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transcription elongation

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https://www.readbyqxmd.com/read/28938651/positive-transcription-elongation-factor-b-p-tefb-is-a-therapeutic-target-in-human-multiple-myeloma
#1
Yu Zhang, Liang Zhou, Yun Leng, Yun Dai, Robert Z Orlowski, Steven Grant
The role of the positive RNA Pol II regulator, P-TEFb (positive transcription elongation factor b), in maintenance of the anti-apoptotic protein Mcl-1 and bortezomib (btz) resistance was investigated in human multiple myeloma (MM) cells. Mcl-1 was up-regulated in all MM lines tested, including bortezomib-resistant lines, human MM xenograft mouse models, and primary CD138(+) MM cells. Mcl-1 over-expression significantly reduced bortezomib lethality, indicating a functional role for Mcl-1 in bortezomib resistance...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28936224/role-of-crrlk1l-cell-wall-sensors-hercules1-and-2-theseus1-and-feronia-in-growth-adaptation-triggered-by-heavy-metals-and-trace-elements
#2
Julia Richter, Marie Ploderer, Gaëlle Mongelard, Laurent Gutierrez, Marie-Theres Hauser
Cell walls are not only a protective barrier surrounding protoplasts but serve as signaling platform between the extracellular environment and the intracellular physiology. Ions of heavy metals and trace elements, summarized to metal ions, bind to cell wall components, trigger their modification and provoke growth responses. To examine if metal ions trigger cell wall sensing receptor like kinases (RLKs) of the Catharanthus roseus RLK1-like (CrRLK1L) family we employed a molecular genetic approach. Quantitative transcription analyses show that HERCULES1 (HERK1), THESEUS1 (THE1), and FERONIA (FER) were differently regulated by cadmium (Cd), nickel (Ni), and lead (Pb)...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28934475/in-vivo-probing-of-nascent-rna-structures-reveals-principles-of-cotranscriptional-folding
#3
Danny Incarnato, Edoardo Morandi, Francesca Anselmi, Lisa M Simon, Giulia Basile, Salvatore Oliviero
Defining the in vivo folding pathway of cellular RNAs is essential to understand how they reach their final native conformation. We here introduce a novel method, named Structural Probing of Elongating Transcripts (SPET-seq), that permits single-base resolution analysis of transcription intermediates' secondary structures on a transcriptome-wide scale, enabling base-resolution analysis of the RNA folding events. Our results suggest that cotranscriptional RNA folding in vivo is a mixture of cooperative folding events, in which local RNA secondary structure elements are formed as they get transcribed, and non-cooperative events, in which 5'-halves of long-range helices get sequestered into transient non-native interactions until their 3' counterparts have been transcribed...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28933854/epigenetic-dna-modification-n6-methyladenine-causes-site-specific-rna-polymerase-ii-transcriptional-pausing
#4
Wei Wang, Liang Xu, Lulu Hu, Jenny Chong, Chuan He, Dong Wang
N6-methyladenine (N6-mA or 6mA) is an epigenetic DNA modification in eukaryotic genomes. In contrast to the well-established roles of 5-methylcytosine for epigenetic regulation of gene expression, the functional roles of N6-mA remain elusive. In particular, the impact of N6-mA modification at DNA template on RNA polymerase II (pol II) transcription elongation is not known. In this work, using the Saccharomyces cerevisiae pol II transcriptional elongation system as a model, we investigated the molecular mechanism of pol II recognition and processing of N6-mA sites via both biochemical and structural approaches...
September 21, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28931938/dynamic-transcriptome-and-phytohormone-profiling-along-the-time-of-light-exposure-in-the-mesocotyl-of-rice-seedling
#5
Fangjun Feng, Hanwei Mei, Peiqing Fan, Yanan Li, Xiaoyan Xu, Haibin Wei, Ming Yan, Lijun Luo
Mesocotyl elongation is an important trait influencing seedling emergence and establishment in rice direct-seeding cultivation and is immediately inhibited after light exposure. Detailed researches on the molecular basis and biological processes underlying light repression of mesocotyl growth could probably provide useful information for key factors controlling this trait. Here we monitored the transcriptome and endogenous phytohormone changes specifically in the elongating mesocotyl in response to light exposure with a time-course...
September 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28931375/identification-of-fasciclin-like-arabinogalactan-proteins-in-textile-hemp-cannabis-sativa-l-in-silico-analyses-and-gene-expression-patterns-in-different-tissues
#6
Gea Guerriero, Lauralie Mangeot-Peter, Sylvain Legay, Marc Behr, Stanley Lutts, Khawar Sohail Siddiqui, Jean-Francois Hausman
BACKGROUND: The fasciclin-like arabinogalactan proteins (FLAs) belong to the arabinogalactan protein (AGP) superfamily and are known to play different physiological roles in plants. This class of proteins was shown to participate in plant growth, development, defense against abiotic stresses and, notably, cell wall biosynthesis. Although some studies are available on the characterization of FLA genes from different species, both woody and herbaceous, no detailed information is available on the FLA family of textile hemp (Cannabis sativa L...
September 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28930680/systematic-kinase-inhibitor-profiling-identifies-cdk9-as-a-synthetic-lethal-target-in-nut-midline-carcinoma
#7
Johannes Brägelmann, Marcel A Dammert, Felix Dietlein, Johannes M Heuckmann, Axel Choidas, Stefanie Böhm, André Richters, Debjit Basu, Verena Tischler, Carina Lorenz, Peter Habenberger, Zhizhou Fang, Sandra Ortiz-Cuaran, Frauke Leenders, Jan Eickhoff, Uwe Koch, Matthäus Getlik, Martin Termathe, Muhammad Sallouh, Zoltán Greff, Zoltán Varga, Hyatt Balke-Want, Christopher A French, Martin Peifer, H Christian Reinhardt, László Örfi, György Kéri, Sascha Ansén, Lukas C Heukamp, Reinhard Büttner, Daniel Rauh, Bert M Klebl, Roman K Thomas, Martin L Sos
Kinase inhibitors represent the backbone of targeted cancer therapy, yet only a limited number of oncogenic drivers are directly druggable. By interrogating the activity of 1,505 kinase inhibitors, we found that BRD4-NUT-rearranged NUT midline carcinoma (NMC) cells are specifically killed by CDK9 inhibition (CDK9i) and depend on CDK9 and Cyclin-T1 expression. We show that CDK9i leads to robust induction of apoptosis and of markers of DNA damage response in NMC cells. While both CDK9i and bromodomain inhibition over time result in reduced Myc protein expression, only bromodomain inhibition induces cell differentiation and a p21-induced cell-cycle arrest in these cells...
September 19, 2017: Cell Reports
https://www.readbyqxmd.com/read/28930676/localized-phosphorylation-of-a-kinesin-1-adaptor-by-a-capsid-associated-kinase-regulates-hiv-1-motility-and-uncoating
#8
Viacheslav Malikov, Mojgan H Naghavi
Although microtubule motors mediate intracellular virus transport, the underlying interactions and control mechanisms remain poorly defined. This is particularly true for HIV-1 cores, which undergo complex, interconnected processes of cytosolic transport, reverse transcription, and uncoating of the capsid shell. Although kinesins have been implicated in regulating these events, curiously, there are no direct kinesin-core interactions. We recently showed that the capsid-associated kinesin-1 adaptor protein, fasciculation and elongation protein zeta-1 (FEZ1), regulates HIV-1 trafficking...
September 19, 2017: Cell Reports
https://www.readbyqxmd.com/read/28923978/mcam-contributes-to-the-establishment-of-cell-autonomous-polarity-in-myogenic-and-chondrogenic-differentiation
#9
Artal Moreno-Fortuny, Laricia Bragg, Giulio Cossu, Urmas Roostalu
Cell polarity has a fundamental role in shaping the morphology of cells and growing tissues. Polarity is commonly thought to be established in response to extracellular signals. Here we used a minimal in vitro assay that enabled us to monitor the determination of cell polarity in myogenic and chondrogenic differentiation in the absence of external signalling gradients. We demonstrate that the initiation of cell polarity is regulated by melanoma cell adhesion molecule (MCAM). We found highly polarized localization of MCAM, Moesin (MSN), Scribble (SCRIB) and Van-Gogh-like 2 (VANGL2) at the distal end of elongating myotubes...
September 18, 2017: Biology Open
https://www.readbyqxmd.com/read/28919888/the-sporothrix-schenckii-gene-encoding-for-the-ribosomal-protein-l6-has-constitutive-and-stable-expression-and-works-as-an-endogenous-control-in-gene-expression-analysis
#10
Elías Trujillo-Esquivel, José A Martínez-Álvarez, Diana M Clavijo-Giraldo, Nahúm V Hernández, Alberto Flores-Martínez, Patricia Ponce-Noyola, Héctor M Mora-Montes
Sporothrix schenckii is one of the causative agents of sporotrichosis, a worldwide-distributed mycosis that affects humans and other mammals. The interest in basic and clinical features of this organism has significantly increased in the last years, yet little progress in molecular aspects has been reported. Gene expression analysis is a set of powerful tools that helps to assess the cell response to changes in the extracellular environment, the genetic networks controlling metabolic pathways, and the adaptation to different growth conditions...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28916594/della-gaf1-complex-is-a-main-component-in-gibberellin-feedback-regulation-of-ga20ox2-in-arabidopsis
#11
Jutarou Fukazawa, Masahiko Mori, Satoshi Watanabe, Chika Miyamoto, Takeshi Ito, Yohsuke Takahashi
Gibberellins (GAs) are phytohormones that regulate many aspects of plant growth and development, including germination, elongation, flowering, and floral development. Negative feedback regulation contributes to homeostasis of the GA level. DELLAs are negative regulators of GA signaling and are rapidly degraded in the presence of GAs. DELLAs regulate many target genes, including AtGA20ox2, encoding the GA-biosynthetic enzyme GA 20-oxidase. As DELLAs do not have an apparent DNA-binding motif, transcription factors that act in association with DELLA are necessary for regulating the target genes...
September 15, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28914981/fna-cytology-of-solitary-fibrous-tumors-and-the-diagnostic-value-of-stat6-immunocytochemistry
#12
Edneia Tani, Johan Wejde, Kristina Åström, Inga-Lill Wingmo, Olle Larsson, Felix Haglund
BACKGROUND: Solitary fibrous tumors (SFTs) are rare mesenchymal tumors commonly located in the pleura, soft tissues, or meninges and are characterized by the NGFI-A-binding protein 2 (NAB2)-signal transducer and activator of transcription 6 (STAT6) fusion gene. Recent studies have indicated that nuclear STAT6 immunohistochemistry is a specific marker for SFTs. METHODS: The authors reviewed fine-needle aspiration (FNA) specimens from extracranial SFTs diagnosed at their institution between 1993 and 2017...
September 15, 2017: Cancer
https://www.readbyqxmd.com/read/28912063/differential-expression-by-chromatin-modifications-of-alcohol-dehydrogenase-1-of-chorispora-bungeana-in-cold-stress
#13
Lijun Liu, Yuan Song, Jun Xu, Dongming Li, Gaopeng Li, Lizhe An
Epigenetic modifications regulate plant genes to cope with a variety of environmental stresses. Chorispora bungeana is an alpine subnival plant with strong tolerance to multiple abiotic stresses, especially cold stress. In this study, we characterized the alcohol dehydrogenase 1 gene from Chorispora bungeana, CbADH1, that is up-regulated in cold conditions. Overexpression of CbADH1 in Arabidopsis thaliana improved cold tolerance, as indicated by a decreased lethal temperature (LT50). Chromatin immunoprecipitation assays showed that histone H3 is removed from the promoter region and the middle-coding region of the gene...
September 11, 2017: Gene
https://www.readbyqxmd.com/read/28904013/integrative-analysis-of-rna-polymerase-ii-and-transcriptional-dynamics-upon-myc-activation
#14
Stefano de Pretis, Theresia R Kress, Marco J Morelli, Arianna Sabò, Chiara Locarno, Alessandro Verrecchia, Mirko Doni, Stefano Campaner, Bruno Amati, Mattia Pelizzola
Overexpression of the MYC transcription factor causes its widespread interaction with regulatory elements in the genome but leads to the up- and down-regulation of discrete sets of genes. The molecular determinants of these selective transcriptional responses remain elusive. Here, we present an integrated time-course analysis of transcription and mRNA dynamics following MYC activation in proliferating mouse fibroblasts, based on chromatin immunoprecipitation, metabolic labeling of newly synthesized RNA, extensive sequencing, and mathematical modeling...
September 13, 2017: Genome Research
https://www.readbyqxmd.com/read/28902388/transcriptional-repression-in-macrophages-basic-mechanisms-and-alterations-in-metabolic-inflammatory-diseases
#15
REVIEW
Eckardt Treuter, Rongrong Fan, Zhiqiang Huang, Tomas Jakobsson, Nicolas Venteclef
Macrophage differentiation and signal responses are coordinated by closely linked transcriptional and epigenomic mechanisms that trigger gene expression. In contrast to well-characterized transcriptional activation pathways in response to diverse metabolic and inflammatory signals, we just begin appreciating that transcriptional repression is equally important. Here we will highlight macrophage pathways that are controlled by multifaceted repression events, along with a discussion of underlying regulatory mechanisms and components...
September 13, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28893556/the-ilk-mmp9-mrtf-axis-is-crucial-for-endmt-differentiation-of-endothelial-cells-in-a-tumor-microenvironment
#16
Wojciech M Ciszewski, Katarzyna Sobierajska, Marta E Wawro, Wanda Klopocka, Natasza Chefczyńska, Angelika Muzyczuk, Kamil Siekacz, Agata Wujkowska, Jolanta Niewiarowska
Increasing evidence indicates that the tumor microenvironment is a critical factor supporting cancer progression, chemoresistance and metastasis. Recently, cancer-associated fibroblasts (CAFs) have been recognized as a crucial tumor stromal component promoting cancer growth and invasiveness via modulation of the extracellular matrix (ECM) structure, tumor metabolism and immune reprogramming. One of the main sources of CAFs are endothelial cells undergoing the endothelial-mesenchymal transition (EndMT). EndMT is mainly promoted by the Transforming Growth Factor-β (TGF-β) family secreted by tumor cells, though the role of particular members in EndMT regulation remains poorly understood...
September 8, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28893534/solution-structure-of-the-n-terminal-domain-of-mediator-subunit-med26-and-molecular-characterization-of-its-interaction-with-eaf1-and-taf7
#17
Zoé Lens, François-Xavier Cantrelle, Riccardo Peruzzini, Xavier Hanoulle, Frédérique Dewitte, Elisabeth Ferreira, Jean-Luc Baert, Didier Monté, Marc Aumercier, Vincent Villeret, Alexis Verger, Isabelle Landrieu
MED26 is a subunit of Mediator, a large complex central to the regulation of gene transcription by RNA Polymerase II (RNA Pol II). MED26 plays a role in the switch between the initiation and elongation phases of RNA Pol II-mediated transcription process. Regulation of these steps requires successive binding of MED26 N-Terminal domain (NTD) to TBP-associated factor 7 (TAF7) and EAF1 (Eleven-nineteen lysine-rich in leukemia-Associated Factor 1). In order to investigate the mechanism of regulation by MED26, MED26-NTD structure was solved by nuclear magnetic resonance spectroscopy (NMR), revealing a 4-helix bundle...
September 9, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28893424/quantifying-the-influence-of-5-rna-modifications-on-rna-polymerase-i-activity
#18
Francis D Appling, Aaron L Lucius, David A Schneider
For ensemble and single-molecule analyses of transcription, the use of synthetic transcription elongation complexes has been a versatile and powerful tool. However, structural analyses demonstrate that short RNA substrates, often employed in these assays, would occupy space within the RNA polymerase. Most commercial RNA oligonucleotides do not carry a 5'-triphosphate as would be present on a natural, de novo synthesized RNA. To examine the effects of 5'-moities on transcription kinetics, we measured nucleotide addition and 3'-dinucleotide cleavage by eukaryotic RNA polymerase I using 5'-hydroxyl and 5'-triphosphate RNA substrates...
September 1, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28892040/structure-of-a-transcribing-rna-polymerase-ii-dsif-complex-reveals-a-multidentate-dna-rna-clamp
#19
Carrie Bernecky, Jürgen M Plitzko, Patrick Cramer
During transcription, RNA polymerase II (Pol II) associates with the conserved elongation factor DSIF. DSIF renders the elongation complex stable and functions during Pol II pausing and RNA processing. We combined cryo-EM and X-ray crystallography to determine the structure of the mammalian Pol II-DSIF elongation complex at a nominal resolution of 3.4 Å. Human DSIF has a modular structure with two domains forming a DNA clamp, two domains forming an RNA clamp, and one domain buttressing the RNA clamp. The clamps maintain the transcription bubble, position upstream DNA, and retain the RNA transcript in the exit tunnel...
September 11, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28886694/comparative-transcriptome-analysis-of-cotton-fiber-development-of-upland-cotton-gossypium-hirsutum-and-chromosome-segment-substitution-lines-from-g-hirsutum-%C3%A3-g-barbadense
#20
Peng-Tao Li, Mi Wang, Quan-Wei Lu, Qun Ge, Md Harun Or Rashid, Ai-Ying Liu, Ju-Wu Gong, Hai-Hong Shang, Wan-Kui Gong, Jun-Wen Li, Wei-Wu Song, Li-Xue Guo, Wei Su, Shao-Qi Li, Xiao-Ping Guo, Yu-Zhen Shi, You-Lu Yuan
BACKGROUND: How to develop new cotton varieties possessing high yield traits of Upland cotton and superior fiber quality traits of Sea Island cotton remains a key task for cotton breeders and researchers. While multiple attempts bring in little significant progresses, the development of Chromosome Segment Substitution Lines (CSSLs) from Gossypium barbadense in G. hirsutum background provided ideal materials for aforementioned breeding purposes in upland cotton improvement. Based on the excellent fiber performance and relatively clear chromosome substitution segments information identified by Simple Sequence Repeat (SSR) markers, two CSSLs, MBI9915 and MBI9749, together with the recurrent parent CCRI36 were chosen to conduct transcriptome sequencing during the development stages of fiber elongation and Secondary Cell Wall (SCW) synthesis (from 10DPA and 28DPA), aiming at revealing the mechanism of fiber development and the potential contribution of chromosome substitution segments from Sea Island cotton to fiber development of Upland cotton...
September 8, 2017: BMC Genomics
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