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Journal articles on the topic 'Tamil Transcriptions'

Author: Grafiati

Published: 4 June 2021

Last updated: 3 February 2022

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1

Ito, Jun, Hidehiro Fukaki, Makoto Onoda, et al. "Auxin-dependent compositional change in Mediator in ARF7- and ARF19-mediated transcription." Proceedings of the National Academy of Sciences 113, no. 23 (2016): 6562–67. http://dx.doi.org/10.1073/pnas.1600739113.

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Mediator is a multiprotein complex that integrates the signals from transcription factors binding to the promoter and transmits them to achieve gene transcription. The subunits of Mediator complex reside in four modules: the head, middle, tail, and dissociable CDK8 kinase module (CKM). The head, middle, and tail modules form the core Mediator complex, and the association of CKM can modify the function of Mediator in transcription. Here, we show genetic and biochemical evidence that CKM-associated Mediator transmits auxin-dependent transcriptional repression in lateral root (LR) formation. The

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2

Georges, Sara A., W. Lee Kraus, Karolin Luger, Jennifer K. Nyborg, and Paul J. Laybourn. "p300-Mediated Tax Transactivation from Recombinant Chromatin: Histone Tail Deletion Mimics Coactivator Function." Molecular and Cellular Biology 22, no. 1 (2002): 127–37. http://dx.doi.org/10.1128/mcb.22.1.127-137.2002.

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ABSTRACT Efficient transcription of the human T-cell leukemia virus type 1 (HTLV-1) genome requires Tax, a virally encoded oncogenic transcription factor, in complex with the cellular transcription factor CREB and the coactivators p300/CBP. To examine Tax transactivation in vitro, we used a chromatin assembly system that included recombinant core histones. The addition of Tax, CREB, and p300 to the HTLV-1 promoter assembled into chromatin activated transcription several hundredfold. Chromatin templates selectively lacking amino-terminal histone tails demonstrated enhanced transcriptional activ

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3

Liu, Zhongle, and Lawrence C. Myers. "Fungal Mediator Tail Subunits Contain Classical Transcriptional Activation Domains." Molecular and Cellular Biology 35, no. 8 (2015): 1363–75. http://dx.doi.org/10.1128/mcb.01508-14.

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Classical activation domains within DNA-bound eukaryotic transcription factors make weak interactions with coactivator complexes, such as Mediator, to stimulate transcription. How these interactions stimulate transcription, however, is unknown. The activation of reporter genes by artificial fusion of Mediator subunits to DNA binding domains that bind to their promoters has been cited as evidence that the primary role of activators is simply to recruit Mediator. We have identified potent classical transcriptional activation domains in the C termini of several tail module subunits ofSaccharomyce

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4

McCulloch, Vicki, and Gerald S. Shadel. "Human Mitochondrial Transcription Factor B1 Interacts with the C-Terminal Activation Region of h-mtTFA and Stimulates Transcription Independently of Its RNA Methyltransferase Activity." Molecular and Cellular Biology 23, no. 16 (2003): 5816–24. http://dx.doi.org/10.1128/mcb.23.16.5816-5824.2003.

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ABSTRACT A significant advancement in understanding mitochondrial gene expression is the recent identification of two new human mitochondrial transcription factors, h-mtTFB1 and h-mtTFB2. Both proteins stimulate transcription in collaboration with the high-mobility group box transcription factor, h-mtTFA, and are homologous to rRNA methyltransferases. In fact, the dual-function nature of h-mtTFB1 was recently demonstrated by its ability to methylate a conserved rRNA substrate. Here, we demonstrate that h-mtTFB1 binds h-mtTFA both in HeLa cell mitochondrial extracts and in direct-binding assays

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5

Alff, Peter J., Nandini Sen, Elena Gorbunova, Irina N. Gavrilovskaya, and Erich R. Mackow. "The NY-1 Hantavirus Gn Cytoplasmic Tail Coprecipitates TRAF3 and Inhibits Cellular Interferon Responses by Disrupting TBK1-TRAF3 Complex Formation." Journal of Virology 82, no. 18 (2008): 9115–22. http://dx.doi.org/10.1128/jvi.00290-08.

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ABSTRACT Pathogenic hantaviruses replicate within human endothelial cells and cause two diseases, hemorrhagic fever with renal syndrome and hantavirus pulmonary syndrome. In order to replicate in endothelial cells pathogenic hantaviruses inhibit the early induction of beta interferon (IFN-β). Expression of the cytoplasmic tail of the pathogenic NY-1 hantavirus Gn protein is sufficient to inhibit RIG-I- and TBK1-directed IFN responses. The formation of TBK1-TRAF3 complexes directs IRF-3 phosphorylation, and both IRF-3 and NF-κB activation are required for transcription from the IFN-β promoter.

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6

Talbert, Paul B., and Steven Henikoff. "The Yin and Yang of Histone Marks in Transcription." Annual Review of Genomics and Human Genetics 22, no. 1 (2021): 147–70. http://dx.doi.org/10.1146/annurev-genom-120220-085159.

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Nucleosomes wrap DNA and impede access for the machinery of transcription. The core histones that constitute nucleosomes are subject to a diversity of posttranslational modifications, or marks, that impact the transcription of genes. Their functions have sometimes been difficult to infer because the enzymes that write and read them are complex, multifunctional proteins. Here, we examine the evidence for the functions of marks and argue that the major marks perform a fairly small number of roles in either promoting transcription or preventing it. Acetylations and phosphorylations on the histone

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7

Sims, Jennifer K., and Judd C. Rice. "PR-Set7 Establishes a Repressive trans-Tail Histone Code That Regulates Differentiation." Molecular and Cellular Biology 28, no. 14 (2008): 4459–68. http://dx.doi.org/10.1128/mcb.00410-08.

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ABSTRACT Posttranslational modifications of the DNA-associated histone proteins play fundamental roles in eukaryotic transcriptional regulation. We previously discovered a novel trans-tail histone code involving monomethylated histone H4 lysine 20 (H4K20) and H3 lysine 9 (H3K9); however, the mechanisms that establish this code and its function in transcription were unknown. In this report, we demonstrate that H3K9 monomethylation is dependent upon the PR-Set7 H4K20 monomethyltransferase but independent of its catalytic function, indicating that PR-Set7 recruits an H3K9 monomethyltransferase to

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8

WANG, Guannan, Jianyin LONG, Isao MATSUURA, Dongming HE, and Fang LIU. "The Smad3 linker region contains a transcriptional activation domain." Biochemical Journal 386, no. 1 (2005): 29–34. http://dx.doi.org/10.1042/bj20041820.

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Transforming growth factor-β (TGF-β)/Smads regulate a wide variety of biological responses through transcriptional regulation of target genes. Smad3 plays a key role in TGF-β/Smad-mediated transcriptional responses. Here, we show that the proline-rich linker region of Smad3 contains a transcriptional activation domain. When the linker region is fused to a heterologous DNA-binding domain, it activates transcription. We show that the linker region physically interacts with p300. The adenovirus E1a protein, which binds to p300, inhibits the transcriptional activity of the linker region, and overe

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9

Ryu, Hong-Yeoul, Dejian Zhao, Jianhui Li, Dan Su, and Mark Hochstrasser. "Histone sumoylation promotes Set3 histone-deacetylase complex-mediated transcriptional regulation." Nucleic Acids Research 48, no. 21 (2020): 12151–68. http://dx.doi.org/10.1093/nar/gkaa1093.

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Abstract Histones are substrates of the SUMO (small ubiquitin-like modifier) conjugation pathway. Several reports suggest histone sumoylation affects transcription negatively, but paradoxically, our genome-wide analysis shows the modification concentrated at many active genes. We find that trans-tail regulation of histone-H2B ubiquitylation and H3K4 di-methylation potentiates subsequent histone sumoylation. Consistent with the known control of the Set3 histone deacetylase complex (HDAC) by H3K4 di-methylation, histone sumoylation directly recruits the Set3 complex to both protein-coding and no

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10

Merrick, David, Kavita Mistry, Jingshing Wu, et al. "Polycystin-1 regulates bone development through an interaction with the transcriptional coactivator TAZ." Human Molecular Genetics 28, no. 1 (2018): 16–30. http://dx.doi.org/10.1093/hmg/ddy322.

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Abstract Polycystin-1 (PC1), encoded by the PKD1 gene that is mutated in the autosomal dominant polycystic kidney disease, regulates a number of processes including bone development. Activity of the transcription factor RunX2, which controls osteoblast differentiation, is reduced in Pkd1 mutant mice but the mechanism governing PC1 activation of RunX2 is unclear. PC1 undergoes regulated cleavage that releases its C-terminal tail (CTT), which translocates to the nucleus to modulate transcriptional pathways involved in proliferation and apoptosis. We find that the cleaved CTT of PC1 (PC1-CTT) sti

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11

Tan, Changming, Siting Zhu, Zee Chen, et al. "Mediator complex proximal Tail subunit MED30 is critical for Mediator core stability and cardiomyocyte transcriptional network." PLOS Genetics 17, no. 9 (2021): e1009785. http://dx.doi.org/10.1371/journal.pgen.1009785.

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Dysregulation of cardiac transcription programs has been identified in patients and families with heart failure, as well as those with morphological and functional forms of congenital heart defects. Mediator is a multi-subunit complex that plays a central role in transcription initiation by integrating regulatory signals from gene-specific transcriptional activators to RNA polymerase II (Pol II). Recently, Mediator subunit 30 (MED30), a metazoan specific Mediator subunit, has been associated with Langer-Giedion syndrome (LGS) Type II and Cornelia de Lange syndrome-4 (CDLS4), characterized by s

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12

Saleh, Moustafa M., Célia Jeronimo, François Robert, and Gabriel E. Zentner. "Connection of core and tail Mediator modules restrains transcription from TFIID-dependent promoters." PLOS Genetics 17, no. 8 (2021): e1009529. http://dx.doi.org/10.1371/journal.pgen.1009529.

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The Mediator coactivator complex is divided into four modules: head, middle, tail, and kinase. Deletion of the architectural subunit Med16 separates core Mediator (cMed), comprising the head, middle, and scaffold (Med14), from the tail. However, the direct global effects of tail/cMed disconnection are unclear. We find that rapid depletion of Med16 downregulates genes that require the SAGA complex for full expression, consistent with their reported tail dependence, but also moderately overactivates TFIID-dependent genes in a manner partly dependent on the separated tail, which remains associate

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13

Svejstrup, Jesper Q. "Transcription: another mark in the tail." EMBO Journal 31, no. 12 (2012): 2753–54. http://dx.doi.org/10.1038/emboj.2012.154.

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14

Parra, Michael A., and John J. Wyrick. "Regulation of Gene Transcription by the Histone H2A N-Terminal Domain." Molecular and Cellular Biology 27, no. 21 (2007): 7641–48. http://dx.doi.org/10.1128/mcb.00742-07.

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ABSTRACT Histone N-terminal domains play critical roles in regulating chromatin structure and gene transcription. Relatively little is known, however, about the role of the histone H2A N-terminal domain in transcription regulation. We have used DNA microarrays to characterize the changes in genome-wide expression caused by mutations in the N-terminal domain of histone H2A. Our results indicate that the N-terminal domain of histone H2A functions primarily to repress the transcription of a large subset of the Saccharomyces cerevisiae genome and that most of the H2A-repressed genes are also repre

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15

Van Dyke, M. W., and M. Sawadogo. "DNA-binding and transcriptional properties of human transcription factor TFIID after mild proteolysis." Molecular and Cellular Biology 10, no. 7 (1990): 3415–20. http://dx.doi.org/10.1128/mcb.10.7.3415.

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The existence of separable functions within the human class II general transcription factor TFIID was probed for differential sensitivity to mild proteolytic treatment. Independent of whether TFIID was bound to DNA or free in solution, partial digestion with either one of a variety of nonspecific endoproteases generated a protease-resistant protein product that retained specific DNA recognition, as revealed by DNase I footprinting. However, in contrast to native TFIID, which interacts with the adenovirus major late (ML) promoter over a very broad DNA region, partially proteolyzed TFIID interac

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16

Van Dyke, M. W., and M. Sawadogo. "DNA-binding and transcriptional properties of human transcription factor TFIID after mild proteolysis." Molecular and Cellular Biology 10, no. 7 (1990): 3415–20. http://dx.doi.org/10.1128/mcb.10.7.3415-3420.1990.

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The existence of separable functions within the human class II general transcription factor TFIID was probed for differential sensitivity to mild proteolytic treatment. Independent of whether TFIID was bound to DNA or free in solution, partial digestion with either one of a variety of nonspecific endoproteases generated a protease-resistant protein product that retained specific DNA recognition, as revealed by DNase I footprinting. However, in contrast to native TFIID, which interacts with the adenovirus major late (ML) promoter over a very broad DNA region, partially proteolyzed TFIID interac

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17

Yarrington, Robert M., Yaxin Yu, Chao Yan, Lu Bai, and David J. Stillman. "A Role for Mediator Core in Limiting Coactivator Recruitment in Saccharomyces cerevisiae." Genetics 215, no. 2 (2020): 407–20. http://dx.doi.org/10.1534/genetics.120.303254.

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Mediator is an essential, multisubunit complex that functions as a transcriptional coactivator in yeast and other eukaryotic organisms. Mediator has four conserved modules, Head, Middle, Tail, and Kinase, and has been implicated in nearly all aspects of gene regulation. The Tail module has been shown to recruit the Mediator complex to the enhancer or upstream activating sequence (UAS) regions of genes via interactions with transcription factors, and the Kinase module facilitates the transition of Mediator from the UAS/enhancer to the preinitiation complex via protein phosphorylation. Here, we

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18

Klupp, Barbara G., Christoph J. Hengartner, Thomas C. Mettenleiter, and Lynn W. Enquist. "Complete, Annotated Sequence of the Pseudorabies Virus Genome." Journal of Virology 78, no. 1 (2004): 424–40. http://dx.doi.org/10.1128/jvi.78.1.424-440.2004.

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ABSTRACT We have obtained the complete DNA sequence of pseudorabies virus (PRV), an alphaherpesvirus also known as Aujeszky's disease virus or suid herpesvirus 1, using sequence fragments derived from six different strains (Kaplan, Becker, Rice, Indiana-Funkhauser, NIA-3, and TNL). The assembled PRV genome sequence comprises 143,461 nucleotides. As expected, it matches the predicted gene arrangement, genome size, and restriction enzyme digest patterns. More than 70 open reading frames were identified with homologs in related alphaherpesviruses; none were unique to PRV. RNA polymerase II transc

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19

Pathak, Prabhat Kumar, Fei Zhang, Shuxia Peng, et al. "Structure of the unique tetrameric STENOFOLIA homeodomain bound with target promoter DNA." Acta Crystallographica Section D Structural Biology 77, no. 8 (2021): 1050–63. http://dx.doi.org/10.1107/s205979832100632x.

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Homeobox transcription factors are key regulators of morphogenesis and development in both animals and plants. In plants, the WUSCHEL-related homeobox (WOX) family of transcription factors function as central organizers of several developmental programs ranging from embryo patterning to meristematic stem-cell maintenance through transcriptional activation and repression mechanisms. The Medicago truncatula STENOFOLIA (STF) gene is a master regulator of leaf-blade lateral development. Here, the crystal structure of the homeodomain (HD) of STF (STF-HD) in complex with its promoter DNA is reported

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20

Wiederhold, Katrin, and Lori A. Passmore. "Cytoplasmic deadenylation: regulation of mRNA fate." Biochemical Society Transactions 38, no. 6 (2010): 1531–36. http://dx.doi.org/10.1042/bst0381531.

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The poly(A) tail of mRNA has an important influence on the dynamics of gene expression. On one hand, it promotes enhanced mRNA stability to allow production of the protein, even after inactivation of transcription. On the other hand, shortening of the poly(A) tail (deadenylation) slows down translation of the mRNA, or prevents it entirely, by inducing mRNA decay. Thus deadenylation plays a crucial role in the post-transcriptional regulation of gene expression, deciding the fate of individual mRNAs. It acts both in basal mRNA turnover, as well as in temporally and spatially regulated translatio

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21

Hirschhorn, J. N., A. L. Bortvin, S. L. Ricupero-Hovasse, and F. Winston. "A new class of histone H2A mutations in Saccharomyces cerevisiae causes specific transcriptional defects in vivo." Molecular and Cellular Biology 15, no. 4 (1995): 1999–2009. http://dx.doi.org/10.1128/mcb.15.4.1999.

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Nucleosomes have been shown to repress transcription both in vitro and in vivo. However, the mechanisms by which this repression is overcome are only beginning to be understood. Recent evidence suggests that in the yeast Saccharomyces cerevisiae, many transcriptional activators require the SNF/SWI complex to overcome chromatin-mediated repression. We have identified a new class of mutations in the histone H2A-encoding gene HTA1 that causes transcriptional defects at the SNF/SWI-dependent gene SUC2. Some of the mutations are semidominant, and most of the predicted amino acid changes are in or n

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22

Kawamura, Akinori, Sumito Koshida, and Shinji Takada. "Activator-to-Repressor Conversion of T-Box Transcription Factors by the Ripply Family of Groucho/TLE-Associated Mediators." Molecular and Cellular Biology 28, no. 10 (2008): 3236–44. http://dx.doi.org/10.1128/mcb.01754-07.

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ABSTRACT The T-box family of transcription factors, defined by a conserved DNA binding domain called the T-box, regulate various aspects of embryogenesis by activating and/or repressing downstream genes. In spite of the biological significance of the T-box proteins, how they regulate transcription remains to be elucidated. Here we show that the Groucho/TLE-associated protein Ripply converts T-box proteins from activators to repressors. In cultured cells, zebrafish Ripply1, an essential component in somite segmentation, and its structural relatives, Ripply2 and -3, suppress the transcriptional

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23

Yu, Xinzhe, and Ping Yi. "Structural Insights of Transcriptionally Active, Full-Length Androgen Receptor Coactivator Complexes." Journal of the Endocrine Society 5, Supplement_1 (2021): A817. http://dx.doi.org/10.1210/jendso/bvab048.1665.

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Abstract Steroid hormone receptors activate gene transcription by binding specific DNA sequences and recruiting coactivators to initiate transcription of their target genes. For most nuclear hormone receptors (NRs), the ligand-dependent activation function domain-2 (AF-2), residing in the C-terminal ligand binding domain (LBD), is a primary contributor to the NR transcriptional activity. In contrast to other steroid receptors such as estrogen receptor-α (ERα), the transcriptional activation function of androgen receptor (AR) is thought to be largely dependent on its ligand-independent activati

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24

Basu, Urmimala, Nandini Mishra, Mohammed Farooqui, Jiayu Shen, Laura C. Johnson, and Smita S. Patel. "The C-terminal tails of the mitochondrial transcription factors Mtf1 and TFB2M are part of an autoinhibitory mechanism that regulates DNA binding." Journal of Biological Chemistry 295, no. 20 (2020): 6823–30. http://dx.doi.org/10.1074/jbc.ra120.013338.

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The structurally homologous Mtf1 and TFB2M proteins serve as transcription initiation factors of mitochondrial RNA polymerases in Saccharomyces cerevisiae and humans, respectively. These transcription factors directly interact with the nontemplate strand of the transcription bubble to drive promoter melting. Given the key roles of Mtf1 and TFB2M in promoter-specific transcription initiation, it can be expected that the DNA binding activity of the mitochondrial transcription factors is regulated to prevent DNA binding at inappropriate times. However, little information is available on how mitoc

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25

Zhang, Fan, Laarni Sumibcay, Alan G. Hinnebusch, and Mark J. Swanson. "A Triad of Subunits from the Gal11/Tail Domain of Srb Mediator Is an In Vivo Target of Transcriptional Activator Gcn4p." Molecular and Cellular Biology 24, no. 15 (2004): 6871–86. http://dx.doi.org/10.1128/mcb.24.15.6871-6886.2004.

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ABSTRACT The Srb mediator is an important transcriptional coactivator for Gcn4p in the yeast Saccharomyces cerevisiae. We show that three subunits of the Gal11/tail domain of mediator, Gal11p, Pgd1p, and Med2p, and the head domain subunit Srb2p make overlapping contributions to the interaction of mediator with recombinant Gcn4p in vitro. Each of these proteins, along with the tail subunit Sin4p, also contributes to the recruitment of mediator by Gcn4p to target promoters in vivo. We found that Gal11p, Med2p, and Pgd1p reside in a stable subcomplex in sin4Δ cells that interacts with Gcn4p in vi

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26

Chang, Jessica, Julie Baker, and Andrea Wills. "Transcriptional dynamics of tail regeneration inXenopus tropicalis." genesis 55, no. 1-2 (2017): e23015. http://dx.doi.org/10.1002/dvg.23015.

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27

Darvekar, Sagar, Sylvia Sagen Johnsen, Agnete Bratsberg Eriksen, Terje Johansen, and Eva Sjøttem. "Identification of two independent nucleosome-binding domains in the transcriptional co-activator SPBP." Biochemical Journal 442, no. 1 (2012): 65–75. http://dx.doi.org/10.1042/bj20111230.

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Transcriptional regulation requires co-ordinated action of transcription factors, co-activator complexes and general transcription factors to access specific loci in the dense chromatin structure. In the present study we demonstrate that the transcriptional co-regulator SPBP [stromelysin-1 PDGF (platelet-derived growth factor)-responsive element binding protein] contains two independent chromatin-binding domains, the SPBP-(1551–1666) region and the C-terminal extended PHD [ePHD/ADD (extended plant homeodomain/ATRX-DNMT3-DNMT3L)] domain. The region 1551–1666 is a novel core nucleosome-interacti

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28

Gallagher, Jennifer E. G., Suk Lan Ser, Michael C. Ayers, Casey Nassif, and Amaury Pupo. "The Polymorphic PolyQ Tail Protein of the Mediator Complex, Med15, Regulates the Variable Response to Diverse Stresses." International Journal of Molecular Sciences 21, no. 5 (2020): 1894. http://dx.doi.org/10.3390/ijms21051894.

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The Mediator is composed of multiple subunits conserved from yeast to humans and plays a central role in transcription. The tail components are not required for basal transcription but are required for responses to different stresses. While some stresses are familiar, such as heat, desiccation, and starvation, others are exotic, yet yeast can elicit a successful stress response. 4-Methylcyclohexane methanol (MCHM) is a hydrotrope that induces growth arrest in yeast. We found that a naturally occurring variation in the Med15 allele, a component of the Mediator tail, altered the stress response

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29

Stallcup, M. R., D. Chen, S. S. Koh, et al. "Co-operation between protein-acetylating and protein-methylating co-activators in transcriptional activation." Biochemical Society Transactions 28, no. 4 (2000): 415–18. http://dx.doi.org/10.1042/bst0280415.

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Nuclear hormone receptors (NRs) activate transcription by binding to specific enhancer elements associated with target genes. Transcriptional activation is accomplished with the help of complexes of co-activator proteins that bind to NRs. p160 co-activators, a family of three related 160 kDa proteins, serve as primary co-activators by binding directly to NRs and recruiting additional secondary co-activators. Some of these (CBP/p300 and p/CAF) can acetylate histones and other proteins in the transcription complex, thus helping to modify chromatin structure and form an active transcription initi

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Paul, Emily, Z. Iris Zhu, David Landsman, and Randall H. Morse. "Genome-Wide Association of Mediator and RNA Polymerase II in Wild-Type and Mediator Mutant Yeast." Molecular and Cellular Biology 35, no. 1 (2014): 331–42. http://dx.doi.org/10.1128/mcb.00991-14.

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Mediator is a large, multisubunit complex that is required for essentially all mRNA transcription in eukaryotes. In spite of the importance of Mediator, the range of its targets and how it is recruited to these is not well understood. Previous work showed that inSaccharomyces cerevisiae, Mediator contributes to transcriptional activation by two distinct mechanisms, one depending on the tail module triad and favoring SAGA-regulated genes, and the second occurring independently of the tail module and favoring TFIID-regulated genes. Here, we use chromatin immunoprecipitation sequencing (ChIP-seq)

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31

Funamoto, Masafumi, Yoichi Sunagawa, Yasufumi Katanasaka, et al. "Histone Acetylation Domains Are Differentially Induced during Development of Heart Failure in Dahl Salt-Sensitive Rats." International Journal of Molecular Sciences 22, no. 4 (2021): 1771. http://dx.doi.org/10.3390/ijms22041771.

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Histone acetylation by epigenetic regulators has been shown to activate the transcription of hypertrophic response genes, which subsequently leads to the development and progression of heart failure. However, nothing is known about the acetylation of the histone tail and globular domains in left ventricular hypertrophy or in heart failure. The acetylation of H3K9 on the promoter of the hypertrophic response gene was significantly increased in the left ventricular hypertrophy stage, whereas the acetylation of H3K122 did not increase in the left ventricular hypertrophy stage but did significantl

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32

Schlissel, M. S. "TRANSCRIPTION:A Tail of Histone Acetylation and DNA Recombination." Science 287, no. 5452 (2000): 438–40. http://dx.doi.org/10.1126/science.287.5452.438.

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Dehlin, E., A. von Gabain, G. Alm, R. Dingelmaier, and O. Resnekov. "Repression of beta interferon gene expression in virus-infected cells is correlated with a poly(A) tail elongation." Molecular and Cellular Biology 16, no. 2 (1996): 468–74. http://dx.doi.org/10.1128/mcb.16.2.468.

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Expression of beta interferon (IFN-beta) is transiently induced when Namalwa B cells (Burkitt lymphoma cell line) are infected by Sendai virus. In this study, we found that an elongation of the IFN-beta mRNA could be detected in virus-infected cells and that such a modification was not observed when the IFN-beta transcript was induced by a nonviral agent, poly(I-C). Treatment of the cells with a transcriptional inhibitor (actinomycin D or 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole) resulted in further elongation of the transcript. Characterization of the elongated IFN-beta transcript by

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Schaefer, T. S., L. K. Sanders, O. K. Park, and D. Nathans. "Functional differences between Stat3alpha and Stat3beta." Molecular and Cellular Biology 17, no. 9 (1997): 5307–16. http://dx.doi.org/10.1128/mcb.17.9.5307.

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Stat3beta is a short form of Stat3 that differs from the longer form (Stat3alpha) by the replacement of the C-terminal 55 amino acid residues of Stat3alpha by 7 residues specific to Stat3beta. In COS cells transfected with Stat3 expression plasmids, both Stat3alpha and Stat3beta were activated for DNA binding and transcription by the same set of growth factors and cytokines and both, when activated, formed homodimers and heterodimers with Stat1. Only Stat3beta was active in the absence of added cytokine or growth factor. Activation of each form, including constitutive activation of Stat3beta,

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Sripichai, Orapan, Christine M. Kiefer, Natarajan V. Bhanu, et al. "Cytokine-mediated increases in fetal hemoglobin are associated with globin gene histone modification and transcription factor reprogramming." Blood 114, no. 11 (2009): 2299–306. http://dx.doi.org/10.1182/blood-2009-05-219386.

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Abstract Therapeutic regulation of globin genes is a primary goal of translational research aimed toward hemoglobinopathies. Signal transduction was used to identify chromatin modifications and transcription factor expression patterns that are associated with globin gene regulation. Histone modification and transcriptome profiling were performed using adult primary CD34+ cells cultured with cytokine combinations that produced low versus high levels of gamma-globin mRNA and fetal hemoglobin (HbF). Embryonic, fetal, and adult globin transcript and protein expression patterns were determined for

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Lee, Jia-Lin, Mei-Jung Wang, and Jeou-Yuan Chen. "Acetylation and activation of STAT3 mediated by nuclear translocation of CD44." Journal of Cell Biology 185, no. 6 (2009): 949–57. http://dx.doi.org/10.1083/jcb.200812060.

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Expression of the type I transmembrane glycoprotein CD44 has recently been recognized as a signature for cancer stem cells. In this study, we demonstrate that CD44, once engaged, is internalized and translocated to the nucleus, where it binds to various promoters, including that of cyclin D1, leading to cell fate change through transcriptional reprogramming. In regulating cyclin D1 expression, the internalized CD44 forms a complex with STAT3 and p300 (acetyltransferase), eliciting STAT3 acetylation at lysine 685 and dimer formation in a cytokine- and growth factor–independent manner. A biparti

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Li, Chuanyin, Tianting Han, Qingrun Li, et al. "MKRN3-mediated ubiquitination of Poly(A)-binding proteins modulates the stability and translation of GNRH1 mRNA in mammalian puberty." Nucleic Acids Research 49, no. 7 (2021): 3796–813. http://dx.doi.org/10.1093/nar/gkab155.

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Abstract The family of Poly(A)-binding proteins (PABPs) regulates the stability and translation of messenger RNAs (mRNAs). Here we reported that the three members of PABPs, including PABPC1, PABPC3 and PABPC4, were identified as novel substrates for MKRN3, whose deletion or loss-of-function mutations were genetically associated with human central precocious puberty (CPP). MKRN3-mediated ubiquitination was found to attenuate the binding of PABPs to the poly(A) tails of mRNA, which led to shortened poly(A) tail-length of GNRH1 mRNA and compromised the formation of translation initiation complex

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Wing, Helen J., Arthur W. Yan, Seth R. Goldman, and Marcia B. Goldberg. "Regulation of IcsP, the Outer Membrane Protease of the Shigella Actin Tail Assembly Protein IcsA, by Virulence Plasmid Regulators VirF and VirB." Journal of Bacteriology 186, no. 3 (2004): 699–705. http://dx.doi.org/10.1128/jb.186.3.699-705.2004.

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ABSTRACT The Shigella outer membrane protease IcsP removes the actin assembly protein IcsA from the bacterial surface, and consequently modulates Shigella actin-based motility and cell-to-cell spread. Here, we demonstrate that IcsP expression is undetectable in mutants lacking either of two transcriptional activators, VirF and VirB. In wild-type Shigella spp., virB expression is entirely dependent on VirF; therefore, to circumvent this regulatory cascade, we independently expressed VirF or VirB in Shigella strains lacking both activators and measured both IcsP levels and transcription from the

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Yang, Zungyoon, Chunyang Zheng, Christophe Thiriet, and Jeffrey J. Hayes. "The Core Histone N-Terminal Tail Domains Negatively Regulate Binding of Transcription Factor IIIA to a Nucleosome Containing a 5S RNA Gene via a Novel Mechanism." Molecular and Cellular Biology 25, no. 1 (2005): 241–49. http://dx.doi.org/10.1128/mcb.25.1.241-249.2005.

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ABSTRACT Reconstitution of a DNA fragment containing a 5S RNA gene from Xenopus borealis into a nucleosome greatly restricts binding of the primary 5S transcription factor, TFIIIA. Consistent with transcription experiments using reconstituted templates, removal of the histone tail domains stimulates TFIIIA binding to the 5S nucleosome greater than 100-fold. However, we show that tail removal increases the probability of 5S DNA unwrapping from the core histone surface by only approximately fivefold. Moreover, using site-specific histone-to-DNA cross-linking, we show that TFIIIA binding neither

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Pande, Amit, Wojciech Makalowski, Jürgen Brosius, and Carsten A. Raabe. "Enhancer occlusion transcripts regulate the activity of human enhancer domains via transcriptional interference: a computational perspective." Nucleic Acids Research 48, no. 7 (2020): 3435–54. http://dx.doi.org/10.1093/nar/gkaa026.

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Abstract Analysis of ENCODE long RNA-Seq and ChIP-seq (Chromatin Immunoprecipitation Sequencing) datasets for HepG2 and HeLa cell lines uncovered 1647 and 1958 transcripts that interfere with transcription factor binding to human enhancer domains. TFBSs (Transcription Factor Binding Sites) intersected by these ‘Enhancer Occlusion Transcripts’ (EOTrs) displayed significantly lower relative transcription factor (TF) binding affinities compared to TFBSs for the same TF devoid of EOTrs. Expression of most EOTrs was regulated in a cell line specific manner; analysis for the same TFBSs across cell l

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Erazo, Tatiana, Sergio Espinosa-Gil, Nora Diéguez-Martínez, Néstor Gómez, and Jose M. Lizcano. "SUMOylation Is Required for ERK5 Nuclear Translocation and ERK5-Mediated Cancer Cell Proliferation." International Journal of Molecular Sciences 21, no. 6 (2020): 2203. http://dx.doi.org/10.3390/ijms21062203.

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The MAP kinase ERK5 contains an N-terminal kinase domain and a unique C-terminal tail including a nuclear localization signal and a transcriptional activation domain. ERK5 is activated in response to growth factors and stresses and regulates transcription at the nucleus by either phosphorylation or interaction with transcription factors. MEK5-ERK5 pathway plays an important role regulating cancer cell proliferation and survival. Therefore, it is important to define the precise molecular mechanisms implicated in ERK5 nucleo-cytoplasmic shuttling. We previously described that the molecular chape

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Reddy, Anireddy S. N., Jie Huang, Naeem H. Syed, Asa Ben-Hur, Suomeng Dong, and Lianfeng Gu. "Decoding co-/post-transcriptional complexities of plant transcriptomes and epitranscriptome using next-generation sequencing technologies." Biochemical Society Transactions 48, no. 6 (2020): 2399–414. http://dx.doi.org/10.1042/bst20190492.

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Next-generation sequencing (NGS) technologies - Illumina RNA-seq, Pacific Biosciences isoform sequencing (PacBio Iso-seq), and Oxford Nanopore direct RNA sequencing (DRS) - have revealed the complexity of plant transcriptomes and their regulation at the co-/post-transcriptional level. Global analysis of mature mRNAs, transcripts from nuclear run-on assays, and nascent chromatin-bound mRNAs using short as well as full-length and single-molecule DRS reads have uncovered potential roles of different forms of RNA polymerase II during the transcription process, and the extent of co-transcriptional

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Proudfoot, Nicholas J. "Post-Transcriptional Regulation: Chasing your own poly(A) tail." Current Biology 4, no. 4 (1994): 359–61. http://dx.doi.org/10.1016/s0960-9822(00)00080-4.

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Hartzog, G. A., and J. W. Tamkun. "A new role for histone tail modifications in transcription elongation." Genes & Development 21, no. 24 (2007): 3209–13. http://dx.doi.org/10.1101/gad.1628707.

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Dang, Chi V. "c‐ MYC mRNA tail tale about glutamine control of transcription." EMBO Journal 36, no. 13 (2017): 1806–8. http://dx.doi.org/10.15252/embj.201796999.

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Vermaak, Danielle, Paul A. Wade, Peter L. Jones, Yun-Bo Shi, and Alan P. Wolffe. "Functional Analysis of the SIN3-Histone Deacetylase RPD3-RbAp48-Histone H4 Connection in the XenopusOocyte." Molecular and Cellular Biology 19, no. 9 (1999): 5847–60. http://dx.doi.org/10.1128/mcb.19.9.5847.

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ABSTRACT We investigated the protein associations and enzymatic requirements for the Xenopus histone deacetylase catalytic subunit RPD3 to direct transcriptional repression in Xenopus oocytes. Endogenous Xenopus RPD3 is present in nuclear and cytoplasmic pools, whereas RbAp48 and SIN3 are predominantly nuclear. We cloned Xenopus RbAp48 and SIN3 and show that expression of RPD3, but not RbAp48 or SIN3, leads to an increase in nuclear and cytoplasmic histone deacetylase activity and transcriptional repression of the TRβA promoter. This repression requires deacetylase activity and nuclear import

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Griffin, K. J., S. L. Amacher, C. B. Kimmel, and D. Kimelman. "Molecular identification of spadetail: regulation of zebrafish trunk and tail mesoderm formation by T-box genes." Development 125, no. 17 (1998): 3379–88. http://dx.doi.org/10.1242/dev.125.17.3379.

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Inhibition of fibroblast growth factor (FGF) signaling prevents trunk and tail formation in Xenopus and zebrafish embryos. While the T-box transcription factor Brachyury (called No Tail in zebrafish) is a key mediator of FGF signaling in the notochord and tail, the pathways activated by FGF in non-notochordal trunk mesoderm have been uncertain. Previous studies have shown that the spadetail gene is required for non-notochordal trunk mesoderm formation; spadetail mutant embryos have major trunk mesoderm deficiencies, but relatively normal tail and notochord development. We demonstrate here that

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Protacio, R. U., G. Li, P. T. Lowary, and J. Widom. "Effects of Histone Tail Domains on the Rate of Transcriptional Elongation through a Nucleosome." Molecular and Cellular Biology 20, no. 23 (2000): 8866–78. http://dx.doi.org/10.1128/mcb.20.23.8866-8878.2000.

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ABSTRACT The N-terminal tail domains of the core histones play important roles in gene regulation, but the exact mechanisms through which they act are not known. Recent studies suggest that the tail domains may influence the ability of RNA polymerase to elongate through the nucleosomal DNA and, thus, that posttranslational modification of the tail domains may provide a control point for gene regulation through effects on the elongation rate. We take advantage of an experimental system that uses bacteriophage T7 RNA polymerase as a probe for aspects of nucleosome transcription that are dominate

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Nagarajan, Roopa, RP Sharmila Devi, VH Savitha, and Lakshmi Venkatesh. "A self-learning module for students of speech-language pathology in phonetic transcription of Tamil." Journal of Indian Speech Language & Hearing Association 30, no. 1 (2016): 17. http://dx.doi.org/10.4103/0974-2131.196254.

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Alff, Peter J., Irina N. Gavrilovskaya, Elena Gorbunova, et al. "The Pathogenic NY-1 Hantavirus G1 Cytoplasmic Tail Inhibits RIG-I- and TBK-1-Directed Interferon Responses." Journal of Virology 80, no. 19 (2006): 9676–86. http://dx.doi.org/10.1128/jvi.00508-06.

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ABSTRACT Hantaviruses cause two diseases with prominent vascular permeability defects, hemorrhagic fever with renal syndrome and hantavirus pulmonary syndrome. All hantaviruses infect human endothelial cells, although it is unclear what differentiates pathogenic from nonpathogenic hantaviruses. We observed dramatic differences in interferon-specific transcriptional responses between pathogenic and nonpathogenic hantaviruses at 1 day postinfection, suggesting that hantavirus pathogenesis may in part be determined by viral regulation of cellular interferon responses. In contrast to pathogenic NY

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