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Thematische Bibliographien / Targeted transcription regulation / Zeitschriftenartikel

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Zeitschriftenartikel zum Thema „Targeted transcription regulation“

Autor: Grafiati

Veröffentlicht am 25. Mai 2024

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1

Braun, Christian J., Peter M. Bruno, Max A. Horlbeck, Luke A. Gilbert, Jonathan S. Weissman, and Michael T. Hemann. "Versatile in vivo regulation of tumor phenotypes by dCas9-mediated transcriptional perturbation." Proceedings of the National Academy of Sciences 113, no. 27 (2016): E3892—E3900. http://dx.doi.org/10.1073/pnas.1600582113.

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Targeted transcriptional regulation is a powerful tool to study genetic mediators of cellular behavior. Here, we show that catalytically dead Cas9 (dCas9) targeted to genomic regions upstream or downstream of the transcription start site allows for specific and sustainable gene-expression level alterations in tumor cells in vitro and in syngeneic immune-competent mouse models. We used this approach for a high-coverage pooled gene-activation screen in vivo and discovered previously unidentified modulators of tumor growth and therapeutic response. Moreover, by using dCas9 linked to an activation

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Li, Conghui, Honghong Wang, Zhinang Yin, et al. "Ligand-induced native G-quadruplex stabilization impairs transcription initiation." Genome Research 31, no. 9 (2021): 1546–60. http://dx.doi.org/10.1101/gr.275431.121.

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G-quadruplexes (G4s) are noncanonical DNA secondary structures formed through the self-association of guanines, and G4s are distributed widely across the genome. G4 participates in multiple biological processes including gene transcription, and G4-targeted ligands serve as potential therapeutic agents for DNA-targeted therapies. However, genome-wide studies of the exact roles of G4s in transcriptional regulation are still lacking. Here, we establish a sensitive G4-CUT&Tag method for genome-wide profiling of native G4s with high resolution and specificity. We find that native G4 signals are

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Ahmed, Mahmoud, Trang Huyen Lai, Trang Minh Pham, et al. "Hierarchical regulation of autophagy during adipocyte differentiation." PLOS ONE 17, no. 1 (2022): e0250865. http://dx.doi.org/10.1371/journal.pone.0250865.

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We previously showed that some adipogenic transcription factors such as CEBPB and PPARG directly and indirectly regulate autophagy gene expression in adipogenesis. The order and effect of these events are undetermined. In this study, we modeled the gene expression, DNA-binding of transcriptional regulators, and histone modifications during adipocyte differentiation and evaluated the effect of the regulators on gene expression in terms of direction and magnitude. Then, we identified the overlap of the transcription factors and co-factors binding sites and targets. Finally, we built a chromatin

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Scott, James N. F., Adam P. Kupinski, and Joan Boyes. "Targeted genome regulation and modification using transcription activator-like effectors." FEBS Journal 281, no. 20 (2014): 4583–97. http://dx.doi.org/10.1111/febs.12973.

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5

Huh, Hyunbin, Dong Kim, Han-Sol Jeong, and Hyun Park. "Regulation of TEAD Transcription Factors in Cancer Biology." Cells 8, no. 6 (2019): 600. http://dx.doi.org/10.3390/cells8060600.

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Transcriptional enhanced associate domain (TEAD) transcription factors play important roles during development, cell proliferation, regeneration, and tissue homeostasis. TEAD integrates with and coordinates various signal transduction pathways including Hippo, Wnt, transforming growth factor beta (TGFβ), and epidermal growth factor receptor (EGFR) pathways. TEAD deregulation affects well-established cancer genes such as KRAS, BRAF, LKB1, NF2, and MYC, and its transcriptional output plays an important role in tumor progression, metastasis, cancer metabolism, immunity, and drug resistance. To da

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Uprety, Bhawana, Amala Kaja, Jannatul Ferdoush, Rwik Sen, and Sukesh R. Bhaumik. "Regulation of Antisense Transcription by NuA4 Histone Acetyltransferase and Other Chromatin Regulatory Factors." Molecular and Cellular Biology 36, no. 6 (2016): 992–1006. http://dx.doi.org/10.1128/mcb.00808-15.

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NuA4 histone lysine (K) acetyltransferase (KAT) promotes transcriptional initiation of TATA-binding protein (TBP)-associated factor (TAF)-dependent ribosomal protein genes. TAFs have also been recently found to enhance antisense transcription from the 3′ end of theGAL10coding sequence. However, it remains unknown whether, like sense transcription of the ribosomal protein genes, TAF-dependent antisense transcription ofGAL10also requires NuA4 KAT. Here, we show that NuA4 KAT associates with theGAL10antisense transcription initiation site at the 3′ end of the coding sequence. Such association of

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Perez-Oquendo, Mabel, and Don L. Gibbons. "Regulation of ZEB1 Function and Molecular Associations in Tumor Progression and Metastasis." Cancers 14, no. 8 (2022): 1864. http://dx.doi.org/10.3390/cancers14081864.

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Zinc finger E-box binding homeobox 1 (ZEB1) is a pleiotropic transcription factor frequently expressed in carcinomas. ZEB1 orchestrates the transcription of genes in the control of several key developmental processes and tumor metastasis via the epithelial-to-mesenchymal transition (EMT). The biological function of ZEB1 is regulated through pathways that influence its transcription and post-transcriptional mechanisms. Diverse signaling pathways converge to induce ZEB1 activity; however, only a few studies have focused on the molecular associations or functional changes of ZEB1 by post-translat

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Imoberdorf, Rachel Maria, Irini Topalidou, and Michel Strubin. "A Role for Gcn5-Mediated Global Histone Acetylation in Transcriptional Regulation." Molecular and Cellular Biology 26, no. 5 (2006): 1610–16. http://dx.doi.org/10.1128/mcb.26.5.1610-1616.2006.

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ABSTRACT Transcriptional activators often require histone acetyltransferases (HATs) for full activity. The common explanation is that activators directly recruit HATs to gene promoters to locally hyperacetylate histones and thereby facilitate transcription complex formation. However, in addition to being targeted to specific loci, HATs such as Gcn5 also modify histones genome-wide. Here we provide evidence for a role of this global HAT activity in regulated transcription. We show that activation by direct recruitment of the transcriptional machinery neither recruits Gcn5 nor induces changes in

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Nourani, Amine, Yannick Doyon, Rhea T. Utley, Stéphane Allard, William S. Lane, and Jacques Côté. "Role of an ING1 Growth Regulator in Transcriptional Activation and Targeted Histone Acetylation by the NuA4 Complex." Molecular and Cellular Biology 21, no. 22 (2001): 7629–40. http://dx.doi.org/10.1128/mcb.21.22.7629-7640.2001.

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ABSTRACT The yeast NuA4 complex is a histone H4 and H2A acetyltransferase involved in transcription regulation and essential for cell cycle progression. We identify here a novel subunit of the complex, Yng2p, a plant homeodomain (PHD)-finger protein homologous to human p33/ING1, which has tumor suppressor activity and is essential for p53 function. Mass spectrometry, immunoblotting, and immunoprecipitation experiments confirm the stable stoichiometric association of this protein with purified NuA4. Yeast cells harboring a deletion of theYNG2 gene show severe growth phenotype and have gene-spec

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Zhang, Yixin, Yanlan Mo, Liyuan Han, Zhenyuan Sun, and Wenzhong Xu. "Exploring Transcriptional Regulation of Hyperaccumulation in Sedum plumbizincicola through Integrated Transcriptome Analysis and CRISPR/Cas9 Technology." International Journal of Molecular Sciences 24, no. 14 (2023): 11845. http://dx.doi.org/10.3390/ijms241411845.

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The cadmium hyperaccumulator Sedum plumbizincicola has remarkable abilities for cadmium (Cd) transport, accumulation and detoxification, but the transcriptional regulation mechanisms responsible for its Cd hyperaccumulation remain unknown. To address this knowledge gap, we conducted a comparative transcriptome study between S. plumbizincicola and the non-hyperaccumulating ecotype (NHE) of Sedum alfredii with or without Cd treatment. Our results revealed many differentially expressed genes involved in heavy metal transport and detoxification that were abundantly expressed in S. plumbizincicola.

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Liu, Liu, Shasha Yin, Charles Brobbey, and Wenjian Gan. "Ubiquitination in cancer stem cell: roles and targeted cancer therapy." STEMedicine 1, no. 3 (2020): e37. http://dx.doi.org/10.37175/stemedicine.v1i3.37.

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Cancer stem cells (CSCs) are a small subset of stem-like cells inside tumors, which possess abilities of unlimited self-renewal, differentiation and proliferation. Extensive studies have suggested that CSCs are one of the major drivers of tumor initiation, metastasis, relapse and therapeutic resistance. Several regulatory networks including transcriptional programs and various signaling pathways tightly control the stemness, proliferation and differentiation of CSCs. Emerging evidence has indicated that post-translational modifications, especially ubiquitination, play a critical role in mainte

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Chapman, Brittany, Jeong Hoon Han, Hong Jo Lee, Isabella Ruud, and Tae Hyun Kim. "Targeted Modulation of Chicken Genes In Vitro Using CRISPRa and CRISPRi Toolkit." Genes 14, no. 4 (2023): 906. http://dx.doi.org/10.3390/genes14040906.

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Engineering of clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-associated protein 9 (Cas9) system has enabled versatile applications of CRISPR beyond targeted DNA cleavage. Combination of nuclease-deactivated Cas9 (dCas9) and transcriptional effector domains allows activation (CRISPRa) or repression (CRISPRi) of target loci. To demonstrate the effectiveness of the CRISPR-mediated transcriptional regulation in chickens, three CRISPRa (VP64, VPR, and p300) and three CRISPRi (dCas9, dCas9-KRAB, and dCas9-KRAB-MeCP2) systems were tested in chicken DF-1 cells. By i

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Jouvenot, Y., V. Ginjala, L. Zhang, et al. "Targeted regulation of imprinted genes by synthetic zinc-finger transcription factors." Gene Therapy 10, no. 6 (2003): 513–22. http://dx.doi.org/10.1038/sj.gt.3301930.

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14

Porter, Baylee A., Maria A. Ortiz, Gennady Bratslavsky, and Leszek Kotula. "Structure and Function of the Nuclear Receptor Superfamily and Current Targeted Therapies of Prostate Cancer." Cancers 11, no. 12 (2019): 1852. http://dx.doi.org/10.3390/cancers11121852.

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The nuclear receptor superfamily comprises a large group of proteins with functions essential for cell signaling, survival, and proliferation. There are multiple distinctions between nuclear superfamily classes defined by hallmark differences in function, ligand binding, tissue specificity, and DNA binding. In this review, we utilize the initial classification system, which defines subfamilies based on structure and functional difference. The defining feature of the nuclear receptor superfamily is that these proteins function as transcription factors. The loss of transcriptional regulation or

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Aranda, Sergi, Gloria Mas, and Luciano Di Croce. "Regulation of gene transcription by Polycomb proteins." Science Advances 1, no. 11 (2015): e1500737. http://dx.doi.org/10.1126/sciadv.1500737.

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The Polycomb group (PcG) of proteins defines a subset of factors that physically associate and function to maintain the positional identity of cells from the embryo to adult stages. PcG has long been considered a paradigmatic model for epigenetic maintenance of gene transcription programs. Despite intensive research efforts to unveil the molecular mechanisms of action of PcG proteins, several fundamental questions remain unresolved: How many different PcG complexes exist in mammalian cells? How are PcG complexes targeted to specific loci? How does PcG regulate transcription? In this review, we

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Perrella, Giorgio, Mhairi L. H. Davidson, Liz O’Donnell, et al. "ZINC-FINGER interactions mediate transcriptional regulation of hypocotyl growth in Arabidopsis." Proceedings of the National Academy of Sciences 115, no. 19 (2018): E4503—E4511. http://dx.doi.org/10.1073/pnas.1718099115.

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Integration of environmental signals and interactions among photoreceptors and transcriptional regulators is key in shaping plant development. TANDEM ZINC-FINGER PLUS3 (TZP) is an integrator of light and photoperiodic signaling that promotes flowering in Arabidopsis thaliana. Here we elucidate the molecular role of TZP as a positive regulator of hypocotyl elongation. We identify an interacting partner for TZP, the transcription factor ZINC-FINGER HOMEODOMAIN 10 (ZFHD10), and characterize its function in coregulating the expression of blue-light–dependent transcriptional regulators and growth-p

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Shao, Jiawei, Meiyan Wang, Guiling Yu, et al. "Synthetic far-red light-mediated CRISPR-dCas9 device for inducing functional neuronal differentiation." Proceedings of the National Academy of Sciences 115, no. 29 (2018): E6722—E6730. http://dx.doi.org/10.1073/pnas.1802448115.

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The ability to control the activity of CRISPR-dCas9 with precise spatiotemporal resolution will enable tight genome regulation of user-defined endogenous genes for studying the dynamics of transcriptional regulation. Optogenetic devices with minimal phototoxicity and the capacity for deep tissue penetration are extremely useful for precise spatiotemporal control of cellular behavior and for future clinic translational research. Therefore, capitalizing on synthetic biology and optogenetic design principles, we engineered a far-red light (FRL)-activated CRISPR-dCas9 effector (FACE) device that i

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Chuang, Kai-Ting, Shyh-Shin Chiou, and Shih-Hsien Hsu. "Recent Advances in Transcription Factors Biomarkers and Targeted Therapies Focusing on Epithelial–Mesenchymal Transition." Cancers 15, no. 13 (2023): 3338. http://dx.doi.org/10.3390/cancers15133338.

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Transcription factors involve many proteins in the process of transactivating or transcribing (none-) encoded DNA to initiate and regulate downstream signals, such as RNA polymerase. Their unique characteristic is that they possess specific domains that bind to specific DNA element sequences called enhancer or promoter sequences. Epithelial–mesenchymal transition (EMT) is involved in cancer progression. Many dysregulated transcription factors—such as Myc, SNAIs, Twists, and ZEBs—are key drivers of tumor metastasis through EMT regulation. This review summarizes currently available evidence rela

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Hirsch, Matthew, and Thomas Elliott. "Stationary-Phase Regulation of RpoS Translation in Escherichia coli." Journal of Bacteriology 187, no. 21 (2005): 7204–13. http://dx.doi.org/10.1128/jb.187.21.7204-7213.2005.

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ABSTRACT In enteric bacteria, adaptation to a number of different stresses is mediated by the RpoS protein, one of several sigma factors that collectively allow a tailored transcriptional response to environmental cues. Stress stimuli including low temperature, osmotic shock, nutrient limitation, and growth to stationary phase (SP) all result in a substantial increase in RpoS abundance and activity. The mechanism of regulation depends on the specific signal but may occur at the level of transcription, translation, protein activity, or targeted proteolysis. In both Escherichia coli and Salmonel

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Neely, Lori A., and Charles S. Hoffman. "Protein Kinase A and Mitogen-Activated Protein Kinase Pathways Antagonistically Regulate Fission Yeast fbp1Transcription by Employing Different Modes of Action at Two Upstream Activation Sites." Molecular and Cellular Biology 20, no. 17 (2000): 6426–34. http://dx.doi.org/10.1128/mcb.20.17.6426-6434.2000.

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ABSTRACT A significant challenge to our understanding of eukaryotic transcriptional regulation is to determine how multiple signal transduction pathways converge on a single promoter to regulate transcription in divergent fashions. To study this, we have investigated the transcriptional regulation of theSchizosaccharomyces pombe fbp1 gene that is repressed by a cyclic AMP (cAMP)-dependent protein kinase A (PKA) pathway and is activated by a stress-activated mitogen-activated protein kinase (MAPK) pathway. In this study, we identified and characterized twocis-acting elements in the fbp1 promote

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Luikenhuis, Sandra, Anton Wutz, and Rudolf Jaenisch. "Antisense Transcription through theXist Locus Mediates Tsix Function in Embryonic Stem Cells." Molecular and Cellular Biology 21, no. 24 (2001): 8512–20. http://dx.doi.org/10.1128/mcb.21.24.8512-8520.2001.

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ABSTRACT Expression of the Xist gene, a key player in mammalian X inactivation, has been proposed to be controlled by the antisense Tsix transcript. Targeted deletion of theTsix promoter encompassing the DPXas34 locus leads to nonrandom inactivation of the mutant X, but it remains unresolved whether this phenotype is caused by loss of Tsixtranscription or by deletion of a crucial DNA element. In this study we determined the role of Tsix transcription in random X inactivation by using mouse embryonic stem (ES) cells as a model system. Two approaches were chosen to modulate Tsixtranscription wit

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Jacobson, Sandra, and Lorraine Pillus. "Molecular Requirements for Gene Expression Mediated by Targeted Histone Acetyltransferases." Molecular and Cellular Biology 24, no. 13 (2004): 6029–39. http://dx.doi.org/10.1128/mcb.24.13.6029-6039.2004.

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ABSTRACT Histone acetyltransferases (HATs) play fundamental roles in regulating gene expression. HAT complexes with distinct subunit composition and substrate specificity act on chromatin-embedded genes with different promoter architecture and chromosomal locations. Because requirements for HAT complexes vary, a central question in transcriptional regulation is how different HAT complexes function in different chromosomal contexts. Here, we have tested the ability of targeted yeast HATs to regulate gene expression of an epigenetically silenced locus. Of a panel of HAT fusion proteins targeted

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Shen, Hongtao, Jing Li, Xiujie Xie, et al. "BRD2 regulation of sigma-2 receptor upon cholesterol deprivation." Life Science Alliance 4, no. 1 (2020): e201900540. http://dx.doi.org/10.26508/lsa.201900540.

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The sigma-2 receptor (S2R) has long been pharmacologically targeted for antipsychotic treatment and tumor imaging. Only recently was it known for its coding gene and for its role implicated in cholesterol homeostasis. Here, we have investigated the transcriptional control of S2R by the Bromo/ExtraTerminal epigenetic reader family (BETs, including BRD2, 3, and 4) upon cholesterol perturbation. Cholesterol deprivation was induced in ARPE19 cells using a blocker of lysosomal cholesterol export. This condition up-regulated S2R mRNA and protein, and also SREBP2 but not SREBP1, both transcription fa

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Wiggins, Amanda K., Guangwei Wei, Epaminondas Doxakis, et al. "Interaction of Brn3a and HIPK2 mediates transcriptional repression of sensory neuron survival." Journal of Cell Biology 167, no. 2 (2004): 257–67. http://dx.doi.org/10.1083/jcb.200406131.

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The Pit1-Oct1-Unc86 domain (POU domain) transcription factor Brn3a controls sensory neuron survival by regulating the expression of Trk receptors and members of the Bcl-2 family. Loss of Brn3a leads to a dramatic increase in apoptosis and severe loss of neurons in sensory ganglia. Although recent evidence suggests that Brn3a-mediated transcription can be modified by additional cofactors, the exact mechanisms are not known. Here, we report that homeodomain interacting protein kinase 2 (HIPK2) is a pro-apoptotic transcriptional cofactor that suppresses Brn3a-mediated gene expression. HIPK2 inter

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Osburn, Deborah L., Gang Shao, H. Martin Seidel, and Ira G. Schulman. "Ligand-Dependent Degradation of Retinoid X Receptors Does Not Require Transcriptional Activity or Coactivator Interactions." Molecular and Cellular Biology 21, no. 15 (2001): 4909–18. http://dx.doi.org/10.1128/mcb.21.15.4909-4918.2001.

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ABSTRACT Cells utilize ubiquitin-mediated proteolysis to regulate the activity of numerous proteins involved in signal transduction, cell cycle control, and transcriptional regulation. For a number of transcription factors, there appears to be a direct correlation between transcriptional activity and protein instability, suggesting that cells use targeted destruction as one method to down-regulate or attenuate gene expression. In this report we demonstrate that retinoid X receptors (RXRs) which function as versatile mediators of nuclear hormone-dependent gene expression are marked for destruct

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Zhang, Xinyue, Jieyu Guo, Xiangxiang Wei, et al. "Bach1: Function, Regulation, and Involvement in Disease." Oxidative Medicine and Cellular Longevity 2018 (October 2, 2018): 1–8. http://dx.doi.org/10.1155/2018/1347969.

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The transcription factor BTB and CNC homology 1 (Bach1) is widely expressed in most mammalian tissues and functions primarily as a transcriptional suppressor by heterodimerizing with small Maf proteins and binding to Maf recognition elements in the promoters of targeted genes. It has a key regulatory role in the production of reactive oxygen species, cell cycle, heme homeostasis, hematopoiesis, and immunity and has been shown to suppress ischemic angiogenesis and promote breast cancer metastasis. This review summarizes how Bach1 controls these and other cellular and physiological and pathologi

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Omelina, E. S., and A. V. Pindyurin. "Optogenetic regulation of endogenous gene transcription in mammals." Vavilov Journal of Genetics and Breeding 23, no. 2 (2019): 219–25. http://dx.doi.org/10.18699/vj19.485.

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Despite the rapid development of approaches aimed to precisely control transcription of exogenous genes in time and space, design of systems providing similar tight regulation of endogenous gene expression is much more challenging. However, finding ways to control the activity of endogenous genes is absolutely necessary for further progress in safe and effective gene therapies and regenerative medicine. In addition, such systems are of particular interest for genetics, molecular and cell biology. An ideal system should ensure tunable and reversible spatio-temporal control over transcriptional

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Shih, H. M., C. C. Chang, H. Y. Kuo, and D. Y. Lin. "Daxx mediates SUMO-dependent transcriptional control and subnuclear compartmentalization." Biochemical Society Transactions 35, no. 6 (2007): 1397–400. http://dx.doi.org/10.1042/bst0351397.

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SUMO (small ubiquitin-related modifier) modification is emerging as an important post-translational control in transcription. In general, SUMO modification is associated with transcriptional repression. Although many SUMO-modified transcription factors and co-activators have been identified, little is known about the mechanism underlying SUMOylation-elicited transcriptional repression. Here, we summarize that SUMO modification of transcription factors such as androgen receptor, glucocorticoid receptor, Smad4 and CBP [CREB (cAMP-response-element-binding protein)-binding protein] co-activator re

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Yu, Le, Ian J. Davis, and Pengda Liu. "Regulation of EWSR1-FLI1 Function by Post-Transcriptional and Post-Translational Modifications." Cancers 15, no. 2 (2023): 382. http://dx.doi.org/10.3390/cancers15020382.

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Ewing sarcoma is the second most common bone tumor in childhood and adolescence. Currently, first-line therapy includes multidrug chemotherapy with surgery and/or radiation. Although most patients initially respond to chemotherapy, recurrent tumors become treatment refractory. Pathologically, Ewing sarcoma consists of small round basophilic cells with prominent nuclei marked by expression of surface protein CD99. Genetically, Ewing sarcoma is driven by a fusion oncoprotein that results from one of a small number of chromosomal translocations composed of a FET gene and a gene encoding an ETS fa

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Mauger, E., and P. H. Scott. "Mitogenic stimulation of transcription by RNA polymerase III." Biochemical Society Transactions 32, no. 6 (2004): 976–77. http://dx.doi.org/10.1042/bst0320976.

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Regulation of protein synthesis is an important aspect of growth control. RNA polymerase (pol) III plays a key role in this process by catalysing production of tRNA and 5 S rRNA. Growth factors trigger a rapid increase in pol III activity and this is essential for cell proliferation. The transcription factor TFIIIB plays a key role in controlling pol III activity and is a target for regulation by a number of mechanisms. This review will focus on how TFIIIB is targeted by these proteins in response to mitogen stimulation.

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Chu, Wing-Keung, Li-Man Hung, Chun-Wei Hou, and Jan-Kan Chen. "MicroRNA 630 Represses NANOG Expression through Transcriptional and Post-Transcriptional Regulation in Human Embryonal Carcinoma Cells." International Journal of Molecular Sciences 23, no. 1 (2021): 46. http://dx.doi.org/10.3390/ijms23010046.

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The pluripotent transcription factor NANOG is essential for maintaining embryonic stem cells and driving tumorigenesis. We previously showed that PKC activity is involved in the regulation of NANOG expression. To explore the possible involvement of microRNAs in regulating the expression of key pluripotency factors, we performed a genome-wide analysis of microRNA expression in the embryonal carcinoma cell line NT2/D1 in the presence of the PKC activator, PMA. We found that MIR630 was significantly upregulated in PMA-treated cells. Experimentally, we showed that transfection of MIR630 mimic into

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Pitts, Stephanie, and Marikki Laiho. "Regulation of RNA Polymerase I Stability and Function." Cancers 14, no. 23 (2022): 5776. http://dx.doi.org/10.3390/cancers14235776.

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RNA polymerase I is a highly processive enzyme with fast initiation and elongation rates. The structure of Pol I, with its in-built RNA cleavage ability and incorporation of subunits homologous to transcription factors, enables it to quickly and efficiently synthesize the enormous amount of rRNA required for ribosome biogenesis. Each step of Pol I transcription is carefully controlled. However, cancers have highjacked these control points to switch the enzyme, and its transcription, on permanently. While this provides an exceptional benefit to cancer cells, it also creates a potential cancer t

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Brown, Jay C. "Role of Polycomb Repressive Complex 2 in Regulation of Human Transcription Factor Gene Expression." Genetics & Genomic Sciences 7, no. 1 (2022): 1–30. http://dx.doi.org/10.24966/ggs-2485/100033.

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For instance, this was the case with 16 of 20 TF families. The results are interpreted to indicate that while individual TFs such as EZH2 may be specific for broadly expressed or tissue targeted genes, this is not a property of most TF families. Most have both broadly expressed and tissue targeted members

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Sayed, Mohammed, and Juw Won Park. "miRinGO: Prediction of Biological Processes Indirectly Targeted by Human microRNAs." Non-Coding RNA 9, no. 1 (2023): 11. http://dx.doi.org/10.3390/ncrna9010011.

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MicroRNAs (miRNAs) are small non-coding RNAs that are known for their role in the post-transcriptional regulation of target genes. Typically, their functions are predicted by first identifying their target genes and then finding biological processes enriched in these targets. Current tools for miRNA functional analysis use only genes with physical binding sites as their targets and exclude other genes that are indirectly targeted transcriptionally through transcription factors. Here, we introduce a method to predict gene ontology (GO) annotations indirectly targeted by microRNAs. The proposed

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Engel, Anja J., Laura-Marie Winterstein, Marina Kithil, Markus Langhans, Anna Moroni, and Gerhard Thiel. "Light-Regulated Transcription of a Mitochondrial-Targeted K+ Channel." Cells 9, no. 11 (2020): 2507. http://dx.doi.org/10.3390/cells9112507.

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The inner membranes of mitochondria contain several types of K+ channels, which modulate the membrane potential of the organelle and contribute in this way to cytoprotection and the regulation of cell death. To better study the causal relationship between K+ channel activity and physiological changes, we developed an optogenetic platform for a light-triggered modulation of K+ conductance in mitochondria. By using the light-sensitive interaction between cryptochrome 2 and the regulatory protein CIB1, we can trigger the transcription of a small and highly selective K+ channel, which is in mammal

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Janostiak, Radoslav, Ariadna Torres-Sanchez, Francesc Posas, and Eulàlia de Nadal. "Understanding Retinoblastoma Post-Translational Regulation for the Design of Targeted Cancer Therapies." Cancers 14, no. 5 (2022): 1265. http://dx.doi.org/10.3390/cancers14051265.

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The retinoblastoma protein (Rb1) is a prototypical tumor suppressor protein whose role was described more than 40 years ago. Together with p107 (also known as RBL1) and p130 (also known as RBL2), the Rb1 belongs to a family of structurally and functionally similar proteins that inhibits cell cycle progression. Given the central role of Rb1 in regulating proliferation, its expression or function is altered in most types of cancer. One of the mechanisms underlying Rb-mediated cell cycle inhibition is the binding and repression of E2F transcription factors, and these processes are dependent on Rb

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Kwon, Geunho, and Kyuho Kang. "Transcriptional regulation of IL10 gene in human macrophages." Journal of Immunology 204, no. 1_Supplement (2020): 152.21. http://dx.doi.org/10.4049/jimmunol.204.supp.152.21.

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Abstract IL-10 is an anti-inflammatory cytokine with a crucial role in immune homeostasis. Dysregulated production of IL-10 has been linked to certain autoimmune and inflammatory diseases. IL-10 is strongly induced by TLR ligands and suppressed by IFN-γ as part of the synergistic activation of inflammatory genes. However, the molecular mechanisms that regulate expression of the IL10 gene, especially in human macrophages, are incompletely understood. By using epigenomic analysis of ATAC-seq and ChIP-seq analysis we have identified human macrophage-specific enhancers in the IL10 gene locus. In t

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Pham, Lan V., Archito T. Tamayo, Changping Li, Carlos Bueso-Ramos, and Richard J. Ford. "An epigenetic chromatin remodeling role for NFATc1 in transcriptional regulation of growth and survival genes in diffuse large B-cell lymphomas." Blood 116, no. 19 (2010): 3899–906. http://dx.doi.org/10.1182/blood-2009-12-257378.

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Abstract The nuclear factor of activated T cells (NFAT) family of transcription factors functions as integrators of multiple signaling pathways by binding to chromatin in combination with other transcription factors and coactivators to regulate genes central for cell growth and survival in hematopoietic cells. Recent experimental evidence has implicated the calcineurin/NFAT signaling pathway in the pathogenesis of various malignancies, including diffuse large B-cell lymphoma (DLBCL). However, the molecular mechanism(s) underlying NFATc1 regulation of genes controlling lymphoma cell growth and

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Calero-Nieto, Fernando, Antonio Di Pietro, M. Isabel G. Roncero, and Concepcion Hera. "Role of the Transcriptional Activator XlnR of Fusarium oxysporum in Regulation of Xylanase Genes and Virulence." Molecular Plant-Microbe Interactions® 20, no. 8 (2007): 977–85. http://dx.doi.org/10.1094/mpmi-20-8-0977.

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Fungal infection of plants involves degradation of the host cell wall through the action of lytic enzymes secreted by the pathogen. The role of these enzymes in virulence is difficult to determine due to their functional redundancy and, therefore, remains controversial. Here, we have studied XlnR, a zinc-finger transcription factor from the vascular wilt pathogen Fusarium oxysporum that is orthologous to the major transcriptional activator of xylanase genes in Aspergillus spp. Transcription of the xlnR gene was activated by inducing carbon sources such as oat spelt xylan (OSX) and repressed by

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Gong, Zehao, Yingqing Luo, Wenfa Zhang, et al. "A SlMYB75-centred transcriptional cascade regulates trichome formation and sesquiterpene accumulation in tomato." Journal of Experimental Botany 72, no. 10 (2021): 3806–20. http://dx.doi.org/10.1093/jxb/erab086.

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Abstract Tomato trichomes act as a mechanical and chemical barrier against pests. An R2R3 MYB transcription factor gene, SlMYB75, is highly expressed in type II, V, and VI trichomes. SlMYB75 protein is located in the nucleus and possesses transcriptional activation activity. Down-regulation of SlMYB75 increased the formation of type II, V, and VI trichomes, accumulation of δ-elemene, β-caryophyllene, and α-humulene in glandular trichomes, and tolerance to spider mites in tomato. In contrast, overexpression of SlMYB75 inhibited trichome formation and sesquiterpene accumulation, and increased pl

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Lee, Sung Kuk, Jack D. Newman, and Jay D. Keasling. "Catabolite Repression of the Propionate Catabolic Genes in Escherichia coli and Salmonella enterica: Evidence for Involvement of the Cyclic AMP Receptor Protein." Journal of Bacteriology 187, no. 8 (2005): 2793–800. http://dx.doi.org/10.1128/jb.187.8.2793-2800.2005.

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ABSTRACT Previous studies with Salmonella enterica serovar Typhimurium LT2 demonstrated that transcriptional activation of the prpBCDE operon requires the function of transcription factor PrpR, sigma-54, and IHF. In this study, we found that transcription from the prpBCDE and prpR promoters was down-regulated by the addition of glucose or glycerol, indicating that these genes may be regulated by the cyclic AMP (cAMP)-cAMP receptor protein (CRP) complex. Targeted mutagenesis of a putative CRP-binding site in the promoter region between prpR and prpBCDE suggested that these genes are under the c

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Block, Gregory J., Christopher H. Eskiw, Graham Dellaire, and David P. Bazett-Jones. "Transcriptional Regulation Is Affected by Subnuclear Targeting of Reporter Plasmids to PML Nuclear Bodies." Molecular and Cellular Biology 26, no. 23 (2006): 8814–25. http://dx.doi.org/10.1128/mcb.00636-06.

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ABSTRACT Whereas the PML protein has been reported to have both transcriptional coactivator and corepressor potential, the contribution of the PML nuclear body (PML NB) itself to transcriptional regulation is not well understood. Here we demonstrate that plasmid DNA artificially tethered to PML or the PML NB-targeting domain of Sp100 is preferentially localized to PML NBs. Using the tethering technique, we targeted a simian virus 40 promoter-driven luciferase reporter plasmid to PML NBs, resulting in the repression of the transgene transcriptional activity. Conversely, the tethering of a cytom

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Bowman, Tamara A., Madeline M. Wong, Linda K. Cox, Joseph J. Baldassare, and John C. Chrivia. "Loss of H2A.Z Is Not Sufficient to Determine Transcriptional Activity of Snf2-Related CBP Activator Protein or p400 Complexes." International Journal of Cell Biology 2011 (2011): 1–8. http://dx.doi.org/10.1155/2011/715642.

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The p400 and SRCAP (Snf2-related CBP activator protein) complexes remodel chromatin by catalyzing deposition of histone H2A.Z into nucleosomes. This remodeling activity has been proposed as a basis for regulation of transcription by these complexes. Transcript levels ofp21orSp1mRNAs after knockdown of p400 or SRCAP reveals that each regulates transcription of these promoters differently. In this study, we asked whether deposition of H2A.Z within specific nucleosomes by p400 or SRCAP dictates transcriptional activity. Our data indicates that nucleosome density at specificp21orSp1promoter positi

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Landeira, David, and Miguel Navarro. "Nuclear repositioning of the VSG promoter during developmental silencing in Trypanosoma brucei." Journal of Cell Biology 176, no. 2 (2007): 133–39. http://dx.doi.org/10.1083/jcb.200607174.

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Interphase nuclear repositioning of chromosomes has been implicated in the epigenetic regulation of RNA polymerase (pol) II transcription. However, little is known about the nuclear position–dependent regulation of RNA pol I–transcribed loci. Trypanosoma brucei is an excellent model system to address this question because its two main surface protein genes, procyclin and variant surface glycoprotein (VSG), are transcribed by pol I and undergo distinct transcriptional activation or downregulation events during developmental differentiation. Although the monoallelically expressed VSG locus is ex

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McAninch, Dale, Ella P. Thomson, and Paul Q. Thomas. "Genome-wide DNA-binding profile of SRY-box transcription factor 3 (SOX3) in mouse testes." Reproduction, Fertility and Development 32, no. 16 (2020): 1260. http://dx.doi.org/10.1071/rd20108.

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Spermatogenesis is the male version of gametogenesis, where germ cells are transformed into haploid spermatozoa through a tightly controlled series of mitosis, meiosis and differentiation. This process is reliant on precisely timed changes in gene expression controlled by several different hormonal and transcriptional mechanisms. One important transcription factor is SRY-box transcription factor 3 (SOX3), which is transiently expressed within the uncommitted spermatogonial stem cell population. Sox3-null mouse testes exhibit a block in spermatogenesis, leading to infertility or subfertility. H

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Bolger, Steven J., Patricia A. Gonzales Hurtado, Jason D. Hoffert, Fahad Saeed, Trairak Pisitkun, and Mark A. Knepper. "Quantitative phosphoproteomics in nuclei of vasopressin-sensitive renal collecting duct cells." American Journal of Physiology-Cell Physiology 303, no. 10 (2012): C1006—C1020. http://dx.doi.org/10.1152/ajpcell.00260.2012.

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Vasopressin regulates transport across the collecting duct epithelium in part via effects on gene transcription. Transcriptional regulation occurs partially via changes in phosphorylation of transcription factors, transcriptional coactivators, and protein kinases in the nucleus. To test whether vasopressin alters the nuclear phosphoproteome of vasopressin-sensitive cultured mouse mpkCCD cells, we used stable isotope labeling and mass spectrometry to quantify thousands of phosphorylation sites in nuclear extracts and nuclear pellet fractions. Measurements were made in the presence and absence o

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Doak, Andrea E., Rose Qu, and Kevin J. Cheung. "Abstract A014: Transcriptional regulation of basal leader cell identity during collective breast cancer invasion." Cancer Research 83, no. 2_Supplement_2 (2023): A014. http://dx.doi.org/10.1158/1538-7445.metastasis22-a014.

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Abstract An early step in breast cancer progression is invasion of tumor cells into surrounding tissues. In many breast cancers, particularly ductal carcinomas, this invasion is accomplished by tumor cells migrating as a cohesive group. This often involves cells that take on heterogeneous roles as either leader or follower cells. Studies in common mouse and human breast cancer models have established that leader cells express high levels of keratin-14 (K14) and other basal epithelial markers. The presence of these K14+ cells promote metastasis and predict poor prognosis. The molecular mechanis

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Xu, Tao, Yongchao Li, Joy D. Van Nostrand, Zhili He, and Jizhong Zhou. "Cas9-Based Tools for Targeted Genome Editing and Transcriptional Control." Applied and Environmental Microbiology 80, no. 5 (2014): 1544–52. http://dx.doi.org/10.1128/aem.03786-13.

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ABSTRACTDevelopment of tools for targeted genome editing and regulation of gene expression has significantly expanded our ability to elucidate the mechanisms of interesting biological phenomena and to engineer desirable biological systems. Recent rapid progress in the study of a clustered, regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) protein system in bacteria has facilitated the development of newly facile and programmable platforms for genome editing and transcriptional control in a sequence-specific manner. The core RNA-guided Cas9 endonuclease in the type

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Nekhai, Sergei, Michael Petukhov, and Denitra Breuer. "Regulation of CDK9 Activity by Phosphorylation and Dephosphorylation." BioMed Research International 2014 (2014): 1–8. http://dx.doi.org/10.1155/2014/964964.

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HIV-1 transcription is regulated by CDK9/cyclin T1, which, unlike a typical cell cycle-dependent kinase, is regulated by associating with 7SK small nuclear ribonuclear protein complex (snRNP). While the protein components of this complex are well studied, the mechanism of the complex formation is still not fully understood. The association of CDK9/cyclin T1 with 7SK snRNP is, in part, regulated by a reversible CDK9 phosphorylation. Here, we present a comprehensive review of the kinases and phosphatases involved in CDK9 phosphorylation and discuss their role in regulation of HIV-1 replication a

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Nylén, Carolina, Wataru Aoi, Ahmed M. Abdelmoez, et al. "IL6 and LIF mRNA expression in skeletal muscle is regulated by AMPK and the transcription factors NFYC, ZBTB14, and SP1." American Journal of Physiology-Endocrinology and Metabolism 315, no. 5 (2018): E995—E1004. http://dx.doi.org/10.1152/ajpendo.00398.2017.

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Adenosine monophosphate-activated protein kinase (AMPK) controls glucose and lipid metabolism and modulates inflammatory responses to maintain metabolic and inflammatory homeostasis during low cellular energy levels. The AMPK activator 5-aminoimidazole-4-carboxamide-1-β-4-ribofuranoside (AICAR) interferes with inflammatory pathways in skeletal muscle, but the mechanisms are undefined. We hypothesized that AMPK activation reduces cytokine mRNA levels by blocking transcription through one or several transcription factors. Three skeletal muscle models were used to study AMPK effects on cytokine m

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