Journal articles: 'Eukaryotic gene regulation'

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Chin, Jason W. "Eukaryotic gene regulation." Chemistry & Biology 7, no. 1 (January 2000): R26. http://dx.doi.org/10.1016/s1074-5521(00)00071-5.

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Lindahl, G. "Gene Regulation: A Eukaryotic Perspective." International Journal of Biochemistry & Cell Biology 35, no. 1 (January 2003): 111–12. http://dx.doi.org/10.1016/s1357-2725(02)00174-7.

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Marsden, P. "Gene Regulation. A Eukaryotic Perspective." Biochemical Education 19, no. 1 (January 1991): 44–45. http://dx.doi.org/10.1016/0307-4412(91)90163-3.

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Goodbourn, Stephen. "Gene regulation: A eukaryotic perspective." Trends in Genetics 7, no. 10 (October 1991): 340. http://dx.doi.org/10.1016/0168-9525(91)90426-q.

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Mellor, Jane. "Gene regulation: A eukaryotic perspective." Trends in Biochemical Sciences 16 (January 1991): 482–83. http://dx.doi.org/10.1016/0968-0004(91)90186-y.

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Bonifer, Constanze. "Developmental regulation of eukaryotic gene loci." Trends in Genetics 16, no. 7 (July 2000): 310–15. http://dx.doi.org/10.1016/s0168-9525(00)02029-1.

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Nakayama, Koh, and Naoyuki Kataoka. "Regulation of Gene Expression under Hypoxic Conditions." International Journal of Molecular Sciences 20, no. 13 (July 3, 2019): 3278. http://dx.doi.org/10.3390/ijms20133278.

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Eukaryotes are often subjected to different kinds of stress. In order to adjust to such circumstances, eukaryotes activate stress–response pathways and regulate gene expression. Eukaryotic gene expression consists of many different steps, including transcription, RNA processing, RNA transport, and translation. In this review article, we focus on both transcriptional and post-transcriptional regulations of gene expression under hypoxic conditions. In the first part of the review, transcriptional regulations mediated by various transcription factors including Hypoxia-Inducible Factors (HIFs) are described. In the second part, we present RNA splicing regulations under hypoxic conditions, which are mediated by splicing factors and their kinases. This work summarizes and discusses the emerging studies of those two gene expression machineries under hypoxic conditions.

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Chen, Lin. "Combinatorial gene regulation by eukaryotic transcription factors." Current Opinion in Structural Biology 9, no. 1 (February 1999): 48–55. http://dx.doi.org/10.1016/s0959-440x(99)80007-4.

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Gagneux, P. "Gene Regulation: A Eukaryotic Perspective, 4th Edition." Journal of Heredity 94, no. 6 (November 1, 2003): 528–29. http://dx.doi.org/10.1093/jhered/esg102.

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Emery-Corbin, Samantha J., Joshua J. Hamey, Brendan R. E. Ansell, Balu Balan, Swapnil Tichkule, Andreas J. Stroehlein, Crystal Cooper, et al. "Eukaryote-Conserved Methylarginine Is Absent in Diplomonads and Functionally Compensated in Giardia." Molecular Biology and Evolution 37, no. 12 (July 23, 2020): 3525–49. http://dx.doi.org/10.1093/molbev/msaa186.

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Abstract Methylation is a common posttranslational modification of arginine and lysine in eukaryotic proteins. Methylproteomes are best characterized for higher eukaryotes, where they are functionally expanded and evolved complex regulation. However, this is not the case for protist species evolved from the earliest eukaryotic lineages. Here, we integrated bioinformatic, proteomic, and drug-screening data sets to comprehensively explore the methylproteome of Giardia duodenalis—a deeply branching parasitic protist. We demonstrate that Giardia and related diplomonads lack arginine-methyltransferases and have remodeled conserved RGG/RG motifs targeted by these enzymes. We also provide experimental evidence for methylarginine absence in proteomes of Giardia but readily detect methyllysine. We bioinformatically infer 11 lysine-methyltransferases in Giardia, including highly diverged Su(var)3-9, Enhancer-of-zeste and Trithorax proteins with reduced domain architectures, and novel annotations demonstrating conserved methyllysine regulation of eukaryotic elongation factor 1 alpha. Using mass spectrometry, we identify more than 200 methyllysine sites in Giardia, including in species-specific gene families involved in cytoskeletal regulation, enriched in coiled-coil features. Finally, we use known methylation inhibitors to show that methylation plays key roles in replication and cyst formation in this parasite. This study highlights reduced methylation enzymes, sites, and functions early in eukaryote evolution, including absent methylarginine networks in the Diplomonadida. These results challenge the view that arginine methylation is eukaryote conserved and demonstrate that functional compensation of methylarginine was possible preceding expansion and diversification of these key networks in higher eukaryotes.

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Schmelling, Nicolas M., and Ilka M. Axmann. "Computational modelling unravels the precise clockwork of cyanobacteria." Interface Focus 8, no. 6 (October 19, 2018): 20180038. http://dx.doi.org/10.1098/rsfs.2018.0038.

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Precisely timing the regulation of gene expression by anticipating recurring environmental changes is a fundamental part of global gene regulation. Circadian clocks are one form of this regulation, which is found in both eukaryotes and prokaryotes, providing a fitness advantage for these organisms. Whereas many different eukaryotic groups harbour circadian clocks, cyanobacteria are the only known oxygenic phototrophic prokaryotes to regulate large parts of their genes in a circadian fashion. A decade of intensive research on the mechanisms and functionality using computational and mathematical approaches in addition to the detailed biochemical and biophysical understanding make this the best understood circadian clock. Here, we summarize the findings and insights into various parts of the cyanobacterial circadian clock made by mathematical modelling. These findings have implications for eukaryotic circadian research as well as synthetic biology harnessing the power and efficiency of global gene regulation.

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Lee, Jun-Yeong, Jawon Song, Lucy LeBlanc, Ian Davis, Jonghwan Kim, and Samuel Beck. "Conserved dual-mode gene regulation programs in higher eukaryotes." Nucleic Acids Research 49, no. 5 (February 23, 2021): 2583–97. http://dx.doi.org/10.1093/nar/gkab108.

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Abstract Recent genomic data analyses have revealed important underlying logics in eukaryotic gene regulation, such as CpG islands (CGIs)-dependent dual-mode gene regulation. In mammals, genes lacking CGIs at their promoters are generally regulated by interconversion between euchromatin and heterochromatin, while genes associated with CGIs constitutively remain as euchromatin. Whether a similar mode of gene regulation exists in non-mammalian species has been unknown. Here, through comparative epigenomic analyses, we demonstrate that the dual-mode gene regulation program is common in various eukaryotes, even in the species lacking CGIs. In cases of vertebrates or plants, we find that genes associated with high methylation level promoters are inactivated by forming heterochromatin and expressed in a context-dependent manner. In contrast, the genes with low methylation level promoters are broadly expressed and remain as euchromatin even when repressed by Polycomb proteins. Furthermore, we show that invertebrate animals lacking DNA methylation, such as fruit flies and nematodes, also have divergence in gene types: some genes are regulated by Polycomb proteins, while others are regulated by heterochromatin formation. Altogether, our study establishes gene type divergence and the resulting dual-mode gene regulation as fundamental features shared in a broad range of higher eukaryotic species.

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QI, He-Yuan, Zhao-Jun ZHANG, Ya-Juan LI, and Xiang-Dong FANG. "Role of chromatin conformation in eukaryotic gene regulation." Hereditas (Beijing) 33, no. 12 (December 21, 2011): 1291–99. http://dx.doi.org/10.3724/sp.j.1005.2011.01291.

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14

Wright, S. "Regulation of eukaryotic gene expression by transcriptional attenuation." Molecular Biology of the Cell 4, no. 7 (July 1993): 661–68. http://dx.doi.org/10.1091/mbc.4.7.661.

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de Jongh, Ronald P. H., Aalt D. J. van Dijk, Mattijs K. Julsing, Peter J. Schaap, and Dick de Ridder. "Designing Eukaryotic Gene Expression Regulation Using Machine Learning." Trends in Biotechnology 38, no. 2 (February 2020): 191–201. http://dx.doi.org/10.1016/j.tibtech.2019.07.007.

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Padmanaban, G. "Specificity in the regulation of eukaryotic gene transcription." Journal of Biosciences 18, no. 1 (March 1993): 27–36. http://dx.doi.org/10.1007/bf02703035.

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17

Brown, David T. "Histone H1 and the dynamic regulation of chromatin function." Biochemistry and Cell Biology 81, no. 3 (June 1, 2003): 221–27. http://dx.doi.org/10.1139/o03-049.

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Eukaryotic DNA is organized in a complex structure called chromatin. Although a primary function of chromatin is compaction of DNA, this must done such that the underlying DNA is potentially accessible to factor-mediated regulatory responses. Chromatin structure clearly plays a dominant role in regulating much of eukaryotic transcription. The demonstration that reversible covalent modification of the core histones contribute to transcriptional activation and repression by altering chromatin structure and the identification of numerous ATP-dependent chromatin remodeling enzymes provide strong support for this view. Chromatin is much more dynamic than was previously thought and regulation of the dynamic properties of chromatin is a key aspect of gene regulation. This review will focus on recent attempts to elucidate the specific contribution of histone H1 to chromatin-mediated regulation of gene expression.Key words: histone H1, chromatin, gene expression.

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SASAI, Masaki, and Tomoki P. TERADA. "Loose Mechanism of Eukaryotic Gene Regulation and Chromatin Dynamics." Seibutsu Butsuri 56, no. 2 (2016): 106–8. http://dx.doi.org/10.2142/biophys.56.106.

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Alvarez-Gonzalez, Rafael. "PARP regulation of eukaryotic gene expression. Survival or death?" Trends in Genetics 17, no. 10 (October 2001): 607–8. http://dx.doi.org/10.1016/s0168-9525(01)02437-4.

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Burnside, Kellie, and Lakshmi Rajagopal. "Regulation of prokaryotic gene expression by eukaryotic-like enzymes." Current Opinion in Microbiology 15, no. 2 (April 2012): 125–31. http://dx.doi.org/10.1016/j.mib.2011.12.006.

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Tarrant, Daniel, and Tobias von der Haar. "Synonymous codons, ribosome speed, and eukaryotic gene expression regulation." Cellular and Molecular Life Sciences 71, no. 21 (July 20, 2014): 4195–206. http://dx.doi.org/10.1007/s00018-014-1684-2.

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Wong, Felix, and Jeremy Gunawardena. "Gene Regulation in and out of Equilibrium." Annual Review of Biophysics 49, no. 1 (May 6, 2020): 199–226. http://dx.doi.org/10.1146/annurev-biophys-121219-081542.

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Determining whether and how a gene is transcribed are two of the central processes of life. The conceptual basis for understanding such gene regulation arose from pioneering biophysical studies in eubacteria. However, eukaryotic genomes exhibit vastly greater complexity, which raises questions not addressed by this bacterial paradigm. First, how is information integrated from many widely separated binding sites to determine how a gene is transcribed? Second, does the presence of multiple energy-expending mechanisms, which are absent from eubacterial genomes, indicate that eukaryotes are capable of improved forms of genetic information processing? An updated biophysical foundation is needed to answer such questions. We describe the linear framework, a graph-based approach to Markov processes, and show that it can accommodate many previous studies in the field. Under the assumption of thermodynamic equilibrium, we introduce a language of higher-order cooperativities and show how it can rigorously quantify gene regulatory properties suggested by experiment. We point out that fundamental limits to information processing arise at thermodynamic equilibrium and can only be bypassed through energy expenditure. Finally, we outline some of the mathematical challenges that must be overcome to construct an improved biophysical understanding of gene regulation.

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Casadesús, Josep, and David Low. "Epigenetic Gene Regulation in the Bacterial World." Microbiology and Molecular Biology Reviews 70, no. 3 (September 2006): 830–56. http://dx.doi.org/10.1128/mmbr.00016-06.

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SUMMARY Like many eukaryotes, bacteria make widespread use of postreplicative DNA methylation for the epigenetic control of DNA-protein interactions. Unlike eukaryotes, however, bacteria use DNA adenine methylation (rather than DNA cytosine methylation) as an epigenetic signal. DNA adenine methylation plays roles in the virulence of diverse pathogens of humans and livestock animals, including pathogenic Escherichia coli, Salmonella, Vibrio, Yersinia, Haemophilus, and Brucella. In Alphaproteobacteria, methylation of adenine at GANTC sites by the CcrM methylase regulates the cell cycle and couples gene transcription to DNA replication. In Gammaproteobacteria, adenine methylation at GATC sites by the Dam methylase provides signals for DNA replication, chromosome segregation, mismatch repair, packaging of bacteriophage genomes, transposase activity, and regulation of gene expression. Transcriptional repression by Dam methylation appears to be more common than transcriptional activation. Certain promoters are active only during the hemimethylation interval that follows DNA replication; repression is restored when the newly synthesized DNA strand is methylated. In the E. coli genome, however, methylation of specific GATC sites can be blocked by cognate DNA binding proteins. Blockage of GATC methylation beyond cell division permits transmission of DNA methylation patterns to daughter cells and can give rise to distinct epigenetic states, each propagated by a positive feedback loop. Switching between alternative DNA methylation patterns can split clonal bacterial populations into epigenetic lineages in a manner reminiscent of eukaryotic cell differentiation. Inheritance of self-propagating DNA methylation patterns governs phase variation in the E. coli pap operon, the agn43 gene, and other loci encoding virulence-related cell surface functions.

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Dillon, Niall, and Pierangela Sabbattini. "Functional gene expression domains: defining the functional unit of eukaryotic gene regulation." BioEssays 22, no. 7 (June 23, 2000): 657–65. http://dx.doi.org/10.1002/1521-1878(200007)22:7<657::aid-bies8>3.0.co;2-2.

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Weiner, Agnes K. M., Mario A. Cerón-Romero, Ying Yan, and Laura A. Katz. "Phylogenomics of the Epigenetic Toolkit Reveals Punctate Retention of Genes across Eukaryotes." Genome Biology and Evolution 12, no. 12 (October 13, 2020): 2196–210. http://dx.doi.org/10.1093/gbe/evaa198.

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Abstract Epigenetic processes in eukaryotes play important roles through regulation of gene expression, chromatin structure, and genome rearrangements. The roles of chromatin modification (e.g., DNA methylation and histone modification) and non-protein-coding RNAs have been well studied in animals and plants. With the exception of a few model organisms (e.g., Saccharomyces and Plasmodium), much less is known about epigenetic toolkits across the remainder of the eukaryotic tree of life. Even with limited data, previous work suggested the existence of an ancient epigenetic toolkit in the last eukaryotic common ancestor. We use PhyloToL, our taxon-rich phylogenomic pipeline, to detect homologs of epigenetic genes and evaluate their macroevolutionary patterns among eukaryotes. In addition to data from GenBank, we increase taxon sampling from understudied clades of SAR (Stramenopila, Alveolata, and Rhizaria) and Amoebozoa by adding new single-cell transcriptomes from ciliates, foraminifera, and testate amoebae. We focus on 118 gene families, 94 involved in chromatin modification and 24 involved in non-protein-coding RNA processes based on the epigenetics literature. Our results indicate 1) the presence of a large number of epigenetic gene families in the last eukaryotic common ancestor; 2) differential conservation among major eukaryotic clades, with a notable paucity of genes within Excavata; and 3) punctate distribution of epigenetic gene families between species consistent with rapid evolution leading to gene loss. Together these data demonstrate the power of taxon-rich phylogenomic studies for illuminating evolutionary patterns at scales of >1 billion years of evolution and suggest that macroevolutionary phenomena, such as genome conflict, have shaped the evolution of the eukaryotic epigenetic toolkit.

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Nützmann, Hans-Wilhelm, Daniel Doerr, América Ramírez-Colmenero, Jesús Emiliano Sotelo-Fonseca, Eva Wegel, Marco Di Stefano, Steven W. Wingett, et al. "Active and repressed biosynthetic gene clusters have spatially distinct chromosome states." Proceedings of the National Academy of Sciences 117, no. 24 (June 3, 2020): 13800–13809. http://dx.doi.org/10.1073/pnas.1920474117.

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While colocalization within a bacterial operon enables coexpression of the constituent genes, the mechanistic logic of clustering of nonhomologous monocistronic genes in eukaryotes is not immediately obvious. Biosynthetic gene clusters that encode pathways for specialized metabolites are an exception to the classical eukaryote rule of random gene location and provide paradigmatic exemplars with which to understand eukaryotic cluster dynamics and regulation. Here, using 3C, Hi-C, and Capture Hi-C (CHi-C) organ-specific chromosome conformation capture techniques along with high-resolution microscopy, we investigate how chromosome topology relates to transcriptional activity of clustered biosynthetic pathway genes inArabidopsis thaliana. Our analyses reveal that biosynthetic gene clusters are embedded in local hot spots of 3D contacts that segregate cluster regions from the surrounding chromosome environment. The spatial conformation of these cluster-associated domains differs between transcriptionally active and silenced clusters. We further show that silenced clusters associate with heterochromatic chromosomal domains toward the periphery of the nucleus, while transcriptionally active clusters relocate away from the nuclear periphery. Examination of chromosome structure at unrelated clusters in maize, rice, and tomato indicates that integration of clustered pathway genes into distinct topological domains is a common feature in plant genomes. Our results shed light on the potential mechanisms that constrain coexpression within clusters of nonhomologous eukaryotic genes and suggest that gene clustering in the one-dimensional chromosome is accompanied by compartmentalization of the 3D chromosome.

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Lohr, D. "Chromatin structure and regulation of the eukaryotic regulatory gene GAL80." Proceedings of the National Academy of Sciences 90, no. 22 (November 15, 1993): 10628–32. http://dx.doi.org/10.1073/pnas.90.22.10628.

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Jurka, J. "Conserved eukaryotic transposable elements and the evolution of gene regulation." Cellular and Molecular Life Sciences 65, no. 2 (November 20, 2007): 201–4. http://dx.doi.org/10.1007/s00018-007-7369-3.

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Willbanks, Amber, Meghan Leary, Molly Greenshields, Camila Tyminski, Sarah Heerboth, Karolina Lapinska, Kathryn Haskins, and Sibaji Sarkar. "The Evolution of Epigenetics: From Prokaryotes to Humans and Its Biological Consequences." Genetics & Epigenetics 8 (January 2016): GEG.S31863. http://dx.doi.org/10.4137/geg.s31863.

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The evolution process includes genetic alterations that started with prokaryotes and now continues in humans. A distinct difference between prokaryotic chromosomes and eukaryotic chromosomes involves histones. As evolution progressed, genetic alterations accumulated and a mechanism for gene selection developed. It was as if nature was experimenting to optimally utilize the gene pool without changing individual gene sequences. This mechanism is called epigenetics, as it is above the genome. Curiously, the mechanism of epigenetic regulation in prokaryotes is strikingly different from that in eukaryotes, mainly higher eukaryotes, like mammals. In fact, epigenetics plays a significant role in the conserved process of embryogenesis and human development. Malfunction of epigenetic regulation results in many types of undesirable effects, including cardiovascular disease, metabolic disorders, autoimmune diseases, and cancer. This review provides a comparative analysis and new insights into these aspects.

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Akıl, Caner, Linh T. Tran, Magali Orhant-Prioux, Yohendran Baskaran, Edward Manser, Laurent Blanchoin, and Robert C. Robinson. "Insights into the evolution of regulated actin dynamics via characterization of primitive gelsolin/cofilin proteins from Asgard archaea." Proceedings of the National Academy of Sciences 117, no. 33 (August 3, 2020): 19904–13. http://dx.doi.org/10.1073/pnas.2009167117.

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Asgard archaea genomes contain potential eukaryotic-like genes that provide intriguing insight for the evolution of eukaryotes. The eukaryotic actin polymerization/depolymerization cycle is critical for providing force and structure in many processes, including membrane remodeling. In general, Asgard genomes encode two classes of actin-regulating proteins from sequence analysis, profilins and gelsolins. Asgard profilins were demonstrated to regulate actin filament nucleation. Here, we identify actin filament severing, capping, annealing and bundling, and monomer sequestration activities by gelsolin proteins from Thorarchaeota (Thor), which complete a eukaryotic-like actin depolymerization cycle, and indicate complex actin cytoskeleton regulation in Asgard organisms. Thor gelsolins have homologs in other Asgard archaea and comprise one or two copies of the prototypical gelsolin domain. This appears to be a record of an initial preeukaryotic gene duplication event, since eukaryotic gelsolins are generally comprise three to six domains. X-ray structures of these proteins in complex with mammalian actin revealed similar interactions to the first domain of human gelsolin or cofilin with actin. Asgard two-domain, but not one-domain, gelsolins contain calcium-binding sites, which is manifested in calcium-controlled activities. Expression of two-domain gelsolins in mammalian cells enhanced actin filament disassembly on ionomycin-triggered calcium release. This functional demonstration, at the cellular level, provides evidence for a calcium-controlled Asgard actin cytoskeleton, indicating that the calcium-regulated actin cytoskeleton predates eukaryotes. In eukaryotes, dynamic bundled actin filaments are responsible for shaping filopodia and microvilli. By correlation, we hypothesize that the formation of the protrusions observed from Lokiarchaeota cell bodies may involve the gelsolin-regulated actin structures.

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Hickey, Donal A., Bernhard F. Benkel, and Charalambos Magoulas. "Molecular biology of enzyme adaptations in higher eukaryotes." Genome 31, no. 1 (January 1, 1989): 272–83. http://dx.doi.org/10.1139/g89-045.

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Multicellular eukaryotes have evolved complex homeostatic mechanisms that buffer the majority of their cells from direct interaction with the external environment. Thus, in these organisms long-term adaptations are generally achieved by modulating the developmental profile and tissue specificity of gene expression. Nevertheless, a subset of eukaryotic genes are still involved in direct responses to environmental fluctuations. It is the adaptative responses in the expression of these genes that buffers many other genes from direct environmental effects. Both microevolutionary and macroevolutionary patterns of change in the structure and regulation of such genes are illustrated by the sequences encoding α-amylases. The molecular biology and evolution of α-amylases in Drosophila and other higher eukaryotes are presented. The amylase system illustrates the effects of both long-term and short-term natural selection, acting on both the structural and regulatory components of a gene–enzyme system. This system offers an opportunity for linking evolutionary genetics to molecular biology, and it allows us to explore the relationship between short-term microevolutionary changes and long-term adaptations.Key words: gene regulation, molecular evolution, eukaryotes, Drosophila, amylase.

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Ito, Shinsuke, Nando Dulal Das, Takashi Umehara, and Haruhiko Koseki. "Factors and Mechanisms That Influence Chromatin-Mediated Enhancer–Promoter Interactions and Transcriptional Regulation." Cancers 14, no. 21 (November 2, 2022): 5404. http://dx.doi.org/10.3390/cancers14215404.

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Eukaryotic gene expression is regulated through chromatin conformation, in which enhancers and promoters physically interact (E–P interactions). How such chromatin-mediated E–P interactions affect gene expression is not yet fully understood, but the roles of histone acetylation and methylation, pioneer transcription factors, and architectural proteins such as CCCTC binding factor (CTCF) and cohesin have recently attracted attention. Moreover, accumulated data suggest that E–P interactions are mechanistically involved in biophysical events, including liquid–liquid phase separation, and in biological events, including cancers. In this review, we discuss various mechanisms that regulate eukaryotic gene expression, focusing on emerging views regarding chromatin conformations that are involved in E–P interactions and factors that establish and maintain them.

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Corry, Gareth N., and D. Alan Underhill. "Subnuclear compartmentalization of sequence-specific transcription factors and regulation of eukaryotic gene expression." Biochemistry and Cell Biology 83, no. 4 (August 1, 2005): 535–47. http://dx.doi.org/10.1139/o05-062.

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To date, the majority of the research regarding eukaryotic transcription factors has focused on characterizing their function primarily through in vitro methods. These studies have revealed that transcription factors are essentially modular structures, containing separate regions that participate in such activities as DNA binding, protein–protein interaction, and transcriptional activation or repression. To fully comprehend the behavior of a given transcription factor, however, these domains must be analyzed in the context of the entire protein, and in certain cases the context of a multiprotein complex. Furthermore, it must be appreciated that transcription factors function in the nucleus, where they must contend with a variety of factors, including the nuclear architecture, chromatin domains, chromosome territories, and cell-cycle-associated processes. Recent examinations of transcription factors in the nucleus have clarified the behavior of these proteins in vivo and have increased our understanding of how gene expression is regulated in eukaryotes. Here, we review the current knowledge regarding sequence-specific transcription factor compartmentalization within the nucleus and discuss its impact on the regulation of such processes as activation or repression of gene expression and interaction with coregulatory factors.Key words: transcription, subnuclear localization, chromatin, gene expression, nuclear architecture.

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Wildeman, Alan G. "Regulation of SV40 early gene expression." Biochemistry and Cell Biology 66, no. 6 (June 1, 1988): 567–77. http://dx.doi.org/10.1139/o88-067.

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The early promoter of the simian virus 40 (SV40) has been used as a model eukaryotic promoter for the study of DN A sequence elements and cellular factors that are involved in transcriptional control and initiation. Site-directed mutagenesis and cell-free transcription systems have enabled the dissection of the functional domains within the 21 bp upstream sequence element and the 72 bp enhancer, and a number of protein factors that bind to various "motifs" within these domains have been identified. This article summarizes recent observations that have led to the conclusion that the SV40 promoter, and particularly, the enhancer region, is composed of multiple sequence elements. Some of these elements are present in cellular genes, and may exhibit tissue-specificity in their action. Furthermore, the proteins that are being identified (e.g., Sp1) may have binding sites within these elements that are sufficiently specific to ensure that only certain sets of genes will be selectively expressed.

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Tuteja, Renu, Abulaish Ansari, and Virander Singh Chauhan. "Emerging Functions of Transcription Factors in Malaria Parasite." Journal of Biomedicine and Biotechnology 2011 (2011): 1–6. http://dx.doi.org/10.1155/2011/461979.

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Transcription is a process by which the genetic information stored in DNA is converted into mRNA by enzymes known as RNA polymerase. Bacteria use only one RNA polymerase to transcribe all of its genes while eukaryotes contain three RNA polymerases to transcribe the variety of eukaryotic genes. RNA polymerase also requires other factors/proteins to produce the transcript. These factors generally termed as transcription factors (TFs) are either associated directly with RNA polymerase or add in building the actual transcription apparatus. TFs are the most common tools that our cells use to control gene expression.Plasmodium falciparumis responsible for causing the most lethal form of malaria in humans. It shows most of its characteristics common to eukaryotic transcription but it is assumed that mechanisms of transcriptional control inP. falciparumsomehow differ from those of other eukaryotes. In this article we describe the studies on the main TFs such as myb protein, high mobility group protein and ApiA2 family proteins from malaria parasite. These studies show that these TFs are slowly emerging to have defined roles in the regulation of gene expression in the parasite.

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Tran, Nham, and Gyorgy Hutvagner. "Biogenesis and the regulation of the maturation of miRNAs." Essays in Biochemistry 54 (April 30, 2013): 17–28. http://dx.doi.org/10.1042/bse0540017.

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Regulation of gene expression is a fundamental process in both prokaryotic and eukaryotic organisms. Multiple regulatory mechanisms are in place to control gene expression at the level of transcription, post-transcription and post-translation to maintain optimal RNA and protein expressions in cells. miRNAs (microRNAs) are abundant short 21–23 nt non-coding RNAs that are key regulators of virtually all eukaryotic biological processes. The levels of miRNAs in an organism are crucial for proper development and sustaining optimal cell functions. Therefore the processing and regulation of the processing of these miRNAs are critical. In the present chapter we highlight the most important steps of miRNA processing, describe the functions of key proteins involved in the maturation of miRNAs, and discuss how the generation and the stability of miRNAs are regulated.

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Naro, Chiara, and Claudio Sette. "Phosphorylation-Mediated Regulation of Alternative Splicing in Cancer." International Journal of Cell Biology 2013 (2013): 1–15. http://dx.doi.org/10.1155/2013/151839.

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Alternative splicing (AS) is one of the key processes involved in the regulation of gene expression in eukaryotic cells. AS catalyzes the removal of intronic sequences and the joining of selected exons, thus ensuring the correct processing of the primary transcript into the mature mRNA. The combinatorial nature of AS allows a great expansion of the genome coding potential, as multiple splice-variants encoding for different proteins may arise from a single gene. Splicing is mediated by a large macromolecular complex, the spliceosome, whose activity needs a fine regulation exerted bycis-acting RNA sequence elements andtrans-acting RNA binding proteins (RBP). The activity of both core spliceosomal components and accessory splicing factors is modulated by their reversible phosphorylation. The kinases and phosphatases involved in these posttranslational modifications significantly contribute to AS regulation and to its integration in the complex regulative network that controls gene expression in eukaryotic cells. Herein, we will review the major canonical and noncanonical splicing factor kinases and phosphatases, focusing on those whose activity has been implicated in the aberrant splicing events that characterize neoplastic transformation.

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Catacalos, Cassandra, Alexander Krohannon, Sahiti Somalraju, Kate D. Meyer, Sarath Chandra Janga, and Kausik Chakrabarti. "Epitranscriptomics in parasitic protists: Role of RNA chemical modifications in posttranscriptional gene regulation." PLOS Pathogens 18, no. 12 (December 22, 2022): e1010972. http://dx.doi.org/10.1371/journal.ppat.1010972.

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“Epitranscriptomics” is the new RNA code that represents an ensemble of posttranscriptional RNA chemical modifications, which can precisely coordinate gene expression and biological processes. There are several RNA base modifications, such as N6-methyladenosine (m6A), 5-methylcytosine (m5C), and pseudouridine (Ψ), etc. that play pivotal roles in fine-tuning gene expression in almost all eukaryotes and emerging evidences suggest that parasitic protists are no exception. In this review, we primarily focus on m6A, which is the most abundant epitranscriptomic mark and regulates numerous cellular processes, ranging from nuclear export, mRNA splicing, polyadenylation, stability, and translation. We highlight the universal features of spatiotemporal m6A RNA modifications in eukaryotic phylogeny, their homologs, and unique processes in 3 unicellular parasites—Plasmodium sp., Toxoplasma sp., and Trypanosoma sp. and some technological advances in this rapidly developing research area that can significantly improve our understandings of gene expression regulation in parasites.

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Pranckeviciene, Erinija, Sergey Hosid, Indiras Maziukas, and Ilya Ioshikhes. "Galaxy Dnpatterntools for Computational Analysis of Nucleosome Positioning Sequence Patterns." International Journal of Molecular Sciences 23, no. 9 (April 28, 2022): 4869. http://dx.doi.org/10.3390/ijms23094869.

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Nucleosomes are basic units of DNA packing in eukaryotes. Their structure is well conserved from yeast to human and consists of the histone octamer core and 147 bp DNA wrapped around it. Nucleosomes are bound to a majority of the eukaryotic genomic DNA, including its regulatory regions. Hence, they also play a major role in gene regulation. For the latter, their precise positioning on DNA is essential. In the present paper, we describe Galaxy dnpatterntools—software package for nucleosome DNA sequence analysis and mapping. This software will be useful for computational biologists practitioners to conduct more profound studies of gene regulatory mechanisms.

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Ray, Swagat, Pól Ó. Catnaigh, and Emma C. Anderson. "Post-transcriptional regulation of gene expression by Unr." Biochemical Society Transactions 43, no. 3 (June 1, 2015): 323–27. http://dx.doi.org/10.1042/bst20140271.

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Unr (upstream of N-ras) is a eukaryotic RNA-binding protein that has a number of roles in the post-transcriptional regulation of gene expression. Originally identified as an activator of internal initiation of picornavirus translation, it has since been shown to act as an activator and inhibitor of cellular translation and as a positive and negative regulator of mRNA stability, regulating cellular processes such as mitosis and apoptosis. The different post-transcriptional functions of Unr depend on the identity of its mRNA and protein partners and can vary with cell type and changing cellular conditions. Recent high-throughput analyses of RNA–protein interactions indicate that Unr binds to a large subset of cellular mRNAs, suggesting that Unr may play a wider role in translational responses to cellular signals than previously thought.

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Yurimoto, Hiroya, Masahide Oku, and Yasuyoshi Sakai. "Yeast Methylotrophy: Metabolism, Gene Regulation and Peroxisome Homeostasis." International Journal of Microbiology 2011 (2011): 1–8. http://dx.doi.org/10.1155/2011/101298.

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Eukaryotic methylotrophs, which are able to obtain all the carbon and energy needed for growth from methanol, are restricted to a limited number of yeast species. When these yeasts are grown on methanol as the sole carbon and energy source, the enzymes involved in methanol metabolism are strongly induced, and the membrane-bound organelles, peroxisomes, which contain key enzymes of methanol metabolism, proliferate massively. These features have made methylotrophic yeasts attractive hosts for the production of heterologous proteins and useful model organisms for the study of peroxisome biogenesis and degradation. In this paper, we describe recent insights into the molecular basis of yeast methylotrophy.

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Pavitt, G. D. "eIF2B, a mediator of general and gene-specific translational control." Biochemical Society Transactions 33, no. 6 (October 26, 2005): 1487–92. http://dx.doi.org/10.1042/bst0331487.

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eIF2B (eukaryotic initiation factor 2B) is a multisubunit protein that is required for protein synthesis initiation and its regulation in all eukaryotic cells. Mutations in eIF2B have also recently been found to cause a fatal human disease called CACH (childhood ataxia with central nervous system hypomyelination) or VWM (vanishing white matter disease). This review provides a general background to translation initiation and mechanisms known to control eIF2B function, before describing molecular genetic and biochemical analysis of eIF2B structure and function, integrating work from studies of the yeast and mammalian eIF2B proteins.

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Szweykowska-Kulińska, Zofia, Artur Jarmołowski, and Marek Figlerowicz. "RNA interference and its role in the regulation of eucaryotic gene expression." Acta Biochimica Polonica 50, no. 1 (March 31, 2003): 217–29. http://dx.doi.org/10.18388/abp.2003_3730.

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Several years ago it was discovered that plant transformation with a transcribed sense transgene could shut down the expression of a homologous endogenous gene. Moreover, it was shown that the introduction into the cell of dsRNA (double-stranded RNA) containing nucleotide sequence complementary to an mRNA sequence causes selective degradation of the latter and thus silencing of a specific gene. This phenomenon, called RNA interference (RNAi) was demonstrated to be present in almost all eukaryotic organisms. RNAi is also capable of silencing transposons in germ line cells and fighting RNA virus infection. Enzymes involved in this process exhibit high homology across species. Some of these enzymes are involved in other cellular processes, for instance developmental timing, suggesting strong interconnections between RNAi and other metabolic pathways. RNAi is probably an ancient mechanism that evolved to protect eukaryotic cells against invasive forms of nucleic acids.

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Zhang, Yan Jessie. "CTD Code: a Combinatorial Code for Eukaryotic Transcription." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C1829. http://dx.doi.org/10.1107/s2053273314081716.

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In eukaryotes, the C-terminal domain of RNA polymerase II (CTD) orchestrates the temporal and spatial control of transcription and is involved in the epigenetic regulation of gene expression. Errors in CTD regulation can result in cell death, cancer and severe developmental defects. The CTD executes its function as transcription modulator through various post-translational modifications on its heptad repeat sequences. Recently, novel modifications on new regulatory sites of CTD have been identified, setting the stage for the possibility of combinatorial mechanisms for transcription regulation. We focused on two well-characterized modification of CTD, namely serine phosphorylation and prolyl isomerization, and discuss the interplay between the enzymes regulating these modification states. Our results established that the selectivity of prolyl isomerization state of CTD on phosphatases can lead to differentiated outcome for the CTD phosphorylation state and therefore, transcription. To further investigate the prolyl selectivity, we developed chemical compounds that can be used to probe such subtle structural variation in the CTD binding proteins. These compounds closely mimic the cis or trans proline state and can be effectively recognized by CTD phosphatases. The application of such chemical probes can help us understand the molecular mechanism of the interplay between phosphorylation and prolyl isomerization state and how that affect the conformational status of CTD in transcription temporally and spatially.

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Gao, Bei, Moxian Chen, and Melvin J. Oliver. "Alternative Splicing: From Abiotic Stress Tolerance to Evolutionary Genomics." International Journal of Molecular Sciences 24, no. 7 (April 4, 2023): 6708. http://dx.doi.org/10.3390/ijms24076708.

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King, Ross D., and Chuan Lu. "An investigation into eukaryotic pseudouridine synthases." Journal of Bioinformatics and Computational Biology 12, no. 04 (August 2014): 1450015. http://dx.doi.org/10.1142/s0219720014500152.

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A common post-transcriptional modification of RNA is the conversion of uridine to its isomer pseudouridine. We investigated the biological significance of eukaryotic pseudouridine synthases using the yeast Saccharomyces cerevisiae. We conducted a comprehensive statistical analysis on growth data from automated perturbation (gene deletion) experiments, and used bi-logistic curve analysis to characterise the yeast phenotypes. The deletant strains displayed different alteration in growth properties, including in some cases enhanced growth and/or biphasic growth curves not seen in wild-type strains under matched conditions. These results demonstrate that disrupting pseudouridine synthases can have a significant qualitative effect on growth. We further investigated the significance of post-transcriptional pseudouridine modification through investigation of the scientific literature. We found that (1) In Toxoplasma gondii, a pseudouridine synthase gene is critical in cellular differentiation between the two asexual forms: Tachyzoites and bradyzoites; (2) Mutation of pseudouridine synthase genes has also been implicated in human diseases (mitochondrial myopathy and sideroblastic anemia (MLASA); dyskeratosis congenita). Taken together, these results are consistent with pseudouridine synthases having a Gene Ontology function of "biological regulation".

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MONTALVETTI, Andrea, Javier PE±A-DÍAZ, Ramón HURTADO, Luis Miguel RUIZ-PÉREZ, and Dolores GONZÁLEZ-PACANOWSKA. "Characterization and regulation of Leishmania major 3-hydroxy-3-methylglutaryl-CoA reductase." Biochemical Journal 349, no. 1 (June 26, 2000): 27–34. http://dx.doi.org/10.1042/bj3490027.

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In eukaryotes the enzyme 3-hydroxy-3-methylglutaryl CoA (HMG-CoA) reductase catalyses the synthesis of mevalonic acid, a common precursor to all isoprenoid compounds. Here we report the isolation and overexpression of the gene coding for HMG-CoA reductase from Leishmania major. The protein from Leishmania lacks the membrane domain characteristic of eukaryotic cells but exhibits sequence similarity with eukaryotic reductases. Highly purified protein was achieved by ammonium sulphate precipitation followed by chromatography on hydroxyapatite. Kinetic parameters were determined for the protozoan reductase, obtaining Km values for the overall reaction of 40.3±5.8 μM for (R,S)-HMG-CoA and 81.4±5.3 μM for NADPH; Vmax was 33.55±1.8 units·mg-1. Gel-filtration experiments suggested an apparent molecular mass of 184 kDa with subunits of 46 kDa. Finally, in order to achieve a better understanding of the role of this enzyme in trypanosomatids, the effect of possible regulators of isoprenoid biosynthesis in cultured promastigote cells was studied. Neither mevalonic acid nor serum sterols appear to modulate enzyme activity whereas incubation with lovastatin results in significant increases in the amount of reductase protein. Western- and Northern-blot analyses indicate that this activation is apparently performed via post-transcriptional control.

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Barrett, Lucy W., Sue Fletcher, and Steve D. Wilton. "Regulation of eukaryotic gene expression by the untranslated gene regions and other non-coding elements." Cellular and Molecular Life Sciences 69, no. 21 (April 27, 2012): 3613–34. http://dx.doi.org/10.1007/s00018-012-0990-9.

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Di Timoteo, Gaia, Francesca Rossi, and Irene Bozzoni. "Circular RNAs in cell differentiation and development." Development 147, no. 16 (August 15, 2020): dev182725. http://dx.doi.org/10.1242/dev.182725.

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ABSTRACTIn recent years, circular RNAs (circRNAs) – a novel class of RNA molecules characterized by their covalently closed circular structure – have emerged as a complex family of eukaryotic transcripts with important biological features. Besides their peculiar structure, which makes them particularly stable molecules, they have attracted much interest because their expression is strongly tissue and cell specific. Moreover, many circRNAs are conserved across eukaryotes, localized in particular subcellular compartments, and can play disparate molecular functions. The discovery of circRNAs has therefore added not only another layer of gene expression regulation but also an additional degree of complexity to our understanding of the structure, function and evolution of eukaryotic genomes. In this Review, we summarize current knowledge of circRNAs and discuss the possible functions of circRNAs in cell differentiation and development.

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Wild, Gary E., Patrizia Papalia, Mark J. Ropeleski, Julio Faria, and Alan BR Thomson. "Applications of Recombinant Dna Technology in Gastrointestinal Medicine and Hepatology: Basic Paradigms of Molecular Cell Biology. Part B: Eukaryotic Gene Transcription and Post-Transcripional Rna Processing." Canadian Journal of Gastroenterology 14, no. 4 (2000): 283–92. http://dx.doi.org/10.1155/2000/385327.

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The transcription of DNA into RNA is the primary level at which gene expression is controlled in eukaryotic cells. Eukaryotic gene transcription involves several different RNA polymerases that interact with a host of transcription factors to initiate transcription. Genes that encode proteins are transcribed into messenger RNA (mRNA) by RNA polymerase II. Ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs) are transcribed by RNA polymerase I and III, respectively. The production of each mRNA in human cells involves complex interactions of proteins (ie, trans-acting factors) with specific sequences on the DNA (ie, cis-acting elements). Cis-acting elements are short base sequences adjacent to or within a particular gene. While the regulation of transcription is a pivotal step in the control of gene expression, a variety of molecular events, collectively known as ’RNA processing’ add an additional level of control of gene expression in eukaryotic cells.

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Journal articles on the topic 'Eukaryotic gene regulation'

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