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Transcriptional elongation

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https://www.readbyqxmd.com/read/28743025/rna-polymerase-i-and-iii-similar-yet-unique
#1
REVIEW
Heena Khatter, Matthias K Vorländer, Christoph W Müller
The majority of non-protein-coding RNAs present in eukaryotic cells comprises rRNAs, tRNAs and U6 snRNA that are involved in protein biosynthesis and are synthesized by DNA-dependent-RNA polymerase I and III. The transcription cycle (initiation, elongation and termination) has similar principles in all three nuclear RNA polymerases with specific features that are reflected back in their structures. Recently, owing to the 'resolution revolution' in electron cryo-microscopy, there has been a significant advancement in the understanding of these molecular machines...
July 22, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28735898/genome-wide-single-molecule-footprinting-reveals-high-rna-polymerase-ii-turnover-at-paused-promoters
#2
Arnaud R Krebs, Dilek Imanci, Leslie Hoerner, Dimos Gaidatzis, Lukas Burger, Dirk Schübeler
Transcription initiation entails chromatin opening followed by pre-initiation complex formation and RNA polymerase II recruitment. Subsequent polymerase elongation requires additional signals, resulting in increased residence time downstream of the start site, a phenomenon referred to as pausing. Here, we harnessed single-molecule footprinting to quantify distinct steps of initiation in vivo throughout the Drosophila genome. This identifies the impact of promoter structure on initiation dynamics in relation to nucleosomal occupancy...
July 19, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28732084/increased-parb-level-affects-expression-of-stress-response-adaptation-and-virulence-operons-and-potentiates-repression-of-promoters-adjacent-to-the-high-affinity-binding-sites-pars3-and-pars4-in-pseudomonas-aeruginosa
#3
Adam Kawalek, Krzysztof Glabski, Aneta Agnieszka Bartosik, Anna Fogtman, Grazyna Jagura-Burdzy
Similarly to its homologs in other bacteria, Pseudomonas aeruginosa partitioning protein ParB facilitates segregation of newly replicated chromosomes. Lack of ParB is not lethal but results in increased frequency of anucleate cells production, longer division time, cell elongation, altered colony morphology and defective swarming and swimming motility. Unlike in other bacteria, inactivation of parB leads to major changes of the transcriptome, suggesting that, directly or indirectly, ParB plays a role in regulation of gene expression in this organism...
2017: PloS One
https://www.readbyqxmd.com/read/28731845/rho-protein-roles-and-mechanisms
#4
Pallabi Mitra, Gairika Ghosh, Md Hafeezunnisa, Ranjan Sen
At the end of the multistep transcription process, the elongating RNA polymerase (RNAP) is dislodged from the DNA template either at specific DNA sequences, called the terminators, or by a nascent RNA-dependent helicase, Rho. In Escherichia coli, about half of the transcription events are terminated by the Rho protein. Rho utilizes its RNA-dependent ATPase activities to translocate along the mRNA and eventually dislodges the RNAP via an unknown mechanism. The transcription elongation factor NusG facilitates this termination process by directly interacting with Rho...
July 21, 2017: Annual Review of Microbiology
https://www.readbyqxmd.com/read/28731049/composite-hemangioendothelioma-with-neuroendocrine-marker-expression-an-aggressive-variant
#5
Kyle D Perry, Alyaa Al-Lbraheemi, Brian P Rubin, Jin Jen, Hongzheng Ren, Jin Sung Jang, Asha Nair, Jaime Davila, Stefan Pambuccian, Andrew Horvai, William Sukov, Henry D Tazelaar, Andrew L Folpe
Aberrant expression of neuroendocrine markers is extremely rare in endothelial neoplasms, with only a single report describing three cases. Although originally classified as conventional angiosarcoma, further assessment of these tumors revealed a strikingly composite morphology composed of retiform and epithelioid elements reminiscent of composite hemangioendothelioma, a rare subtype of hemangioendothelioma. To further investigate these findings, available materials from 11 morphologically distinctive endothelial tumors showing neuroendocrine marker expression were retrieved from our archives...
July 21, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/28724617/human-venous-valve-disease-caused-by-mutations-in-foxc2-and-gjc2
#6
Oliver Lyons, Prakash Saha, Christopher Seet, Adam Kuchta, Andrew Arnold, Steven Grover, Victoria Rashbrook, Amélie Sabine, Gema Vizcay-Barrena, Ash Patel, Francesca Ludwinski, Soundrie Padayachee, Tsutomu Kume, Brenda R Kwak, Glen Brice, Sahar Mansour, Pia Ostergaard, Peter Mortimer, Steve Jeffery, Nigel Brown, Taija Makinen, Tatiana V Petrova, Bijan Modarai, Alberto Smith
Venous valves (VVs) prevent venous hypertension and ulceration. We report that FOXC2 and GJC2 mutations are associated with reduced VV number and length. In mice, early VV formation is marked by elongation and reorientation ("organization") of Prox1(hi) endothelial cells by postnatal day 0. The expression of the transcription factors Foxc2 and Nfatc1 and the gap junction proteins Gjc2, Gja1, and Gja4 were temporospatially regulated during this process. Foxc2 and Nfatc1 were coexpressed at P0, and combined Foxc2 deletion with calcineurin-Nfat inhibition disrupted early Prox1(hi) endothelial organization, suggesting cooperative Foxc2-Nfatc1 patterning of these events...
July 19, 2017: Journal of Experimental Medicine
https://www.readbyqxmd.com/read/28724529/coactivators-and-general-transcription-factors-have-two-distinct-dynamic-populations-dependent-on%C3%A2-transcription
#7
Nikolaos Vosnakis, Marc Koch, Elisabeth Scheer, Pascal Kessler, Yves Mély, Pascal Didier, László Tora
SAGA and ATAC are two distinct chromatin modifying co-activator complexes with distinct enzymatic activities involved in RNA polymerase II (Pol II) transcription regulation. To investigate the mobility of co-activator complexes and general transcription factors in live-cell nuclei, we performed imaging experiments based on photobleaching. SAGA and ATAC, but also two general transcription factors (TFIID and TFIIB), were highly dynamic, exhibiting mainly transient associations with chromatin, contrary to Pol II, which formed more stable chromatin interactions...
July 19, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28722178/cdk9-a-key-player-in-cancer-and-other-diseases
#8
Lia Carolina Franco, Fátima Morales, Silvia Boffo, Antonio Giordano
Cyclin-Dependent Kinase 9 (CDK9) is part of a functional diverse group of enzymes responsible for cell cycle control and progression. It associates mainly with Cyclin T1 and forms the Positive Transcription Elongation Factor b (p-TEFb) complex responsible for regulation of transcription elongation and mRNA maturation. Recent studies have highlighted the importance of CDK9 in many relevant pathologic processes, like cancer, cardiovascular diseases and viral replication. Herein we provide an overview of the different pathways in which CDK9 is directly and indirectly involved...
July 19, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28720596/elongator-regulates-hypocotyl-growth-in-darkness-and-during-photomorphogenesis
#9
Magdalena Woloszynska, Olimpia Gagliardi, Filip Vandenbussche, Steven De Groeve, Luis Alonso Baez, Pia Neyt, Sabine Le Gall, Jorge Fung, Paloma Mas, Dominique Van Der Straeten, Mieke Van Lijsebettens
Elongator promotes RNA polymerase II-mediated transcript elongation through epigenetic activities such as histone acetylation. Elongator regulates growth, development, immune response, sensitivity to drought and abscisic acid. We demonstrate that elo mutants exhibit defective hypocotyl elongation but have a normal apical hook in darkness and are hyposensitive to light during photomorphogenesis. These elo phenotypes are supported by transcriptome changes, i.e. downregulation of circadian clock components, positive regulators of skoto- or photomorphogenesis, hormonal pathways and cell wall biogenesis-related factors...
July 18, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/28720252/the-cryptochrome-photolyase-protein-family-in-diatoms
#10
Sarah König, Matthias Juhas, Stefanie Jäger, Tilman Kottke, Claudia Büchel
The cryptochrome - photolyase family (CPF) consists of homologous flavoproteins having completely different functions involving DNA repair, circadian rhythm and/or photoreception. From the original photolyases, working either as (6-4) or cyclobutane pyrimidine dimer photolyases, the animal- and plant-type cryptochromes, respectively, evolved and also the more intermediate DASH cryptochromes. Whereas animal cryptochromes work mostly in clock-related functions, plant cryptochromes are also directly involved in developmental processes such as hypocotyl elongation or flower induction...
July 8, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28717009/acetylation-on-histone-h3-lysine-9-mediates-a-switch-from-transcription-initiation-to-elongation
#11
Leah A Gates, Jiejun Shi, Aarti D Rohira, Qin Feng, Bokai Zhu, Mark T Bedford, Cari A Sagum, Sung Yun Jung, Jun Qin, Ming-Jer Tsai, Sophia Y Tsai, Wei Li, Charles E Foulds, Bert W O'Malley
The transition from transcription initiation to elongation is a key regulatory step in gene expression, which requires RNA polymerase II (Pol II) to escape promoter proximal pausing on chromatin. While elongation factors promote pause release leading to transcription elongation, the role of epigenetic modifications during this critical transition step is poorly understood. Two histone marks on histone H3, lysine 4 trimethylation (H3K4me3) and lysine 9 acetylation (H3K9ac), co-localize on active gene promoters and are associated with active transcription...
July 17, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28715973/the-molecular-basis-for-human-immunodeficiency-virus-latency
#12
Uri Mbonye, Jonathan Karn
Although potent combination antiretroviral therapy can effectively block viral replication in the host, human immunodeficiency virus (HIV) persists due to the existence of latent but replication-competent proviruses residing primarily in a very small population of resting memory CD4(+) T cells. Viral latency is established when the expression of the autoregulatory viral trans-activating factor Tat is reduced to subthreshold levels. The absence of Tat reduces HIV transcription and protein production to levels that make the host cell invisible to the immune system and refractory to antiretroviral treatment...
July 17, 2017: Annual Review of Virology
https://www.readbyqxmd.com/read/28710288/post-transcriptional-control-of-gene-expression-following-stress-the-role-of-rna-binding-proteins
#13
REVIEW
Robert Harvey, Veronica Dezi, Mariavittoria Pizzinga, Anne E Willis
The ability of mammalian cells to modulate global protein synthesis in response to cellular stress is essential for cell survival. While control of protein synthesis is mediated by the regulation of eukaryotic initiation and elongation factors, RNA-binding proteins (RBPs) provide a crucial additional layer to post-transcriptional regulation. RBPs bind specific RNA through conserved RNA-binding domains and ensure that the information contained within the genome and transcribed in the form of RNA is exported to the cytoplasm, chemically modified, and translated prior to folding into a functional protein...
July 14, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28710103/transcription-elongation-factors-are-potential-targets-in-glioblastoma
#14
(no author information available yet)
JMJD6 promotes transcription pause-release and elongation and glioblastoma cell survival in vivo.
July 14, 2017: Cancer Discovery
https://www.readbyqxmd.com/read/28708834/osmph1-regulates-plant-height-and-improves-grain-yield-in-rice
#15
Yongxing Zhang, Chunsheng Yu, Jianzhong Lin, Jun Liu, Bin Liu, Jian Wang, Aobo Huang, Hongyu Li, Tao Zhao
Plant height is a major trait affecting yield potential in rice. Using a large-scale hybrid transcription factor approach, we identified the novel MYB-like transcription factor OsMPH1 (MYB-like gene of Plant Height 1), which is involved in the regulation of plant height in rice. Overexpression of OsMPH1 leads to increases of plant height and grain yield in rice, while knockdown of OsMPH1 leads to the opposite phenotypes. Microscopy of longitudinal stem sections indicated that a change in internode cell length resulted in the change in plant height...
2017: PloS One
https://www.readbyqxmd.com/read/28708516/peroxisome-proliferator-activated-receptor-ppar-isoforms-are-differentially-expressed-in-peri-implantation-porcine-conceptuses
#16
Agnieszka Blitek, Magdalena Szymanska
Peroxisome proliferator-activated receptors (PPARs) are members of the nuclear receptor family of ligand-dependent transcription factors. PPARs are critical regulators of glucose homeostasis and lipid metabolism, and affect cell proliferation and differentiation. In the current study, we examined (1) the profiles of PPARA, PPARD, and PPARG mRNA expression and DNA binding activity in porcine conceptuses collected on Days 10-11 (spherical and tubular conceptuses), 11-12 (filamentous conceptuses), 13-14, and 15-16 (elongated conceptuses) of pregnancy, (2) the presence of PPARA, PPARD, and PPARG proteins in Days 10, 12, and 15 conceptuses...
June 13, 2017: Theriogenology
https://www.readbyqxmd.com/read/28707908/mechanical-properties-of-transcription
#17
Stuart A Sevier, Herbert Levine
The mechanical properties of transcription have recently been shown to play a central role in gene expression. However, a full physical characterization of this central biological process is lacking. In this Letter, we introduce a simple description of the basic physical elements of transcription where RNA elongation, RNA polymerase rotation, and DNA supercoiling are coupled. The resulting framework describes the relative amount of RNA polymerase rotation and DNA supercoiling that occurs during RNA elongation...
June 30, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28706132/identification-of-a-novel-metastasis-inducing-lncrna-which-suppresses-the-kai1-cd82-metastasis-suppressor-gene-and-is-upregulated-in-triple-negative-breast-cancer
#18
Ronni Aram, Iris Dotan, Agnes Hotz-Wagenblatt, Dan Canaani
Inactivation of tumor/metastasis suppressor genes via epigenetic silencing is a frequent event in human cancers. KAI1/CD82 is a metastasis suppressor gene whose normal protecting activity is deficient in twelve different solid malignancies. Here we have identified and characterized a primarily nuclear non-polyadenylated, antisense (as)-lncRNA, initiating upstream of the KAI1 human metastasis suppressor gene transcription start site; and elongating in the opposite direction to KAI1 mRNA. We show that the KAI1 promoter is bi-directional giving rise to KAI1 mRNA and its as-lncRNA...
June 28, 2017: Oncotarget
https://www.readbyqxmd.com/read/28704511/genetic-variation-analysis-and-relationships-among-environmental-strains-of-scedosporium-apiospermum-sensu-stricto-in-bangkok-thailand
#19
Thanwa Wongsuk, Potjaman Pumeesat, Natthanej Luplertlop
The Scedosporium apiospermum species complex is an emerging filamentous fungi that has been isolated from environment. It can cause a wide range of infections in both immunocompetent and immunocompromised individuals. We aimed to study the genetic variation and relationships between 48 strains of S. apiospermum sensu stricto isolated from soil in Bangkok, Thailand. For PCR, sequencing and phylogenetic analysis, we used the following genes: actin; calmodulin exons 3 and 4; the second largest subunit of the RNA polymerase II; ß-tubulin exon 2-4; manganese superoxide dismutase; internal transcribed spacer; transcription elongation factor 1α; and beta-tubulin exons 5 and 6...
2017: PloS One
https://www.readbyqxmd.com/read/28702047/transcriptome-analysis-of-al-induced-genes-in-buckwheat-fagopyrum-esculentum-moench-root-apex-new-insight-into-al-toxicity-and-resistance-mechanisms-in-an-al-accumulating-species
#20
Jia Meng Xu, Wei Fan, Jian Feng Jin, He Qiang Lou, Wei Wei Chen, Jian Li Yang, Shao Jian Zheng
Relying on Al-activated root oxalate secretion, and internal detoxification and accumulation of Al, buckwheat is highly Al resistant. However, the molecular mechanisms responsible for these processes are still poorly understood. It is well-known that root apex is the critical region of Al toxicity that rapidly impairs a series of events, thus, resulting in inhibition of root elongation. Here, we carried out transcriptome analysis of the buckwheat root apex (0-1 cm) with regards to early response (first 6 h) to Al stress (20 μM), which is crucial for identification of both genes and processes involved in Al toxicity and tolerance mechanisms...
2017: Frontiers in Plant Science
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