Relevant bibliographies by topics / Transcriptional study

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  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
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Academic literature on the topic 'Transcriptional study'

Author: Grafiati
Published: 25 June 2022

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Journal articles on the topic "Transcriptional study"

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Wang, Yaolai, Jiaming Qi, Jie Shao, and Xu-Qing Tang. "Signaling Mechanism of Transcriptional Bursting: A Technical Resolution-Independent Study." Biology 9, no. 10 (October 19, 2020): 339. http://dx.doi.org/10.3390/biology9100339.

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Gene transcription has been uncovered to occur in sporadic bursts. However, due to technical difficulties in differentiating individual transcription initiation events, it remains debated as to whether the burst size, frequency, or both are subject to modulation by transcriptional activators. Here, to bypass technical constraints, we addressed this issue by introducing two independent theoretical methods including analytical research based on the classic two-model and information entropy research based on the architecture of transcription apparatus. Both methods connect the signaling mechanism of transcriptional bursting to the characteristics of transcriptional uncertainty (i.e., the differences in transcriptional levels of the same genes that are equally activated). By comparing the theoretical predictions with abundant experimental data collected from published papers, the results exclusively support frequency modulation. To further validate this conclusion, we showed that the data that appeared to support size modulation essentially supported frequency modulation taking into account the existence of burst clusters. This work provides a unified scheme that reconciles the debate on burst signaling.
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Nishimura, Akiko, Takeshi Ono, Akinori Ishimoto, Jennifer J. Dowhanick, Margaret A. Frizzell, Peter M. Howley, and Hiroyuki Sakai. "Mechanisms of Human Papillomavirus E2-Mediated Repression of Viral Oncogene Expression and Cervical Cancer Cell Growth Inhibition." Journal of Virology 74, no. 8 (April 15, 2000): 3752–60. http://dx.doi.org/10.1128/jvi.74.8.3752-3760.2000.

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ABSTRACT The papillomavirus E2 gene product plays a pivotal role in viral replication. E2 has multiple functions, including (i) transcriptional activation and repression of viral promoters and (ii) the enhancement of viral DNA replication. It was previously reported that E2 suppressed the growth of papillomavirus-positive cervical carcinoma cell lines. In the present study, we investigated the mechanisms of E2 growth inhibition. We found that the transcriptional activation function of E2 is required for inhibition of the growth of HeLa cells as well as for transcriptional repression of the viralE6/E7 promoter. It had been previously postulated that transcriptional repression of the E6/E7 promoter results from E2 binding its cognate sites proximal to the E6/E7promoter and displacing other cellular transcriptional factors. In this study, we report a requirement for the transcription activation function for the binding of E2 to transcriptionally active templates.
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Babu, M. Madan. "Computational approaches to study transcriptional regulation." Biochemical Society Transactions 36, no. 4 (July 22, 2008): 758–65. http://dx.doi.org/10.1042/bst0360758.

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In recent years, a number of technical and experimental advances have allowed us to obtain an unprecedented amount of information about living systems on a genomic scale. Although the complete genomes of many organisms are available due to the progress made in sequencing technology, the challenge to understand how the individual genes are regulated within the cell remains. Here, I provide an overview of current computational methods to investigate transcriptional regulation. I will first discuss how representing protein–DNA interactions as a network provides us with a conceptual framework to understand the organization of regulatory interactions in an organism. I will then describe methods to predict transcription factors and cis-regulatory elements using information such as sequence, structure and evolutionary conservation. Finally, I will discuss approaches to infer genome-scale transcriptional regulatory networks using experimentally characterized interactions from model organisms and by reverse-engineering regulatory interactions that makes use of gene expression data and genomewide location data. The methods summarized here can be exploited to discover previously uncharacterized transcriptional pathways in organisms whose genome sequence is known. In addition, such a framework and approach can be invaluable to investigate transcriptional regulation in complex microbial communities such as the human gut flora or populations of emerging pathogens. Apart from these medical applications, the concepts and methods discussed can be used to understand the combinatorial logic of transcriptional regulation and can be exploited in biotechnological applications, such as in synthetic biology experiments aimed at engineering regulatory circuits for various purposes.
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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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Rossi, Alessandra, Ilenia Pacella, and Silvia Piconese. "RNA Flow Cytometry for the Study of T Cell Metabolism." International Journal of Molecular Sciences 22, no. 8 (April 9, 2021): 3906. http://dx.doi.org/10.3390/ijms22083906.

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T cells undergo activation and differentiation programs along a continuum of states that can be tracked through flow cytometry using a combination of surface and intracellular markers. Such dynamic behavior is the result of transcriptional and post-transcriptional events, initiated and sustained by the activation of specific transcription factors and by epigenetic remodeling. These signaling pathways are tightly integrated with metabolic routes in a bidirectional manner: on the one hand, T cell receptors and costimulatory molecules activate metabolic reprogramming; on the other hand, metabolites modify T cell transcriptional programs and functions. Flow cytometry represents an invaluable tool to analyze the integration of phenotypical, functional, metabolic and transcriptional features, at the single cell level in heterogeneous T cell populations, and from complex microenvironments, with potential clinical application in monitoring the efficacy of cancer immunotherapy. Here, we review the most recent advances in flow cytometry-based analysis of gene expression, in combination with indicators of mitochondrial activity, with the aim of revealing and characterizing major metabolic pathways in T cells.
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SINHA, Anupama, Douglas V. FALLER, and Gerald V. DENIS. "Bromodomain analysis of Brd2-dependent transcriptional activation of cyclin A1." Biochemical Journal 387, no. 1 (March 22, 2005): 257–69. http://dx.doi.org/10.1042/bj20041793.

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Cyclin A is regulated primarily through transcription control during the mammalian cell cycle. A dual mechanism of cyclin A transcriptional repression involves, on the one hand, promoter-bound inhibitory complexes of E2F transcription factors and RB (retinoblastoma) family proteins, and on the other, chromatin-directed histone deacetylase activity that is recruited to the cyclin A promoter early in the cell cycle in association with these RB proteins. This dual regulation maintains transcriptional silence of the cyclin A locus until its transcription is required in S-phase. At that time, RB family members dissociate from E2F proteins and nucleosomal restructuring of the locus takes place, to permit transcriptional activation and resultant S-phase progression to proceed. We have identified a double bromo-domain-containing protein Brd2, which exhibits apparent ‘scaffold’ or transcriptional adapter functions and mediates recruitment of both E2F transcription factors and chromatin-remodelling activity to the cyclin A promoter. We have shown previously that Brd2-containing nuclear, multiprotein complexes contain E2F-1 and -2. In the present study, we show that, in S-phase, they also contain histone H4-directed acetylase activity. Overexpression of Brd2 in fibroblasts accelerates the cell cycle through increased expression of cyclin A and its associated cyclin-dependent kinase activity. Chromatin immunoprecipitation studies show that Brd2 is physically present at the cyclin A promoter and its overexpression promotes increased histone H4 acetylation at the promoter as it becomes transcriptionally active, suggesting a new model for the dual regulation of cyclin A.
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Cipolletti, Manuela, Sara Pescatori, and Filippo Acconcia. "Real-Time Challenging of ERα Y537S Mutant Transcriptional Activity in Living Cells." Endocrines 2, no. 1 (March 10, 2021): 54–64. http://dx.doi.org/10.3390/endocrines2010006.

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Metastatic estrogen receptor α (ERα)-expressing breast cancer (BC) occurs after prolonged patient treatment with endocrine therapy (ET) (e.g., aromatase inhibitors—AI; 4OH-tamoxifen—4OH-Tam). Often these metastatic BCs express a mutated ERα variant (e.g., Y537S), which is transcriptionally hyperactive, sustains uncontrolled proliferation, and renders tumor cells insensitive to ET drugs. Therefore, new molecules blocking hyperactive Y537S ERα mutation transcriptional activity are requested. Here we generated an MCF-7 cell line expressing the Y537S ERα mutation stably expressing an estrogen-responsive element (ERE) promoter, which activity can be monitored in living cells. Characterization of this cell line shows both hyperactive basal transcriptional activity with respect to normal MCF-7 cells, which stably express the same ERE-based promoter and a decreased effect of selective ER downregulators (SERDs) in reducing Y537S ERα mutant transcriptional activity with respect to wild type ERα transcriptional activity. Kinetic profiles of Y537S ERα mutant-based transcription produced by both drugs inducing receptor degradation and siRNA-mediated depletion of specific proteins (e.g., FOXA1 and caveolin1) reveals biphasic dynamics of the inhibition of the receptor-regulated transcriptional effects. Overall, we report a new model where to study the behavior of the Y537S ERα mutant that can be used for the identification of new targets and pathways regulating the Y537S ERα transcriptional activity.
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Teves, Sheila S., and Steven Henikoff. "The heat shock response: A case study of chromatin dynamics in gene regulation." Biochemistry and Cell Biology 91, no. 1 (February 2013): 42–48. http://dx.doi.org/10.1139/bcb-2012-0075.

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Recent studies in transcriptional regulation using the Drosophila heat shock response system have elucidated many of the dynamic regulatory processes that govern transcriptional activation and repression. The classic view that the control of gene expression occurs at the point of RNA polymerase II (Pol II) recruitment is now giving way to a more complex outlook of gene regulation. Promoter chromatin dynamics coordinate with transcription factor binding to maintain the promoters of active genes accessible. For a large number of genes, the rate-limiting step in Pol II progression occurs during its initial elongation, where Pol II transcribes 30–50 bp and pauses for further signals. These paused genes have unique genic chromatin architecture and dynamics compared with genes where Pol II recruitment is rate limiting for expression. Further elongation of Pol II along the gene causes nucleosome turnover, a continuous process of eviction and replacement, which suggests a potential mechanism for Pol II transit along a nucleosomal template. In this review, we highlight recent insights into transcription regulation of the heat shock response and discuss how the dynamic regulatory processes involved at each transcriptional stage help to generate faithful yet highly responsive gene expression.
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ARAO, Yukitomo, Etsuko YAMAMOTO, Naoto MIYATAKE, Yuichi NINOMIYA, Taisuke UMEHARA, Hiroyuki KAWASHIMA, Shoichi MASUSHIGE, Tadao HASEGAWA, and Shigeaki KATO. "A synthetic oestrogen antagonist, tamoxifen, inhibits oestrogen-induced transcriptional, but not post-transcriptional, regulation of gene expression." Biochemical Journal 313, no. 1 (January 1, 1996): 269–74. http://dx.doi.org/10.1042/bj3130269.

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Oestrogen (E2) regulates the expression of its target genes at transcriptional and post-transcriptional levels. To clarify the mechanism of E2-induced post-transcriptional regulation, with attention to the involvement of the oestrogen receptor (ER), we studied the effect of tamoxifen (TAM), a synthetic E2 antagonist that inhibits ER-mediated transcription, on E2-induced transcriptional and post-transcriptional regulation of the chicken ovalbumin (OVA) gene in chick oviducts. Run-on analysis with oviduct nuclei isolated from E2-treated chicks showed that TAM treatment completely blocked E2-induced transcription of the OVA gene within 24 h without affecting ER gene expression. Likewise, the rate of transcription fell to below the limit of detection after E2 withdrawal from the chicks. Reflecting the transcription rate, OVA mRNA accumulated linearly in E2-treated chicks, and E2 withdrawal caused a rapid loss of OVA mRNA. However, in the chicks treated with TAM and E2, OVA mRNA was degraded slowly over 48 h with a half-life of 24 h, suggesting that TAM does not inhibit E2-induced mRNA stabilization. Moreover, E2-induced mRNA stabilization was observed even when transcription of the OVA gene was blocked by a transcription inhibitor. Western-blot analysis showed that the remaining OVA mRNA was translatable. Thus the present study indicates that E2 regulates expression of the OVA gene via distinct pathways at transcriptional and post-transcriptional levels.
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Sadka, Avi, Qiaoping Qin, Jianrong Feng, Macarena Farcuh, Lyudmila Shlizerman, Yunting Zhang, David Toubiana, and Eduardo Blumwald. "Ethylene Response of Plum ACC Synthase 1 (ACS1) Promoter is Mediated through the Binding Site of Abscisic Acid Insensitive 5 (ABI5)." Plants 8, no. 5 (May 2, 2019): 117. http://dx.doi.org/10.3390/plants8050117.

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The enzyme 1-amino-cyclopropane-1-carboxylic acid synthase (ACS) participates in the ethylene biosynthesis pathways and it is tightly regulated transcriptionally and post-translationally. Notwithstanding its major role in climacteric fruit ripening, the transcriptional regulation of ACS during ripening is not fully understood. We studied fruit ripening in two Japanese plum cultivars, the climacteric Santa Rosa (SR) and its non-climacteric bud sport mutant, Sweet Miriam (SM). As the two cultivars show considerable difference in ACS expression, they provide a good system for the study of the transcriptional regulation of the gene. To investigate the differential transcriptional regulation of ACS1 genes in the SR and SM, their promoter regions, which showed only minor sequence differences, were isolated and used to identify the binding of transcription factors interacting with specific ACS1 cis-acting elements. Three transcription factors (TFs), abscisic acid-insensitive 5 (ABI5), GLABRA 2 (GL2), and TCP2, showed specific binding to the ACS1 promoter. Synthetic DNA fragments containing multiple cis-acting elements of these TFs fused to β-glucuronidase (GUS), showed the ABI5 binding site mediated ethylene and abscisic acid (ABA) responses of the promoter. While TCP2 and GL2 showed constant and similar expression levels in SM and SR fruit during ripening, ABI5 expression in SM fruits was lower than in SR fruits during advanced fruit ripening states. Overall, the work demonstrates the complex transcriptional regulation of ACS1.
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Dissertations / Theses on the topic "Transcriptional study"

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Durand, Alexandre. "Structural study of the transcriptional co-activator SAGA." Thesis, Strasbourg, 2014. http://www.theses.fr/2014STRAJ051/document.

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Le complexe SAGA (Spt-Ada-Gcn5 acetyl transferase) est un co-activateur transcriptionel, conservé chez les eucaryotes, qui participent à la transcription d’environ 10% des gènes chez la levure, où il fait le lien entre les composants du complexe de pré-initiation, tel que la TATA-box Binding Protein (TBP) et des activateurs, et modifie les histones dans le contexte de la chromatine (acétylation et déubiquitination). Ces travaux de thèse ont permis de décrire l’architecture moléculaire du complexe observée par microscopie électronique. Nous avons pu (i) localiser le module de déubiquitination au sein du complexe entier et ainsi (ii) définir une zone d’interaction avec le nucléosome ; (iii) montrer la présence de deux sites d’interaction avec la protéine TBP situé au niveau d’une « pince »moléculaire ; (iv) observer un lien fonctionnel entre le module de déubiquitination, en particulier de la protéine Sgf73, et les conformations adoptées par cette pince
The SAGA complex (Spt-Ada-Gcn5 acetyl transferase) is a transcriptional coactivator, highly conserved in eukaryotes, involved in the transcription of 10% of the genes in yeast, where it bridges the components of the pre-initiation complex such as the TATA-box Binding Protein (TBP) and activators, as well as modifies histones in the chromatin template (acetylation and deubiquitination). This work has revealed the molecular architecture of the complex observed by electron microscopy. We could (i) localize the deubiquitination module within the whole complex and thus (ii) define the interaction surface with the nucleosome; (iii) reveal the presence of two TBP-interacting surfaces localized at the tips of a molecular clamp; (iv) observe a functional link between the deubiquitination module, in particular the Sgf73 protein, and the conformation adopted by this clamp
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Ameur, Adam. "A Bioinformatics Study of Human Transcriptional Regulation." Doctoral thesis, Uppsala universitet, Centrum för bioinformatik, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-9346.

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Regulation of transcription is a central mechanism in all living cells that now can be investigated with high-throughput technologies. Data produced from such experiments give new insights to how transcription factors (TFs) coordinate the gene transcription and thereby regulate the amounts of proteins produced. These studies are also important from a medical perspective since TF proteins are often involved in disease. To learn more about transcriptional regulation, we have developed strategies for analysis of data from microarray and massively parallel sequencing (MPS) experiments. Our computational results consist of methods to handle the steadily increasing amount of data from high-throughput technologies. Microarray data analysis tools have been assembled in the LCB-Data Warehouse (LCB-DWH) (paper I), and other analysis strategies have been developed for MPS data (paper V). We have also developed a de novo motif search algorithm called BCRANK (paper IV). The analysis has lead to interesting biological findings in human liver cells (papers II-V). The investigated TFs appeared to bind at several thousand sites in the genome, that we have identified at base pair resolution. The investigated histone modifications are mainly found downstream of transcription start sites, and correlated to transcriptional activity. These histone marks are frequently found for pairs of genes in a bidirectional conformation. Our results suggest that a TF can bind in the shared promoter of two genes and regulate both of them. From a medical perspective, the genes bound by the investigated TFs are candidates to be involved in metabolic disorders. Moreover, we have developed a new strategy to detect single nucleotide polymorphisms (SNPs) that disrupt the binding of a TF (paper IV). We further demonstrated that SNPs can affect transcription in the immediate vicinity. Ultimately, our method may prove helpful to find disease-causing regulatory SNPs.
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Koch, Frédéric. "From enhancer transcription to initiation and elongation : a study of eukaryotic transcriptional regulation during lymphocyte development." Thesis, Aix-Marseille 2, 2011. http://www.theses.fr/2011AIX22097.

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La régulation transcriptionnelle des eucaryotes supérieurs est un processus hautement contrôlé du point de vue spatial et temporel lors du développement, ou en réaction à l’environnement. La transcription ciblée des gènes codant requiert l’assemblage d’un complexe de pré-initiation (PIC) aux promoteurs comprenant l’ARN Polymérase (Pol) II et les facteurs généraux de transcription (GTFs) et dépend de la médiation d’un signal par les facteurs activateurs de transcription (TFs). Les années récentes ont montré que la transition de l’initiation vers l’élongation productive de la transcription représente une étape clé de la régulation de l’expression des gènes. Ce processus est également contrôlé par la structure de la chromatine, les modifications d’histones et par la présence d’éléments cis-régulateurs tels que les ‘enhancers’ ou les ‘silencers’. Au cours de ma thèse, nous avons entrepris de décrypter les mécanismes de régulation transcriptionnelle impliqués dans les étapes du développement lymphocytaire. Nous avons essentiellement travaillé sur des thymocytes primaires murins isolés au stade de différenciation double positif (DP, CD4+/CD8+) pour lequel de nombreuses séquences de type ‘enhancers’ ont été caractérisées dans la littérature scientifique. Nous avons également utilisé des lymphocytes B humains (Raji) immortalisés pour certaines des expériences impliquant des manipulation génétiques complexes permettant l’étude de mutants du domaine carboxy-terminal (CTD) de Pol II. En couplant des approches d’analyse à l’échelle du génome au séquençage à haut-débit, nous avons établi des cartographies fines de la localisation de Pol II, des GTFs, des TFs,de modifications d’histones (ChIP-Seq) et de nucléosomes (MNase-seq) ainsi que la caractérisation de populations variées d’ARN par RNA-seq. Nos principaux résultats ont révélé (i) l’assemblage du PIC et la transcription des enhancers tissus-spécifiques, (ii) l’existence de plateforme d’initiation de la transcription (TIPs) aux enhancers et aux promoteurs tissus-spécifique, (ii) que le contenu en GC représente l’un des principaux éléments promoteurs mammifères en permettant une ouverture transcription-indépendante de la chromatine, (iv) l’importance d’une nouvelle modification post-traductionnelle du domaine CTD de Pol II pour la progression de l’enzyme en élongation et finalement (v) que la modification de l’histone H3 sur le résidu K36 methylé corrèle avec l’épissage des transcrits Pol II. Globalement, les résultats les plus important de ce manuscrit consistent dans la mise en évidence de la transcription des enhancers comme caractérisant l’expression des gènes tissus-spécifiques et dans l’importance des ilots CpG comme éléments promoteurs mammifères permettant la formation d’une structure ouverte de la chromatine
Transcriptional regulation in higher eukaryotes resembles a tightly controlled temporal and spatial process, as exemplified during development or an organism’s response to environmental stimuli. Directed transcription requires the assembly of the preinitiation complex (PIC) at the promoter of protein-coding genes, including RNA Polymerase (Pol) II and the general transcription factors (GTFs), mediated by activating transcription factors (TFs). Several rate-limiting steps further control the progression of Pol II initiation to productive elongation of the gene. This process is further controlled by chromatin structure, histone modifications as well as cis-regulatory elements, such as enhancers or silencers. We set out to decipher some of these regulatory mechanisms during the tightly controlled process of lymphocyte development. Our work primarily made use of primary mouse thymocytes in CD4+/CD8+ double positive (DP, CD4+/CD8+) stage during T-cell development. To our advantage, many developmentally important cis-regulatory regions are well characterized in this cell population. For genetic manipulations, we made use of the Raji B-cell lymphoma cell-line. Using high throughput genome-wide approaches based on next generation sequencing (NGS), we performed both localization studies of Pol II, GTFs, TFs, histone modifying enzymes, histone modifications and nucleosomes as well as deep-sequencing of different RNA transcript populations. In summary, we find that (i) PICs assemble at tissue-specific enhancers leading to local transcription, (ii) large transcription initiation platforms (TIPs) at tissue-specific promoters and enhancers exist, which correlate with high CG-content of the DNA and transcription factor binding sites (TFBS), (iii) GC-content regulates the nucleosomal structure and initiation, including directionality, at promoters, (iv) Pol II is phosphorylated at a new residue of it C-terminal domain (CTD) in the 3’ regions of genes and (v) splicing events can influence the chromatin structure. Altogether, these results show that PIC formation at and transcription of enhancers are important for the regulation of T-cell target genes, that CpG islands represent important if not the major regulatory promoter element in mammals guiding tissue-specific gene expression and nucleosome structure, as well as novel mechanisms of Pol II elongation and the effect on chromatin structure
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Liu, Ching-Ti. "Study on transcriptional regulation of protein complexes in Saccharomyces cerevisiae." Diss., Restricted to subscribing institutions, 2006. http://proquest.umi.com/pqdweb?did=1276392271&sid=1&Fmt=2&clientId=1564&RQT=309&VName=PQD.

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Mandke, Pooja P. "Study of MicroRNA-34a mediated post transcriptional regulation of MDM4." Wright State University / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=wright1347648257.

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Watanabe, Satoshi. "Structural study of the oxidative-stress sensing SoxR transcriptional activator." 京都大学 (Kyoto University), 2007. http://hdl.handle.net/2433/136799.

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Lin, Ling. "Genetic Approaches to Study Transcriptional Activation and Tumor Suppression: A Dissertation." eScholarship@UMMS, 2012. https://escholarship.umassmed.edu/gsbs_diss/610.

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The development of methods and techniques is the driving force of scientific research. In this work, we described two large-scale screens in studying transcriptional activation and tumor suppression. In Part I, we studied transcriptional activation mechanisms by deriving and characterizing activation defective mutants. Promoter-specific transcriptional activators stimulate transcription through direct interactions with one or more components of the transcription machinery, termed the “target.” The identification of direct in vivo targets of activators has been a major challenge. We perform a large-scale genetic screen to derive and characterize tra1 alleles that are selectively defective for interaction with Gal4 in vivo. Utilizing these mutants, we demonstrated that Tra is an essential target for Gal4 activation, Gal4 and Tra1 bind cooperatively at the promoter and the Gal4–Tra1 interaction occurs predominantly on the promoter. In addition, we demonstrated that the Gal4-interaction site on Tra1 is highly selective. In Part II, we described a functional genomics approach to discover new tumor suppressor genes. A goal of contemporary cancer research is to identify the genes responsible for neoplastic transformation. Cells that are immortalized but non-tumorigenic were stably transduced with pools of short hairpin RNAs (shRNAs) and tested for their ability to form tumors in mice. ShRNAs in any resulting tumors were identified by sequencing to reveal candidate TSGs, which were then validated both experimentally and clinically by analysis of human tumor samples. Using this approach, we identified and validated 33 candidate TSGs. We found that most candidate TSGs were down-regulated in >70% of human lung squamous cell carcinoma (hLSCC) samples, and 17 candidate TSGs negatively regulate FGFR signalling pathway, and their ectopic expression inhibited growth of hLSCC xenografts. Furthermore, we suggest that by examining at the expression level of TSGs in lung cancer patients, we can predict their drug responsiveness to FGFR inhibitors. In conclusion, we have identified many new lung squamous cell cancer TSGs, using an experimental strategy that can be broadly applied to find TSGs in other tumor types.
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Cridland, Nigel A. "A study of cellular factors interacting with the Xenopus laevis vitellogenin B2 gene promoter." Thesis, University of Oxford, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.276525.

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Edwards, Helen Jane. "Transcriptional and post-transcriptional regulation of MDR1 expression during oxidative stress and recovery : a spatial and temporal study of MDR1 mRNA localization." Thesis, Imperial College London, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.438197.

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Romanish, Mark Taras. "Regulatory elements within repeated elements : a case study of NAIP transcriptional innovation." Thesis, University of British Columbia, 2009. http://hdl.handle.net/2429/12271.

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Neuronal Apoptosis Inhibitory Protein (NAIP, also known as BIRC1) is a member of the conserved Inhibitor of Apoptosis Protein (IAP) family. However, it is no longer principally considered an apoptosis inhibitor since its domain structure and functions in innate immunity also warrant inclusion in the Nod-Like Receptor (NLR) superfamily. Lineage-specific rearrangement and expansion of this locus have yielded different copy numbers among primates and rodents, providing an interesting case study in which to study transcriptional regulatory changes by a rapidly evolving gene. In the first stage of my thesis, I show that NAIP has multiple promoters sharing no similarity between human and rodents. Moreover, I demonstrate that multiple, domesticated long terminal repeats (LTRs) of endogenous retroviral (ERV) elements provide NAIP promoter function in human, mouse and rat. In human, an LTR serves as a tissue-specific promoter active primarily in testis. However, in rodents, our evidence indicates that an ancestral LTR common to all rodent genes is the major, constitutive promoter for these genes and that a second LTR found in two of the mouse genes is a minor promoter. Thus, independently acquired LTRs have assumed regulatory roles for orthologous genes, a remarkable evolutionary scenario. It is also demonstrated that 5’ flanking regions of IAP family genes as a group, in both human and mouse, are enriched for LTR insertions compared to average genes. In the second stage of my thesis, I demonstrate that several of the human NAIP paralogues are expressed, and that novel transcripts arise from both internal and upstream transcription start sites. Remarkably, two internal start sites initiate within Alu short interspersed element (SINE) retrotransposons, and a third novel transcription start site exists within the final intron of the GUSBP1 gene, upstream of only two NAIP copies. One Alu functions alone as a promoter in transient assays, while the other likely combines with upstream L1 sequences to form a composite promoter. The novel transcripts encode shortened open reading frames and I show that corresponding proteins are translated in a number of cell lines and primary tissues, in some cases above the level of full length NAIP. Interestingly, some NAIP isoforms lack their caspase-sequestering motifs, indicating that they have novel functions. My results support an important role for transposable elements in NAIP evolution, particularly as transcriptional regulatory modules, and illustrate a fascinating example of regulatory innovations adopted by a rapidly evolving gene.
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Books on the topic "Transcriptional study"

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Park-Youhanaie, Mary. Medical transcription made easy: The complete home study course. [United States: M. Park-Youhanaie?], 1999.

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Clay, Calvert, ed. Descriptive phonetics transcription workbook. 2nd ed. New York: Thieme, 1986.

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1477-1547, Schöner Johann, ed. Johann Schoner's globe of 1515: Transcription and study. Philadelphia: American Philosophical Society, 2010.

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Transcription, American Association for Medical. The model curriculum for medical transcription. 3rd ed. Modesto, California: American Association for Medical Transcription, 2005.

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The epic of Pābūjī: A study, transcription, and translation. Cambridge [England]: Cambridge University Press, 1991.

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Compton, Arthur J. Phonetic transcription of foreign accent. San Francisco, CA: Carousel House, 2004.

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Categorically speaking: A reference work and study guide for realtime writing. 2nd ed. Lafayette, Colo: White-Boucke Pub., 2006.

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Boucke, Laurie. CATegorically speaking: A reference work and study guide for realtime writing. Lafayette, Colo: White Boucke Pub., 1996.

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Stuart, Denis. Manorial records: An introduction to their transcription and translation. Chichester, Sussex: Phillimore, 1992.

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M, Sunnarborg Edith, ed. Introduction to medical office transcription. 3rd ed. Boston: McGraw-Hill/Irwin, 2007.

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Book chapters on the topic "Transcriptional study"

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Clement, Sandra L., and Jens Lykke-Andersen. "A Tethering Approach to Study Proteins that Activate mRNA Turnover in Human Cells." In Post-Transcriptional Gene Regulation, 121–33. Totowa, NJ: Humana Press, 2008. http://dx.doi.org/10.1007/978-1-59745-033-1_8.

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Trachsel, Hans, Michael Altmann, and Sylviane Blum. "Initiation Factor-Dependent Extracts: A Tool To Study Translation Initiation In Eukaryotes." In Post-transcriptional Control of Gene Expression, 93–98. Berlin, Heidelberg: Springer Berlin Heidelberg, 1996. http://dx.doi.org/10.1007/978-3-642-60929-9_8.

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Kadonaga, James T., Michael R. Briggs, and Robert Tjian. "Eukaryotic Transcriptional Specificity Conferred by DNA-Binding Proteins." In New Frontiers in the Study of Gene Functions, 87–98. Boston, MA: Springer US, 1987. http://dx.doi.org/10.1007/978-1-4613-1845-3_7.

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Tushir-Singh, Jogender, and Sanchita Bhatnagar. "In Vitro Assay to Study Histone Ubiquitination During Transcriptional Regulation." In Methods in Molecular Biology, 235–44. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-6518-2_17.

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Antunes, Ana, and Bruno Dupuy. "Molecular Methods to Study Transcriptional Regulation of Clostridium difficile Toxin Genes." In Methods in Molecular Biology, 93–115. Totowa, NJ: Humana Press, 2010. http://dx.doi.org/10.1007/978-1-60327-365-7_7.

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Waddell, Simon J., and Philip D. Butcher. "Use of DNA Arrays to Study Transcriptional Responses to Antimycobacterial Compounds." In Methods in Molecular Biology, 75–91. Totowa, NJ: Humana Press, 2010. http://dx.doi.org/10.1007/978-1-60327-279-7_6.

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Shukla, Surendra K., Ryan J. King, and Pankaj K. Singh. "Transcriptional Profiling Using RNA-Seq to Study Hypoxia-Mediated Gene Regulation." In Methods in Molecular Biology, 55–66. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-7665-2_6.

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Casson, Stuart A., Matthew W. B. Spencer, and Keith Lindsey. "Laser-Capture Microdissection to Study Global Transcriptional Changes During Plant Embryogenesis." In Methods in Molecular Biology, 111–20. Totowa, NJ: Humana Press, 2008. http://dx.doi.org/10.1007/978-1-59745-273-1_9.

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Chávez Montes, Ricardo A., Joanna Serwatowska, and Stefan de Folter. "Laser-Assisted Microdissection to Study Global Transcriptional Changes During Plant Embryogenesis." In Somatic Embryogenesis: Fundamental Aspects and Applications, 495–506. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-33705-0_27.

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Belostotsky, Dmitry A. "Gene-Specific and Genome-Wide ChIP Approaches to Study Plant Transcriptional Networks." In Plant Systems Biology, 3–12. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60327-563-7_1.

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Conference papers on the topic "Transcriptional study"

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Ahmad, Salma, Hanan Nazar, Nouralhuda Alatieh, Maryam Al-Mansoob, Zainab Farooq, Muna Yusuf, and Allal Ouhtit. "Validation of Novel Transcriptional Targets that Underpin CD44-promoted breast cancer cell invasion." In Qatar University Annual Research Forum & Exhibition. Qatar University Press, 2021. http://dx.doi.org/10.29117/quarfe.2021.0153.

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Introduction: Breast cancer (BC) is the most common cancer worldwide, and metastasis is its worst aspect and the first cause of death. Metastasis is a multistep process, where an invasion is a recurring event. The process of BC cell invasion involves three major factors, including cell adhesion molecules (CAM), proteinases and Growth factors.CD44, a family of CAM proteins and the hyaluronic acid (HA) cell surface receptor, acts as cell differentiation, cell migration/invasion and apoptosis regulator. Rationale: We have previously established a tetracycline (Tet)-OFF-regulated expression system, both in vitro and in vivo (Hill et al, 2006). As a complementary approach, the highly metastatic MDA-MB-231 BC cells expressing high levels of endogenous CD44s (the standard form of CD44), was cultured in the presence and absence of 50 µg/ml of HA. RNA samples were isolated from both cell experimental models, and microarray analysis (12K CHIP from Affymetrix) was applied. More than 200 CD44s transcriptional target genes were identified and were sub-divided into groups of genes based on their function: cell motility, cytoskeletal organization, ability to degrade ECM, and cell survival. Hypothesis: Among these 200 identified genes, we selected seven genes (ICAP-1, KYNU, AHR, SIRT1, SRSF8, PRAD1, and SOD2) and hypothesized that based on evidence from literature, these genes are potential novel targets of CD44-downstream signaling mediating BC cell invasion. Specific Aims: Pursuant to this goal, we proposed the following objectives: 1- Structural validation of ICAP-1, KYNU, AHR, SIRT1, SRSF8, PRAD1 and SOD2 as novel transcriptional targets of CD44/HA-downstream signaling at both RNA and Protein level using reverse transcription polymerase chain reaction (RT-PCR) and Western Blot respectively. 2-Functional validation of ICAP-1, KYNU, AHR, SIRT1, SRSF8, PRAD1and SOD2 as novel transcriptional targets that underpin CD44-promoted BC cell migration using wound healing assay after the transfection with siRNA. Innovation/Consclusion: This study validated seven transcriptional targets of CD44/HA-downstream signaling promoting BC cell invasion. Ongoing experiments aim to dissect the signaling pathways that link CD44 activation by HA to the transcription of these seven genes.
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Khajamoinuddin, Syed, Bhanu Kamapantula, Michael Mayo, Edward Perkins, and Preetam Ghosh. "Abundance of connected motifs in transcriptional networks, a case study using random forests regression." In 9th EAI International Conference on Bio-inspired Information and Communications Technologies (formerly BIONETICS). ACM, 2016. http://dx.doi.org/10.4108/eai.3-12-2015.2262520.

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Liu, Yuwen, Jie Zhou, and Kevin P. White. "Abstract 4935: A quantitative model to study cell-type-specific transcriptional regulation between MCF-7 and LNCaP." 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.am2012-4935.

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High, K. A., J. P. Evans, J. L. Ware, D. W. Stafford, and H. R. Roberts. "HEMOPHILIA B IN CANINES IS DUE TO A POST-TRANSCRIPTIONAL DEFECT." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644017.

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Factor IX is a vitamin K dependent plasma proteinsynthesized in the liver; a deficiency of Factor IX results in hemophilia B. An animal model for hemophilia B exists in dogs; affected animals have severe disease, with activity levels of less than 1%. The purpose of the current study is to determine the molecular basis of canine hemophilia. In previous work, we had shown that the Factor IX gene in hemophilic dogs appeared to be at least partly intact; thus, genomic DNA from normal, carrier and hemophilic dogs, when probed with sequences from the 4th, 7th, and 8th exons of the human gene, gave identical patterns on Southern blot. We have now completed the mapping of the hemophilic gene, using probes from the first, second, third and sixth exons, and have shown it to beentirely intact, that is, free of any large deletions or rearrangements, as determined by Southern blotting. In addition, using the guanidinium thiocyanate technique, we h^ve prepared total RNA from normal and -hemophilic dog livers add analyzed these samples by Northern blotting. The results show that the hemophilic dog synthesizes a Factor IX transcript of approximately 3 kilobases, that is, of the same size asthe normal dog. In addition, baaed on signal intensity, the transcript appears to be produced in roughlyequivalent amounts in the normal and hemophilic dogs.We conclude that the defect responsible for canine hemophilia B interferes with the production of the normal Factor IX protein at a post-transcriptional level. Moreover, since the hemophilic dogs produce Factor IX mRNA it should be possible to elucidate the gene defect in the hemophilic animals by preparing normal and hemophilic canine liver cDNA libraries and isolating and characterizing the respective Factor IX cDNAs.
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Schmid, Virginia, and David Mole. "Abstract LB-239: Studying effects of disease associated polymorphism on a transcriptional pathway: A case study in renal cell cancer." In Proceedings: AACR Annual Meeting 2018; April 14-18, 2018; Chicago, IL. American Association for Cancer Research, 2018. http://dx.doi.org/10.1158/1538-7445.am2018-lb-239.

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Onel, Buket, Clement Lin, and Danzhou Yang. "Abstract 685: Structural study of the 3'-end G-quadruplex formed in the human PDGFR-β promoter: Insight into a transcriptional inhibitor element." In Proceedings: AACR Annual Meeting 2018; April 14-18, 2018; Chicago, IL. American Association for Cancer Research, 2018. http://dx.doi.org/10.1158/1538-7445.am2018-685.

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Bettinson, Mat, and Steven Bird. "Learning Through Transcription." In Proceedings of the Fifth Workshop on the Use of Computational Methods in the Study of Endangered Languages. Stroudsburg, PA, USA: Association for Computational Linguistics, 2022. http://dx.doi.org/10.18653/v1/2022.computel-1.11.

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Chamberlain, C., P. Colman, A. Ranger, G. Johnson, C. Otoul, C. Stach, T. Dörner, M. Urowitz, and F. Hiepe. "90 Safety, efficacy and transcriptional changes following repeated administration of dapirolizumab pegol in patients with systemic lupus erythematosus: results from a phase i study." In LUPUS 2017 & ACA 2017, (12th International Congress on SLE &, 7th Asian Congress on Autoimmunity). Lupus Foundation of America, 2017. http://dx.doi.org/10.1136/lupus-2017-000215.90.

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Bromberg, Natalia, Gustavo Campos Molina, Elisa Napolitano Ferreira, Dirce Maria Carraro, Helena Brentani, and Maria Mitzi Brentani. "Abstract 532: A transcriptional sketch of breast cancer fibroblasts: The validation of cDNA libraries for expression profile study using a high-throughput sequencing technology." In Proceedings: AACR 102nd Annual Meeting 2011‐‐ Apr 2‐6, 2011; Orlando, FL. American Association for Cancer Research, 2011. http://dx.doi.org/10.1158/1538-7445.am2011-532.

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Van Laere, Steven J., Naoto Ueno, Pascal Finetti, Peter B. Vermeulen, Anthony Lucci, Daniel Birnbaum, Fredika Robertson, et al. "Abstract 328: An integrated analysis of three distinct IBC/non-IBC Affymetrix gene expression data sets to study the transcriptional heterogeneity both between IBC and non-IBC and within IBC." In Proceedings: AACR 102nd Annual Meeting 2011‐‐ Apr 2‐6, 2011; Orlando, FL. American Association for Cancer Research, 2011. http://dx.doi.org/10.1158/1538-7445.am2011-328.

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Reports on the topic "Transcriptional study"

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Pichersky, Eran, Alexander Vainstein, and Natalia Dudareva. Scent biosynthesis in petunia flowers under normal and adverse environmental conditions. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7699859.bard.

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The ability of flowering plants to prosper throughout evolution, and for many crop plants to set fruit, is strongly dependent on their ability to attract pollinators. To that end many plants synthesize a spectrum of volatile compounds in their flowers. Scent is a highly dynamic trait that is strongly influenced by the environment. However, with high temperature conditions becoming more common, the molecular interplay between this type of stress and scent biosynthesis need to be investigated. Using petunia as a model system, our project had three objectives: (1) Determine the expression patterns of genes encoding biosynthetic scent genes (BSGs) and of several genes previously identified as encoding transcription factors involved in scent regulation under normal and elevated temperature conditions. (2) Examine the function of petunia transcription factors and a heterologous transcription factor, PAPl, in regulating genes of the phenylpropanoid/benzenoid scent pathway. (3) Study the mechanism of transcriptional regulation by several petunia transcription factors and PAPl of scent genes under normal and elevated temperature conditions by examining the interactions between these transcription factors and the promoters of target genes. Our work accomplished the first two goals but was unable to complete the third goal because of lack of time and resources. Our general finding was that when plants grew at higher temperatures (28C day/22C night, vs. 22C/16C), their scent emission decreased in general, with the exception of a few volatiles such as vanillin. To understand why, we looked at gene transcription levels, and saw that generally there was a good correlation between levels of transcriptions of gene specifying enzymes for specific scent compounds and levels of emission of the corresponding scent compounds. Enzyme activity levels, however, showed little difference between plants growing at different temperature regimes. Plants expressing the heterologous gene PAPl showed general increase in scent emission in control temperature conditions but emission decreased at the higher temperature conditions, as seen for control plants. Finally, expression of several transcription factor genes decreased at high temperature, but expression of new transcription factor, EOB-V, increased, implicating it in the decrease of transcription of BSGs. The major conclusion of this work is that high temperature conditions negatively affect scent emission from plants, but that some genetic engineering approaches could ameliorate this problem.
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Arazi, Tzahi, Vivian Irish, and Asaph Aharoni. Micro RNA Targeted Transcription Factors for Fruit Quality Improvement. United States Department of Agriculture, July 2008. http://dx.doi.org/10.32747/2008.7592651.bard.

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Fruits are unique to flowering plants and represent an important component of human and animal diets. Development and maturation of tomato fruit is a well-programmed process, and yet, only a limited number of factors involved in its regulation have been characterized. Micro-RNAs (miRNAs) are small, endogenous RNAs that regulate gene expression in animals and plants. Plant miRNAs have a vital role in the generation of plant forms through post-transcriptional regulation of the accumulation of developmental regulators, especially transcription factors. Recently, we and others have demonstrated that miRNAs and other type of small RNAs are expressed in tomato fruit, and target putative transcription factors during its development and maturation. The original objectives of the approved proposal were: 1. To identify fruit miRNA transcription factor target genes through a bioinformatic approach. 2. To identify fruit miRNA transcription factor target genes up-regulated in tomato Dicer-like 1 silenced fruit. 3. To establish the biological functions of selected transcription factors and examine their utility for improving fleshy fruit quality trait. This project was approved by BARD as a feasibility study to allow initial experiments to peruse objective 2 as described above in order to provide initial evidence that miRNAs do play a role in fruit development. The approach planned to achieve objective 2, namely to identify miRNA transcription factor targets was to clone and silence the expression of a tomato DCL1 homolog in different stages of fruit development and examine alterations to gene expression in such a fruit in order to identify pathways and target genes that are regulated by miRNA via DCL1. In parallel, we characterized two transcription factors that are regulated by miRNAs in the fruit. We report here on the cloning of tomato DCL1 homolog, characterization of its expression in fruit flesh and peel of wild type and ripening mutants and generation of transgenic plants that silence SlDCL1 specifically in the fruit. Our results suggest that the tomato homolog of DCL1, which is the major plant enzyme involved in miRNA biogenesis, is present in fruit flesh and peel and differentially expressed during various stages of fruit development. In addition, its expression is altered in ripening mutants. We also report on the cloning and expression analysis of Sl_SBP and Sl_ARF transcription factors, which serve as targets of miR157 and miR160, respectively. Our data suggest that Sl_SBP levels are highest during fruit ripening supporting a role for this gene in that process. On the other hand Sl_ARF is strongly expressed in green fruit up to breaker indicating a role for that gene at preripening stage which is consistent with preliminary in_situ analyses that suggest expression in ovules of immature green fruit. The results of this feasibility study together with our previous results that miRNAs are expressed in the fruit indeed provide initial evidence that these regulators and their targets play roles in fruit development and ripening. These genes are expected to provide novel means for genetic improvement of tomato fleshy fruit.
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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.

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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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Levy, Avraham A., and Virginia Walbot. Regulation of Transposable Element Activities during Plant Development. United States Department of Agriculture, August 1992. http://dx.doi.org/10.32747/1992.7568091.bard.

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We have studied the regulation of the maize Ac and MuDR transposable elements activities during plant development. Ac was studied in an heterologous system (transgenic tobacco plants and cell suspensions) while MuDR was studied in the native maize background. The focus of this study was on the transcriptional regulation of Ac and MuDR. For Ac, the major achievements were to show that 1-It is autoregulated in a way that the Ac-encoded transposase can repress the activity of its own promoter; 2-It is expressed at low basal level in all the plant organs that were studied, and its activity is stronger in dividing tissues -- a behaviour reminiscent of housekeeping genes; 3- the activity of Ac promoter is cell cycle regulated -- induced at early S-phase and increasing until mitosis; 4- host factor binding sites were identified at both extremities of Ac and may be important for transposition. For MuDR, It was shown that it encodes two genes, mudrA and mudrB, convergently transcribed from near-identical promoters in the terminal inverted repeats. Distinct 5' start sites, alternative splicing, production of antisense RNA and tissue specificity were all shown to be involved in the regulation of MuDR.
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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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Fromm, A., Avihai Danon, and Jian-Kang Zhu. Genes Controlling Calcium-Enhanced Tolerance to Salinity in Plants. United States Department of Agriculture, March 2003. http://dx.doi.org/10.32747/2003.7585201.bard.

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The specific objectives of the proposed research were to identify, clone and characterize downstream cellular target(s) of SOS3 in Arabidopsis thaliana, to analyze the Ca2+-binding characteristics of SOS3 and the sos3-1 mutant and their interactions with SOS3 cellular targets to analyze the SOS3 cell-specific expression patterns, and its subcellular localization, and to assess the in vivo role of SOS3 target protein(s) in plant tolerance to salinity stress. In the course of the study, in view of recent opportunities in identifying Ca2+ - responsive genes using microarrays, the group at Weizmann has moved into identifying Ca2+-responsive stress genes by using a combination of aqeuorin-based measurements of cytosolic Ca and analysis by DNA microarrays of early Ca-responsive genes at the whole genome level. Analysis of SOS3 (University of Arizona) revealed its expression in both roots and shoots. However, the expression of this gene is not induced by stress. This is reminiscent of other stress proteins that are regulated by post-transcriptional mechanisms such as the activation by second messengers like Ca. Further analysis of the expression of the gene using promoter - GUS fusions revealed expression in lateral root primordial. Studies at the Weizmann Institute identified a large number of genes whose expression is up-regulated by a specific cytosolic Ca burst evoked by CaM antagonists. Fewer genes were found to be down-regulated by the Ca burst. Among the up-regulated genes many are associated with early stress responses. Moreover, this study revealed a large number of newly identified Ca-responsive genes. These genes could be useful to investigate yet unknown Ca-responsive gene networks involved in plant response to stress.
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Levin, Ilan, Avtar K. Handa, Avraham Lalazar, and Autar K. Mattoo. Modulating phytonutrient content in tomatoes combining engineered polyamine metabolism with photomorphogenic mutants. United States Department of Agriculture, December 2006. http://dx.doi.org/10.32747/2006.7587724.bard.

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Fruit constitutes a major component of our diet, providing fiber, vitamins, minerals, and many other phytonutrients that promote good health. Fleshy fruits, such as tomatoes, already contain high levels of several of these ingredients. Nevertheless, efforts have been invested in increasing and diversifying the content of phytonutrients, such as carotenoids and flavonoids, in tomato fruits. Increasing levels of phytonutrients, such as lycopene, is highly justified from the perspective of the lycopene extraction industry due to cost effectiveness reasons. Diversifying phytonutrients, in particular those that contribute to fruit color, could potentially provide an array of attractive colors to our diet. Our major goal was to devise a novel strategy for developing tomato fruits with enhanced levels of phytochemicals known to promote good health with special emphasis on lycopene content. A further important goal was to analyze global gene expression of selected genetic lines produced throughout this study in order is to dissect the molecular mechanisms regulating phytonutrients accumulation in the tomato fruit. To achieve these goals we proposed to: 1. combine, by classical breeding, engineered polyamine metabolism with photomorphogenic high pigment mutants in order generate tomato plant with exceptionally high levels of phytonutrients; 2. use gene transfer technology for genetic introduction of key genes that promote phytonutrient accumulation in the tomato fruit, 3. Analyze accumulation patterns of the phytonutrients in the tomato fruit during ripening; 4. Analyze global gene expression during fruit ripening in selected genotypes identified in objectives 1 and 2, and 5. Identify and analyze regulatory mechanisms of chloroplast disassembly and chromoplast formation. During the 3 years research period we have carried out most of the research activities laid out in the original proposal and our key conclusions are as follows: 1. the engineered polyamine metabolism strategy proposed by the US collaborators can not increase lycopene content either on its own or in combination with an hp mutant (hp-2ᵈᵍ); 2. The hp-2ᵈᵍ affects strongly the transcriptional profile of the tomato fruit showing a strong tendency for up- rather than down-regulation of genes, 3. Ontology assignment of these miss-regulated genes revealed a consistent up-regulation of genes related to chloroplast biogenesis and photosynthesis in hp-2ᵈᵍ mutants throughout fruit development; 4. A tendency for up-regulation was also usually observed in structural genes involved in phytonutrientbiosynthesis; however this up-regulation was not as consistent. 5. Microscopic observations revealed a significantly higher number of chloroplasts in pericarp cells of mature-green hp-2ᵈᵍ/hp-2ᵈᵍ fruits in comparison to their normal fully isogenic counterparts. 6. The relative abundance of chloroplasts could be observed from early stages of fruit development. Cumulatively these results suggest that: 1. the overproduction of secondary metabolites, characterizing hp-2ᵈᵍ/hp-2ᵈᵍ fruits, is more due to chloroplast number rather then to transcriptional activation of structural genes of the relevant metabolic pathways, and 2. The molecular trigger increasing metabolite levels in hp-2ᵈᵍ mutant fruits should be traced at early stage of fruit development.
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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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9

Chen, Junping, Zach Adam, and Arie Admon. The Role of FtsH11 Protease in Chloroplast Biogenesis and Maintenance at Elevated Temperatures in Model and Crop Plants. United States Department of Agriculture, May 2013. http://dx.doi.org/10.32747/2013.7699845.bard.

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specific objectives of this proposal were to: 1) determine the location, topology, and oligomerization of FtsH11 protease; 2) identify the substrate/s of FtsH11 and the downstream components involved in maintaining thermostability of chloroplasts; 3) identify new elements involved in FtsH11 protease regulatory network related to HT adaptation processes in chloroplast; 4) Study the role of FtsH11 homologs from crop species in HT tolerance. Background to the topic: HT-tolerant varieties that maintain high photosynthetic efficiency at HT, and cope better with daily and seasonal temperature fluctuations are in great need to alleviate the effect of global warming on food production. Photosynthesis is a very complex process requiring accurate coordination of many complex systems and constant adjustments to the changing environments. Proteolytic activities mediated by various proteases in chloroplast are essential part of this process and critical for maintaining normal chloroplast functions under HT. However, little is known about mechanisms that contribute to adaptation of photosynthetic processes to HT. Our study has shown that a chloroplast-targeted Arabidopsis FtsH11 protease plays an essential and specific role in maintaining thermostability of thylakoids and normal photosynthesis at moderate HT. We hypothesized that FtsH11 homologs recently identified in other plant species might have roles similarly to that of AtFtsH1. Thus, dissecting the underlying mechanisms of FtsH11 in the adaptation mechanisms in chloroplasts to HT stress and other elements involved will aid our effort to produce more agricultural products in less favorable environments. Major conclusions, solutions, achievements - Identified the chloroplast inner envelope membrane localization of FtsH11. - Revealed a specific association of FtsH11 with the a and b subunits of CPN60. - Identified the involvement of ARC6, a protein coordinates chloroplast division machineries in plants, in FtsH11 mediated HT adaptation process in chloroplast. -Reveal possible association of a polyribonucleotide nucleotidyltransferase (cpPNPase), coded by At3G03710, with FtsH11 mediated HT adaptation process in chloroplast. - Mapped 4 additional loci in FtsH11 mediated HT adaptation network in chloroplast. - Demonstrated importance of the proteolytic activity of FtsH11 for thermotolerance, in addition to the ATPase activity. - Demonstrated a conserved role of plant FtsH11 proteases in chloroplast biogenesis and in maintaining structural and functional thermostability of chloroplast at elevated temperatures. Implications, both scientific and agricultural:Three different components interacting with FtsH11 were identified during the course of this study. At present, it is not known whether these proteins are directly involved in FtsH11mediated thermotolerance network in chloroplast and/or how these elements are interrelated. Studies aiming to connect the dot among biological functions of these networks are underway in both labs. Nevertheless, in bacteria where it was first studied, FtsH functions in heat shock response by regulating transcription level of σ32, a heat chock factor regulates HSPsexpression. FtsH also involves in control of biosynthesis of membrane components and quality control of membrane proteins etc. In plants, both Arc 6 and CPN60 identified in this study are essential in chloroplast division and developments as mutation of either one impairs chloroplast division in Arabidopsis. The facts that we have found the specific association of both α and β CPN60 with FtsH11 protein biochemically, the suppression/ enhancement of ftsh11 thermosensitive phenotype by arc6 /pnp allele genetically, implicate inter-connection of these networks via FtsH11 mediated network(s) in regulating the dynamic adaptation processes of chloroplast to temperature increases at transcriptional, translational and post-translational levels. The conserved role of FtsH11 proteases in maintaining thermostability of chloroplast at HT demonstrated here provides a foundation for improving crop photosynthetic performance at high temperatures.
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10

Paran, Ilan, and Allen Van Deynze. Regulation of pepper fruit color, chloroplasts development and their importance in fruit quality. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7598173.bard.

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Pepper exhibits large natural variation in chlorophyll content in the immature fruit. To dissect the genetic and molecular basis of this variation, we conducted QTL mapping for chlorophyll content in a cross between light and dark green-fruited parents, PI 152225 and 1154. Two major QTLs, pc1 and pc10, that control chlorophyll content by modulation of chloroplast compartment size in a fruit-specific manner were detected in chromosomes 1 and 10, respectively. The pepper homolog of GOLDEN2- LIKE transcription factor (CaGLK2) was found as underlying pc10, similar to its effect on tomato fruit chloroplast development. A candidate gene for pc1was found as controlling chlorophyll content in pepper by the modulation of chloroplast size and number. Fine mapping of pc1 aided by bulked DNA and RNA-seq analyses enabled the identification of a zinc finger transcription factor LOL1 (LSD-One-Like 1) as a candidate gene underlying pc1. LOL1 is a positive regulator of oxidative stress- induced cell death in Arabidopsis. However, over expression of the rice ortholog resulted in an increase of chlorophyll content. Interestingly, CaAPRR2 that is linked to the QTL and was found to affect immature pepper fruit color in a previous study, did not have a significant effect on chlorophyll content in the present study. Verification of the candidate's function was done by generating CRISPR/Cas9 knockout mutants of the orthologues tomato gene, while its knockout experiment in pepper by genome editing is under progress. Phenotypic similarity as a consequence of disrupting the transcription factor in both pepper and tomato indicated its functional conservation in controlling chlorophyll content in the Solanaceae. A limited sequence diversity study indicated that null mutations in CaLOL1 and its putative interactorCaMIP1 are present in C. chinensebut not in C. annuum. Combinations of mutations in CaLOL1, CaMIP1, CaGLK2 and CaAPRR2 are required for the creation of the extreme variation in chlorophyll content in Capsicum.
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