012.7593390.bard.
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The proposed research was directed at determining the activation/binding domains and gene regulation of the PBAN-R’s thereby providing information for the design and screening of potential PBAN-R-blockers and to indicate possible ways of preventing the process from proceeding to its completion. Our specific aims included: (1) The identification of the PBAN-R binding domain by a combination of: (a) in silico modeling studies for identifying specific amino-acid side chains that are likely to be involved in binding PBAN with the receptor and; (b) bioassays to verify the modeling studies using mutant receptors, cell lines and pheromone glands (at tissue and organism levels) against selected, designed compounds to confirm if compounds are agonists or antagonists. (2) The elucidation ofthemolecular regulationmechanisms of PBAN-R by:(a) age-dependence of gene expression; (b) the effect of hormones and; (c) PBAN-R characterization in male hair-pencil complexes. Background to the topic Insects have several closely related G protein-coupled receptors (GPCRs) belonging to the pyrokinin/PBAN family, one with the ligand pheromone biosynthesis activating neuropeptide or pyrokinin-2 and another with diapause hormone or pyrokinin-1 as a ligand. We were unable to identify the diapause hormone receptor from Helicoverpa zea despite considerable effort. A third, related receptor is activated by a product of the capa gene, periviscerokinins. The pyrokinin/PBAN family of GPCRs and their ligands has been identified in various insects, such as Drosophila, several moth species, mosquitoes, Triboliumcastaneum, Apis mellifera, Nasoniavitripennis, and Acyrthosiphon pisum. Physiological functions of pyrokinin peptides include muscle contraction, whereas PBAN regulates pheromone production in moths plus other functions indicating the pleiotropic nature of these ligands. Based on the alignment of annotated genomic sequences, the primary and secondary structures of the pyrokinin/PBAN family of receptors have similarity with the corresponding structures of the capa or periviscerokinin receptors of insects and the neuromedin U receptors found in vertebrates. Major conclusions, solutions, achievements Evolutionary trace analysisof receptor extracellular domains exhibited several class-specific amino acid residues, which could indicate putative domains for activation of these receptors by ligand recognition and binding. Through site-directed point mutations, the 3rd extracellular domain of PBAN-R was shown to be critical for ligand selection. We identified three receptors that belong to the PBAN family of GPCRs and a partial sequence for the periviscerokinin receptor from the European corn borer, Ostrinianubilalis. Functional expression studies confirmed that only the C-variant of the PBAN-R is active. We identified a non-peptide agonist that will activate the PBAN-receptor from H. zea. We determined that there is transcriptional control of the PBAN-R in two moth species during the development of the pupa to adult, and we demonstrated that this transcriptional regulation is independent of juvenile hormone biosynthesis. This transcriptional control also occurs in male hair-pencil gland complexes of both moth species indicating a regulatory role for PBAN in males. Ultimate confirmation for PBAN's function in the male tissue was revealed through knockdown of the PBAN-R using RNAi-mediated gene-silencing. Implications, both scientific and agricultural The identification of a non-peptide agonist can be exploited in the future for the design of additional compounds that will activate the receptor and to elucidate the binding properties of this receptor. The increase in expression levels of the PBAN-R transcript was delineated to occur at a critical period of 5 hours post-eclosion and its regulation can now be studied. The mysterious role of PBAN in the males was elucidated by using a combination of physiological, biochemical and molecular genetics techniques.
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Sessa, Guido, and Gregory Martin. Role of GRAS Transcription Factors in Tomato Disease Resistance and Basal Defense. United States Department of Agriculture, 2005. http://dx.doi.org/10.32747/2005.7696520.bard.
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The research problem: Bacterial spot and bacterial speck diseases of tomato are causedby strains of Xanthomonas campestris pv. vesicatoria (Xcv) and Pseudomonas syringae pv.tomato (Pst), respectively. These bacteria colonize aerial parts of the plant and causesignificant losses in tomato production worldwide. Protection against Xcv and Pst bycultural practices or chemical control has been unsuccessful and there are only limitedsources of genetic resistance to these pathogens. In previous research supported in part byBARD IS-3237-01, we extensively characterized changes in tomato gene expression uponthe onset of spot and speck disease resistance. A remarkable finding of these studies wasthe inducibility in tomato leaves by both Xcv and Pst strains of genes encodingtranscriptional activator of the GRAS family, which has not been previously linked todisease resistance. Goals: Central goals of this research were to investigate the role of GRAS genes in tomatoinnate immunity and to assess their potential use for disease control.Specific objectives were to: 1. Identify GRAS genes that are induced in tomato during thedefense response and analyze their role in disease resistance by loss-of-function experiments.2. Overexpress GRAS genes in tomato and characterize plants for possible broad-spectrumresistance. 3. Identify genes whose transcription is regulated by GRAS family. Our main achievements during this research program are in three major areas:1. Identification of tomato GRAS family members induced in defense responses andanalysis of their role in disease resistance. Genes encoding tomato GRAS family memberswere retrieved from databases and analyzed for their inducibility by Pst avirulent bacteria.Real-time RT-PCR analysis revealed that six SlGRAS transcripts are induced during theonset of disease resistance to Pst. Further expression analysis of two selected GRAS genesshowed that they accumulate in tomato plants in response to different avirulent bacteria orto the fungal elicitor EIX. In addition, eight SlGRAS genes, including the Pst-induciblefamily members, were induced by mechanical stress in part in a jasmonic acid-dependentmanner. Remarkably, SlGRAS6 gene was found to be required for tomato resistance to Pstin virus-induced gene silencing (VIGS) experiments.2. Molecular analysis of pathogen-induced GRAS transcriptional activators. In aheterologous yeast system, Pst-inducible GRAS genes were shown to have the ability toactivate transcription in agreement with their putative function of transcription factors. Inaddition, deletion analysis demonstrated that short sequences at the amino-terminus ofSlGRAS2, SlGRAS4 and SlGRAS6 are sufficient for transcriptional activation. Finally,defense-related SlGRAS proteins were found to localize to the cell nucleus. 3. Disease resistance and expression profiles of transgenic plants overexpressing SlGRASgenes. Transgenic plants overexpressing SlGRAS3 or SlGRAS6 were generated. Diseasesusceptibility tests revealed that these plants are not more resistant to Pst than wild-typeplants. Gene expression profiles of the overexpressing plants identified putative direct orindirect target genes regulated by SlGRAS3 and SlGRAS6. Scientific and agricultural significance: Our research activities established a novel linkbetween the GRAS family of transcription factors, plant disease resistance and mechanicalstress response. SlGRAS6 was found to be required for disease resistance to Pstsuggesting that this and possibly other GRAS family members are involved in thetranscriptional reprogramming that takes place during the onset of disease resistance.Their nuclear localization and transcriptional activation ability support their proposed roleas transcription factors or co-activators. However, the potential of utilizing GRAS familymembers for the improvement of plant disease resistance in agriculture has yet to bedemonstrated.
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Amir, Rachel, David J. Oliver, Gad Galili, and Jacline V. Shanks. The Role of Cysteine Partitioning into Glutathione and Methionine Synthesis During Normal and Stress Conditions. United States Department of Agriculture, January 2013. http://dx.doi.org/10.32747/2013.7699850.bard.
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The objective of this research is to study the nature of the competition for cysteine (Cys), the first organic sulfur-containing compound, between its two main metabolites, glutathione (GSH) and methionine (Met). GSH plays a central role in protecting plants during various stresses, while Met, an essential amino acid, regulates essential processes and metabolites in plant cells through its metabolite S-adenosyl-Met. Our results, which are based on flux analysis and measurements of Met- metabolites, show that the flux towards Met synthesis is high during non-stress conditions, however the flux is significantly reduced under stress conditions, when there is high synthesis of GSH. Under oxidative stress the expression level of the regulatory enzyme of Met synthesis, cystathionine g-synthase (CGS) was reduced. By using three different systems, we have found that that GSH down regulates the expression level of CGS, thus reducing Met synthesis. We have found that this regulation occurs at the post-transcriptional level, and further studies have shown that it occurs at post-translationaly. To reveal how oxidative stress affects the flux towards Met and GSH, flux analysis was performed. We have found that the level of Met is significantly reduced, while the level of glutathione significantly increases during stress. Under stress conditions most of the glutathione is converted from GSH to GSSG (the oxidised form of glutathione). These results suggest that under normal growth conditions, Cys is channelled towards both pathways to support GSH accumulation and the synthesis of growth-essential Met metabolites. However, during oxidative stress, when a high level of GSH is required to protect the plants, the levels of GSH increase while those of CGS are reduced. This reduction leaves more Cys available for GSH synthesis under stress conditions. In addition we have also studied the effects of high GSH level on the transcriptome profile. The analysis revealed that GSH affects the expression level of many major genes coding to enzymes or proteins associated with photosynthesis, starch degradation, hormone metabolism (especially genes associated with jasmonate), biotic stress (especially genes associated with PR-proteins), cytochrome P450 genes, regulation of transcription and signaling (especially genes associated with receptor kinases and calcium). These results suggest that indeed GSH levels affect different pathways and metabolites in plants.
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Barg, Rivka, Erich Grotewold, and Yechiam Salts. Regulation of Tomato Fruit Development by Interacting MYB Proteins. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7592647.bard.
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Background to the topic: Early tomato fruit development is executed via extensive cell divisions followed by cell expansion concomitantly with endoreduplication. The signals involved in activating the different modes of growth during fruit development are still inadequately understood. Addressing this developmental process, we identified SlFSM1 as a gene expressed specifically during the cell-division dependent stages of fruit development. SlFSM1 is the founder of a class of small plant specific proteins containing a divergent SANT/MYB domain (Barg et al 2005). Before initiating this project, we found that low ectopic over-expression (OEX) of SlFSM1 leads to a significant decrease in the final size of the cells in mature leaves and fruits, and the outer pericarp is substantially narrower, suggesting a role in determining cell size and shape. We also found the interacting partners of the Arabidopsis homologs of FSM1 (two, belonging to the same family), and cloned their tomato single homolog, which we named SlFSB1 (Fruit SANT/MYB–Binding1). SlFSB1 is a novel plant specific single MYB-like protein, which function was unknown. The present project aimed at elucidating the function and mode of action of these two single MYB proteins in regulating tomato fruit development. The specific objectives were: 1. Functional analysis of SlFSM1 and its interacting protein SlFSB1 in relation to fruit development. 2. Identification of the SlFSM1 and/or SlFSB1 cellular targets. The plan of work included: 1) Detailed phenotypic, histological and cellular analyses of plants ectopically expressing FSM1, and plants either ectopically over-expressing or silenced for FSB1. 2) Extensive SELEX analysis, which did not reveal any specific DNA target of SlFSM1 binding, hence the originally offered ChIP analysis was omitted. 3) Genome-wide transcriptional impact of gain- and loss- of SlFSM1 and SlFSB1 function by Affymetrix microarray analyses. This part is still in progress and therefore results are not reported, 4) Search for additional candidate partners of SlFSB1 revealed SlMYBI to be an alternative partner of FSB1, and 5) Study of the physical basis of the interaction between SlFSM1 and SlFSB1 and between FSB1 and MYBI. Major conclusions, solutions, achievements: We established that FSM1 negatively affects cell expansion, particularly of those cells with the highest potential to expand, such as the ones residing inner to the vascular bundles in the fruit pericarp. On the other hand, FSB1 which is expressed throughout fruit development acts as a positive regulator of cell expansion. It was also established that besides interacting with FSM1, FSB1 interacts also with the transcription factor MYBI, and that the formation of the FSB1-MYBI complex is competed by FSM1, which recognizes in FSB1 the same region as MYBI does. Based on these findings a model was developed explaining the role of this novel network of the three different MYB containing proteins FSM1/FSB1/MYBI in the control of tomato cell expansion, particularly during fruit development. In short, during early stages of fruit development (Phase II), the formation of the FSM1-FSB1 complex serves to restrict the expansion of the cells with the greatest expansion potential, those non-dividing cells residing in the inner mesocarp layers of the pericarp. Alternatively, during growth phase III, after transcription of FSM1 sharply declines, FSB1, possibly through complexing with the transcription factor MYBI serves as a positive regulator of the differential cell expansion which drives fruit enlargement during this phase. Additionally, a novel mechanism was revealed by which competing MYB-MYB interactions could participate in the control of gene expression. Implications, both scientific and agricultural: The demonstrated role of the FSM1/FSB1/MYBI complex in controlling differential cell growth in the developing tomato fruit highlights potential exploitations of these genes for improving fruit quality characteristics. Modulation of expression of these genes or their paralogs in other organs could serve to modify leaf and canopy architecture in various crops.
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Stern, David B., and Gadi Schuster. Manipulation of Gene Expression in the Chloroplast: Control of mRNA Stability and Transcription Termination. United States Department of Agriculture, December 1993. http://dx.doi.org/10.32747/1993.7568750.bard.
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Chloroplasts are the site of photosynthesis and of other essential biosynthetic activities in plant cells. Chloroplasts are semi-autonomous organelles, since they contain their own genomes and protein biosynthetic machinery, but depend on the coordinate expression of nuclear genes to assemble macromolecular complexes. The bioeingineering of plants requires manipulation of chloroplast gene expression, and thus a knowledge of the molecular mechanisms that modulate mRNA and protein production. In this proposal the heterotrophic green alga Chlamydomonas reinhardtii has been used as a model system to understand the control and interrelationships between transcription termination, mRNA 3' end processing and mRNA stability in chloroplasts. Chlamydomonas is a unique and ideal system in which to address these issues, because the chloroplast can be easily manipulated by genetic transformation techniques. This research uncovered new and important information on chloroplast mRNA 3' end formation and mRNA stability. In particular, the 3' untranslated regions of chloroplast mRNAs were shown not to be efficient transcription terminators. The endonucleolytic site in the 3' untranslated region was characterized by site directed mutagensis and the role of several 3' untranslated regions in modulating RNA stability and translation has been studied. This information will allow us to experimentally manipulate the expression of chloroplast genes in vivo by post-transcriptional mechanisms, and should be widely applicable to other higher plant systems.
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Dubcovsky, Jorge, Tzion Fahima, Ann Blechl, and Phillip San Miguel. Validation of a candidate gene for increased grain protein content in wheat. United States Department of Agriculture, January 2007. http://dx.doi.org/10.32747/2007.7695857.bard.
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High Grain Protein Content (GPC) of wheat is important for improved nutritional value and industrial quality. However, selection for this trait is limited by our poor understanding of the genes involved in the accumulation of protein in the grain. A gene with a large effect on GPC was detected on the short arm of chromosome 6B in a Triticum turgidum ssp. dicoccoides accession from Israel (DIC, hereafter). During the previous BARD project we constructed a half-million clones Bacterial Artificial Chromosome (BAC) library of tetraploid wheat including the high GPC allele from DIC and mapped the GPC-B1 locus within a 0.3-cM interval. Our long-term goal is to provide a better understanding of the genes controlling grain protein content in wheat. The specific objectives of the current project were to: (1) complete the positional cloning of the GPC-B1 candidate gene; (2) characterize the allelic variation and (3) expression profile of the candidate gene; and (4) validate this gene by using a transgenic RNAi approach to reduce the GPC transcript levels. To achieve these goals we constructed a 245-kb physical map of the GPC-B1 region. Tetraploid and hexaploid wheat lines carrying this 245-kb DIC segment showed delayed senescence and increased GPC and grain micronutrients. The complete sequencing of this region revealed five genes. A high-resolution genetic map, based on approximately 9,000 gametes and new molecular markers enabled us to delimit the GPC-B1 locus to a 7.4-kb region. Complete linkage of the 7.4-kb region with earlier senescence and increase in GPC, Zn, and Fe concentrations in the grain suggested that GPC-B1 is a single gene with multiple pleiotropic effects. The annotation of this 7.4-kb region identified a single gene, encoding a NAC transcription factor, designated as NAM-B1. Allelic variation studies demonstrated that the ancestral wild wheat allele encodes a functional NAC transcription factor whereas modern wheat varieties carry a non-functional NAM-B1 allele. Quantitative PCR showed that transcript levels for the multiple NAMhomologues were low in flag leaves prior to anthesis, after which their levels increased significantly towards grain maturity. Reduction in RNA levels of the multiple NAMhomologues by RNA interference delayed senescence by over three weeks and reduced wheat grain protein, Zn, and Fe content by over 30%. In the transgenic RNAi plants, residual N, Zn and Fe in the dry leaves was significantly higher than in the control plants, confirming a more efficient nutrient remobilization in the presence of higher levels of GPC. The multiple pleiotropic effects of NAM genes suggest a central role for these genes as transcriptional regulators of multiple processes during leaf senescence, including nutrient remobilization to the developing grain. The cloning of GPC-B1 provides a direct link between the regulation of senescence and nutrient remobilization and an entry point to characterize the genes regulating these two processes. This may contribute to their more efficient manipulation in crops and translate into food with enhanced nutritional value. The characterization of the GPC-B1 gene will have a significant impact on wheat production in many regions of the world and will open the door for the identification of additional genes involved in the accumulation of protein in the grain.
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Porat, Ron, Gregory T. McCollum, Amnon Lers, and Charles L. Guy. Identification and characterization of genes involved in the acquisition of chilling tolerance in citrus fruit. United States Department of Agriculture, December 2007. http://dx.doi.org/10.32747/2007.7587727.bard.
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Citrus, like many other tropical and subtropical fruit are sensitive to chilling temperatures. However, application of a pre-storage temperature conditioning (CD) treatment at 16°C for 7 d or of a hot water brushing (HWB) treatment at 60°C for 20 sec remarkably enhances chilling tolerance and reduces the development of chilling injuries (CI) upon storage at 5°C. In the current research, we proposed to identify and characterize grapefruit genes that are induced by CD, and may contribute to the acquisition of fruit chilling tolerance, by two different molecular approaches: cDNA array analysis and PCR cDNA subtraction. In addition, following the recent development and commercialization of the new Affymetrix Citrus Genome Array, we further performed genome-wide transcript profiling analysis following exposure to CD and chilling treatments. To conduct the cDNA array analysis, we constructed cDNA libraries from the peel tissue of CD- and HWB-treated grapefruit, and performed an EST sequencing project including sequencing of 3,456 cDNAs from each library. Based on the obtained sequence information, we chose 70 stress-responsive and chilling-related genes and spotted them on nylon membranes. Following hybridization the constructed cDNA arrays with RNA probes from control and CD-treated fruit and detailed confirmations by RT-PCR analysis, we found that six genes: lipid-transfer protein, metallothionein-like protein, catalase, GTP-binding protein, Lea5, and stress-responsive zinc finger protein, showed higher transcript levels in flavedo of conditioned than in non-conditioned fruit stored at 5 ᵒC. The transcript levels of another four genes: galactinol synthase, ACC oxidase, temperature-induced lipocalin, and chilling-inducible oxygenase, increased only in control untreated fruit but not in chilling-tolerant CD-treated fruit. By PCR cDNA subtraction analysis we identified 17 new chilling-responsive and HWB- and CD-induced genes. Overall, characterization of the expression patterns of these genes as well as of 11 more stress-related genes by RNA gel blot hybridizations revealed that the HWB treatment activated mainly the expression of stress-related genes(HSP19-I, HSP19-II, dehydrin, universal stress protein, EIN2, 1,3;4-β-D-glucanase, and SOD), whereas the CD treatment activated mainly the expression of lipid modification enzymes, including fatty acid disaturase2 (FAD2) and lipid transfer protein (LTP). Genome wide transcriptional profiling analysis using the newly developed Affymetrix Citrus GeneChip® microarray (including 30,171 citrus probe sets) revealed the identification of three different chilling-related regulons: 1,345 probe sets were significantly affected by chilling in both control and CD-treated fruits (chilling-response regulon), 509 probe sets were unique to the CD-treated fruits (chilling tolerance regulon), and 417 probe sets were unique to the chilling-sensitive control fruits (chilling stress regulon). Overall, exposure to chilling led to expression governed arrest of general cellular metabolic activity, including concretive down-regulation of cell wall, pathogen defense, photosynthesis, respiration, and protein, nucleic acid and secondary metabolism. On the other hand, chilling enhanced various adaptation processes, such as changes in the expression levels of transcripts related to membranes, lipid, sterol and carbohydrate metabolism, stress stimuli, hormone biosynthesis, and modifications in DNA binding and transcription factors.
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Fromm, Hillel, Paul Michael Hasegawa, and Aaron Fait. Calcium-regulated Transcription Factors Mediating Carbon Metabolism in Response to Drought. United States Department of Agriculture, June 2013. http://dx.doi.org/10.32747/2013.7699847.bard.
Full textAbstract:
Original objectives: The long-term goal of the proposed research is to elucidate the transcription factors, genes and metabolic networks involved in carbon metabolism and partitioning in response to water deficit. The proposed research focuses on the GTLcalcium/calmodulinbindingTFs and the gene and metabolic networks modulated by these TFs in Arabidopsis thaliana. The specific objectives are as follows. Objective-1 (USA): Physiological analyses of GTL1 loss- and gain-of-function plants under water sufficient and drought stress conditions Objective 2 (USA / Israel-TAU): Characterizion of GTL target genes and bioinformatic analysis of data to eulcidate gene-network topology. Objective-3 (Israel-TAU): Regulation of GTLmediated transcription by Ca²⁺/calmodulin: mechanism and biological significance. Objective-4 (Israel-BGU): Metabolic networks and carbon partitioning in response to drought. Additional direction: In the course of the project we added another direction, which was reported in the 2nd annual report, to elucidate genes controlling drought avoidance. The TAU team has isolated a few unhydrotropic (hyd) mutants and are in the process of mapping these mutations (of hyd13 and hyd15; see last year's report for a description of these mutants under salt stress) in the Arabidopsis genome by map-based cloning and deep sequencing. For this purpose, each hyd mutant was crossed with a wild type plant of the Landsberg ecotype, and at the F2 stage, 500-700 seedlings showing the unhydrotropic phenotype were collected separately and pooled DNA samples were subkected to the Illumina deep sequencing technology. Bioinformatics were used to identify the exact genomic positions of the mutations (based on a comparison of the genomic sequences of the two Arabidopsis thaliana ecotypes (Columbia and Landsberg). Background: To feed the 9 billion people or more, expected to live on Earth by the mid 21st century, the production of high-quality food must increase substantially. Based on a 2009 Declaration of the World Summit on Food Security, a target of 70% more global food production by the year 2050 was marked, an unprecedented food-production growth rate. Importantly, due to the larger areas of low-yielding land globally, low-yielding environments offer the greatest opportunity for substantial increases in global food production. Nowadays, 70% of the global available water is used by agriculture, and 40% of the world food is produced from irrigated soils. Therefore, much needs to be done towards improving the efficiency of water use by plants, accompanied by increased crop yield production under water-limiting conditions. Major conclusions, solutions and achievements: We established that AtGTL1 (Arabidopsis thaliana GT-2 LIKE1) is a focal determinant in water deficit (drought) signaling and tolerance, and water use efficiency (WUE). The GTL1 transcription factor is an upstream regulator of stomatal development as a transrepressor of AtSDD1, which encodes a subtilisin protease that activates a MAP kinase pathway that negatively regulates stomatal lineage and density. GTL1 binds to the core GT3 cis-element in the SDD1 promoter and transrepresses its expression under water-sufficient conditions. GTL1 loss-of-function mutants have reduced stomatal number and transpiration, and enhanced drought tolerance and WUE. In this case, higher WUE under water sufficient conditions occurs without reduction in absolute biomass accumulation or carbon assimilation, indicating that gtl1-mediated effects on stomatal conductance and transpiration do not substantially affect CO₂ uptake. These results are proof-of-concept that fine-tuned regulation of stomatal density can result in drought tolerance and higher WUE with maintenance of yield stability. Implications: Accomplishments during the IS-4243-09R project provide unique tools for continued discovery research to enhance plant drought tolerance and WUE.
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Gafni, Yedidya, Moshe Lapidot, and Vitaly Citovsky. Dual role of the TYLCV protein V2 in suppressing the host plant defense. United States Department of Agriculture, January 2013. http://dx.doi.org/10.32747/2013.7597935.bard.
Full textAbstract:
TYLCV-Is is a major tomato pathogen, causing extensive crop losses in Israel and the U.S. We have identified a TYLCV-Is protein, V2, which acts as a suppressor of RNA silencing. Intriguingly, the counter-defense function of V2 may not be limited to silencing suppression. Our recent data suggest that V2 interacts with the tomato CYP1 protease. CYP1 belongs to the family of papain-like cysteine proteases which participate in programmed cell death (PCD) involved in plant defense against pathogens. Based on these data we proposed a model for dual action of V2 in suppressing the host antiviral defense: V2 targets SGS3 for degradation and V2 inhibits CYP1 activity. To study this we proposed to tackle three specific objectives. I. Characterize the role of V2 in SGS3 proteasomal degradation ubiquitination, II. Study the effects of V2 on CYP1 maturation, enzymatic activity, and accumulation and, III. Analyze the effects of the CYP1-V2 interaction on TYLCV-Is infection. Here we describe results from our study that support our hypothesis: the involvement of the host's innate immune system—in this case, PCD—in plant defense against TYLCV-Is. Also, we use TYLCV-Is to discover the molecular pathway(s) by which this plant virus counters this defense. Towards the end of our study we discovered an interesting involvement of the C2 protein encoded by TYLCV-Is in inducing Hypersensitive Response in N. benthamianaplants which is not the case when the whole viral genome is introduced. This might lead to a better understanding of the multiple processes involved in the way TYLCV is overcoming the defense mechanisms of the host plant cell. In a parallel research supporting the main goal described, we also investigated Agrobacteriumtumefaciens-encoded F-box protein VirF. It has been proposed that VirF targets a host protein for the UPS-mediated degradation, very much the way TYLCV V2 does. In our study, we identified one such interactor, an Arabidopsistrihelix-domain transcription factor VFP3, and further show that its very close homolog VFP5 also interacted with VirF. Interestingly, interactions of VirF with either VFP3 or VFP5 did not activate the host UPS, suggesting that VirF might play other UPS-independent roles in bacterial infection. Another target for VirF is VFP4, a transcription factor that both VirF and its plant functional homolog VBF target to degradation by UPS. Using RNA-seqtranscriptome analysis we showed that VFP4 regulates numerous plant genes involved in disease response, including responses to viral and bacterial infections. Detailed analyses of some of these genes indicated their involvement in plant protection against Agrobacterium infection. Thus, Agrobacterium may facilitate its infection by utilizing the host cell UPS to destabilize transcriptional regulators of the host disease response machinery that limits the infection.
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Friedman, Haya, Julia Vrebalov, and James Giovannoni. Elucidating the ripening signaling pathway in banana for improved fruit quality, shelf-life and food security. United States Department of Agriculture, October 2014. http://dx.doi.org/10.32747/2014.7594401.bard.
Full textAbstract:
Background : Banana being a monocot and having distinct peel and pulp tissues is unique among the fleshy fruits and hence can provide a more comprehensive understanding of fruit ripening. Our previous research which translated ripening discoveries from tomato, led to the identification of six banana fruit-associated MADS-box genes, and we confirmed the positive role of MaMADS1/2 in banana ripening. The overall goal was to further elucidate the banana ripening signaling pathway as mediated by MADS-boxtranscriptional regulators. Specific objectives were: 1) characterize transcriptional profiles and quality of MaMADS1/2 repressed fruit; 2) reveal the role of additional MaMADSgenes in ripening; 3) develop a model of fruit MaMADS-box mode of action; and 4) isolate new components of the banana ripening signaling pathway. Major conclusion: The functions of the banana MaMADS1-5 have been examined by complimenting the rinor the TAGL1-suppressed lines of tomato. Only MaMADS5 exhibited partial complementation of TAGL1-suppressed and rinlines, suggesting that while similar genes play corresponding roles in ripening, evolutionary divergence makes heterologous complementation studies challenging. Nevertheless, the partial complementation of tomato TAGL1-surpessed and rinlines with MaMADS5 suggests this gene is likely an important ripening regulator in banana, worthy of further study. RNA-seqtranscriptome analysis during ripening was performed on WT and MaMADS2-suppressed lines revealing additional candidate genes contributing to ripening control mechanisms. In summary, we discovered 39 MaMADS-box genes in addition to homologues of CNR, NOR and HB-1 expressed in banana fruits, and which were shown in tomato to play necessary roles in ripening. For most of these genes the expression in peel and pulp was similar. However, a number of key genes were differentially expressed between these tissues indicating that the regulatory components which are active in peel and pulp include both common and tissue-specific regulatory systems, a distinction as compared to the more uniform tomato fruit pericarp. Because plant hormones are well documented to affect fruit ripening, the expressions of genes within the auxin, gibberellin, abscisic acid, jasmonic acid, salicylic and ethylene signal transduction and synthesis pathways were targeted in our transcriptome analysis. Genes’ expression associated with these pathways generally declined during normal ripening in both peel and pulp, excluding cytokinin and ethylene, and this decline was delayed in MaMADS2-suppressed banana lines. Hence, we suggest that normal MaMADS2 activity promotes the observed downward expression within these non-ethylene pathways (especially in the pulp), thus enabling ripening progression. In contrast, the expressions of ACSand ACOof the ethylene biosynthesis pathway increase in peel and pulp during ripening and are delayed/inhibited in the transgenic bananas, explaining the reduced ethylene production of MaMADS2-suppressed lines. Inferred by the different genes’ expression in peel and pulp of the gibberellins, salicylic acid and cytokinins pathways, it is suggested that hormonal regulation in these tissues is diverse. These results provide important insights into possible avenues of ripening control in the diverse fruit tissues of banana which was not previously revealed in other ripening systems. As such, our transcriptome analysis of WT and ripening delayed banana mutants provides a starting point for further characterization of ripening. In this study we also developed novel evidence that the cytoskeleton may have a positive role in ripening as components of this pathway were down-regulated by MaMADS2 suppression. The mode of cytoskeleton involvement in fruit ripening remains unclear but presents a novel new frontier in ripening investigations. In summary, this project yielded functional understanding of the role and mode of action of MaMADS2 during ripening, pointing to both induction of ethylene and suppression of non-ethylene hormonal singling pathways. Furthermore, our data suggest important roles for cytoskeleton components and MaMADS5 in the overall banana ripening control network. Implications: The project revealed new molecular components/genes involved in banana ripening and refines our understanding of ripening responses in the peel and pulp tissues of this important species. This information is novel as compared to that derived from the more uniform carpel tissues of other highly studied ripening systems including tomato and grape. The work provides specific target genes for potential modification through genetic engineering or for exploration of useful genetic diversity in traditional breeding. The results from the project might point toward improved methods or new treatments to improve banana fruit storage and quality.