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Transcriptional elongation

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https://www.readbyqxmd.com/read/29656028/rice-transcription-factor-osdof11-modulates-sugar-transport-by-promoting-expression-of-sucrose-transporter-and-sweet-genes
#1
Yunfei Wu, Sang-Kyu Lee, Youngchul Yoo, Jinhuan Wei, Suk-Yoon Kwon, Sang-Won Lee, Jong-Seong Jeon, Gynheung An
Sucrose is produced in mesophyll cells and transferred into phloem cells before it is delivered long-distance to sink tissues. However, little is known about how sucrose transport is regulated in plants. Here, we identified T-DNA insertional mutants in Oryza sativa DNA BINDING WITH ONE FINGER 11 (OsDOF11), which is expressed in the vascular cells of photosynthetic organs and in various sink tissues. The osdof11 mutant plants are semi-dwarf and have fewer tillers and smaller panicles. Although sucrose enhanced root elongation in young wild-type (WT) seedlings, this did not occur in osdof11 seedlings due to reduced sucrose uptake...
April 12, 2018: Molecular Plant
https://www.readbyqxmd.com/read/29651162/quantitative-methods-to-monitor-rna-biomarkers-in-myotonic-dystrophy
#2
Marzena Wojciechowska, Krzysztof Sobczak, Piotr Kozlowski, Saam Sedehizadeh, Agnieszka Wojtkowiak-Szlachcic, Karol Czubak, Robert Markus, Anna Lusakowska, Anna Kaminska, J David Brook
Myotonic dystrophy type 1 (DM1) and type 2 (DM2) are human neuromuscular disorders associated with mutations of simple repetitive sequences in affected genes. The abnormal expansion of CTG repeats in the 3'-UTR of the DMPK gene elicits DM1, whereas elongated CCTG repeats in intron 1 of ZNF9/CNBP triggers DM2. Pathogenesis of both disorders is manifested by nuclear retention of expanded repeat-containing RNAs and aberrant alternative splicing. The precise determination of absolute numbers of mutant RNA molecules is important for a better understanding of disease complexity and for accurate evaluation of the efficacy of therapeutic drugs...
April 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29651114/a-mechanistic-framework-for-auxin-dependent-arabidopsis-root-hair-elongation-to-low-external-phosphate
#3
Rahul Bhosale, Jitender Giri, Bipin K Pandey, Ricardo F H Giehl, Anja Hartmann, Richard Traini, Jekaterina Truskina, Nicola Leftley, Meredith Hanlon, Kamal Swarup, Afaf Rashed, Ute Voß, Jose Alonso, Anna Stepanova, Jeonga Yun, Karin Ljung, Kathleen M Brown, Jonathan P Lynch, Liam Dolan, Teva Vernoux, Anthony Bishopp, Darren Wells, Nicolaus von Wirén, Malcolm J Bennett, Ranjan Swarup
Phosphate (P) is an essential macronutrient for plant growth. Roots employ adaptive mechanisms to forage for P in soil. Root hair elongation is particularly important since P is immobile. Here we report that auxin plays a critical role promoting root hair growth in Arabidopsis in response to low external P. Mutants disrupting auxin synthesis (taa1) and transport (aux1) attenuate the low P root hair response. Conversely, targeting AUX1 expression in lateral root cap and epidermal cells rescues this low P response in aux1...
April 12, 2018: Nature Communications
https://www.readbyqxmd.com/read/29650642/setd2-regulates-quiescence-and-differentiation-of-adult-hematopoietic-stem-cells-by-restricting-rna-polymerase-ii-elongation
#4
Yile Zhou, Xiaomei Yan, Xiaomin Feng, Jiachen Bu, Yunzhu Dong, Peipei Lin, Yoshihiro Hayashi, Rui Huang, Andre Olsson, Paul R Andreassen, H Leighton Grimes, Qian-Fei Wang, Tao Cheng, Zhijian Xiao, Jie Jin, Gang Huang
SET domain containing 2 (Setd2), encoding a histone methyltransferase, is associated with many hematopoietic diseases when mutated. By generating a novel exon 6 conditional knockout mouse model, we described an essential role of Setd2 in maintaining the adult hematopoietic stem cells. Loss of Setd2 results in leukopenia, anemia, and increased platelet accompanied with hypocellularity, erythroid dysplasia, and mild fibrosis in bone marrow. Setd2 knockout mice show significantly decreased hematopoietic stem and progenitor cells except for erythroid progenitors...
April 12, 2018: Haematologica
https://www.readbyqxmd.com/read/29649811/transcription-elongation-factor-p-tefb-is-involved-in-il-17f-signaling-in-airway-smooth-muscle-cells
#5
Masayuki Nakajima, Mio Kawaguchi, Masashi Matsuyama, Kyoko Ota, Junichi Fujita, Satoshi Matsukura, Shau-Ku Huang, Yuko Morishima, Yukio Ishii, Hiroaki Satoh, Tohru Sakamoto, Nobuyuki Hizawa
BACKGROUND: IL-17F is involved in the pathogenesis of several inflammatory diseases, including asthma and COPD. However, the effects of steroids on the function of IL-17F signaling mechanisms are largely unknown. One of the transcription elongation factors, positive transcription elongation factor b (P-TEFb) composed of cyclin T1 and cyclin-dependent kinase 9 (CDK9), is known as a novel checkpoint regulator of gene expression via bromodomain-containing protein 4 (Brd4). METHODS: Human airway smooth muscle cells were stimulated with IL-17F and the expression of IL-8 was evaluated by real-time PCR and ELISA...
April 12, 2018: International Archives of Allergy and Immunology
https://www.readbyqxmd.com/read/29648621/the-mef2-transcriptional-target-dmpk-induces-loss-of-sarcomere-structure-and-cardiomyopathy
#6
Amin Damanafshan, Ies Elzenaar, Benoit Samson-Couterie, Ingeborg van der Made, Meriem Bourajjaj, Maarten M van den Hoogenhof, Henk A van Veen, Daisy I Picavet, Abdelaziz Beqqali, Elisabeth Ehler, Leon J De Windt, Yigal M Pinto, Ralph J van Oort
Aim: The pathology of heart failure is characterized by poorly contracting and dilated ventricles. At the cellular level, this is associated with lengthening of individual cardiomyocytes and loss of sarcomeres. While it is known that the transcription factor myocyte enhancer factor -2 (MEF2) is involved in this cardiomyocyte remodeling, the underlying mechanism remains to be elucidated. Here, we aim to mechanistically link MEF2 target genes with loss of sarcomeres during cardiomyocyte remodeling...
April 10, 2018: Cardiovascular Research
https://www.readbyqxmd.com/read/29643171/fungal-morphogenesis-from-the-polarized-growth-of-hyphae-to-complex-reproduction-and-infection-structures
#7
REVIEW
Meritxell Riquelme, Jesús Aguirre, Salomon Bartnicki-García, Gerhard H Braus, Michael Feldbrügge, Ursula Fleig, Wilhelm Hansberg, Alfredo Herrera-Estrella, Jörg Kämper, Ulrich Kück, Rosa R Mouriño-Pérez, Norio Takeshita, Reinhard Fischer
Filamentous fungi constitute a large group of eukaryotic microorganisms that grow by forming simple tube-like hyphae that are capable of differentiating into more-complex morphological structures and distinct cell types. Hyphae form filamentous networks by extending at their tips while branching in subapical regions. Rapid tip elongation requires massive membrane insertion and extension of the rigid chitin-containing cell wall. This process is sustained by a continuous flow of secretory vesicles that depends on the coordinated action of the microtubule and actin cytoskeletons and the corresponding motors and associated proteins...
June 2018: Microbiology and Molecular Biology Reviews: MMBR
https://www.readbyqxmd.com/read/29643073/the-plant-hormone-ethylene-restricts-arabidopsis-growth-via-the-epidermis
#8
Irina Ivanova Vaseva, Enas Qudeimat, Thomas Potuschak, Yunlong Du, Pascal Genschik, Filip Vandenbussche, Dominique Van Der Straeten
The gaseous hormone ethylene plays a key role in plant growth and development, and it is a major regulator of stress responses. It inhibits vegetative growth by restricting cell elongation, mainly through cross-talk with auxins. However, it remains unknown whether ethylene controls growth throughout all plant tissues or whether its signaling is confined to specific cell types. We employed a targeted expression approach to map the tissue site(s) of ethylene growth regulation. The ubiquitin E3 ligase complex containing Skp1, Cullin1, and the F-box protein EBF1 or EBF2 (SCFEBF1/2 ) target the degradation of EIN3, the master transcription factor in ethylene signaling...
April 11, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29627732/responses-of-grapevine-rootstocks-to-drought-through-altered-root-system-architecture-and-root-transcriptomic-regulations
#9
Kubilay Yıldırım, Adem Yağcı, Seda Sucu, Sümeyye Tunç
Roots are the major interface between the plant and various stress factors in the soil environment. Alteration of root system architecture (RSA) (root length, spread, number and length of lateral roots) in response to environmental changes is known to be an important strategy for plant adaptation and productivity. In light of ongoing climate changes and global warming predictions, the breeding of drought-tolerant grapevine cultivars is becoming a crucial factor for developing a sustainable viticulture. Root-trait modeling of grapevine rootstock for drought stress scenarios, together with high-throughput phenotyping and genotyping techniques, may provide a valuable background for breeding studies in viticulture...
March 31, 2018: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29624124/architecture-of-the-rna-polymerase-ii-elongation-complex-new-insights-into-spt4-5-and-elf1
#10
Haruhiko Ehara, Shun-Ichi Sekine
Transcription by RNA polymerase II (Pol II) is accomplished with the aid of numerous accessory factors specific to each transcriptional stage. The structure of the Pol II elongation complex (EC) bound with Spt4/5, Elf1, and TFIIS unveiled the sophisticated basal EC architecture essential for transcription elongation and other transcription-related events.
April 6, 2018: Transcription
https://www.readbyqxmd.com/read/29621707/identification-of-cd-responsive-rna-helicase-genes-and-expression-of-a-putative-bnrh-24-mediated-by-mir158-in-canola-brassica-napus
#11
Xian Duo Zhang, Jia Yun Sun, Yuan Yuan You, Jian Bo Song, Zhi Min Yang
RNA helicases play crucial roles in RNA splicing, transport, editing and degradation, protein translation initiation and siRNA-mediated gene silencing. However, knowledge about their functionality in rapeseed (Brassica napus) is rare. In the study, we identified and annotated 271 RNA helicase genes from B. napus using bioinformatics and high-throughput RNA-sequencing (RNA-seq). Three subfamilies DEAD-box, DEAH-box, or DExD/H-box have been identified. One hundred and ninety-five RNA helicases were confirmed by RNA-seq and 49 were identified to differentially respond to cadmium (Cd) stress (> 1...
April 2, 2018: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/29618629/targeted-recruitment-of-the-basal-transcriptional-machinery-by-lnk-clock-components-controls-the-circadian-rhythms-of-nascent-rnas-in-arabidopsis
#12
Yuan Ma, Sergio Gil, Klaus D Grasser, Paloma Mas
The rhythms of steady-state mRNA expression pervade nearly all circadian systems. However, the mechanisms behind the rhythmic transcriptional synthesis and its correlation with circadian expression remain fully unexplored, particularly in plants. Here, we discovered a multi-functional protein complex that orchestrates the rhythms of transcriptional activity in Arabidopsis thaliana. The expression of the circadian oscillator genes TOC1 (TIMING OF CAB EXPRESSION1/PSEUDO-RESPONSE REGULATOR1) and PRR5 (PSEUDO-RESPONSE REGULATOR5) initially relies on the modular function of the clock-related factor RVE8: its MYB domain provides the DNA binding specificity, while its LCL domain recruits the clock components, LNKs, to target promoters...
April 4, 2018: Plant Cell
https://www.readbyqxmd.com/read/29610279/h3k36me3-mediated-mismatch-repair-preferentially-protects-actively-transcribed-genes-from-mutation
#13
Yaping Huang, Liya Gu, Guo-Min Li
Histone H3 trimethylation at lysine 36 (H3K36me3) is an important histone mark involved in both transcription elongation and DNA mismatch repair (MMR). It is known that H3K36me3 recruits the mismatch-recognition protein MutSα to replicating chromatin via its physical interaction with MutSα's PWWP domain, but the exact role of H3K36me3 in transcription is undefined. Using chromatin immunoprecipitation combined with whole genome  DNA sequencing analysis, we demonstrate here that H3K36me3, together with MutSα, is involved in protecting against mutation, preferentially in actively transcribed genomic regions...
April 2, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29608805/rebuilding-the-bridge-between-transcription-and-translation
#14
Irina Artsimovitch
In Bacteria, ribosomes may bind to the nascent RNA emerging from the transcribing RNA polymerase and initiate translation. Transcription-translation coupling plays diverse roles in cellular physiology, including attenuation control, mRNA surveillance, and maintenance of genome integrity. While the existence of coupling is broadly accepted, its mechanism and ubiquity are debated. Structural evidence supports mutually exclusive modes of RNA polymerase-ribosome contacts. In a model based on nuclear magnetic resonance data, NusG binds to a ribosomal protein S10 and acts as an adapter between RNA polymerase and the 30S subunit...
April 2, 2018: Molecular Microbiology
https://www.readbyqxmd.com/read/29602239/inflammatory-factor-receptor-toll-like-receptor-4-controls-telomeres-through-heterochromatin-protein-1-isoforms-in-liver-cancer-stem-cell
#15
Qidi Zheng, Jie Xu, Zhuojia Lin, Yanan Lu, Xiaoru Xin, Xiaonan Li, Yuxin Yang, Qiuyu Meng, Chen Wang, Wujun Xiong, Dongdong Lu
Toll-like receptor 4 (TLR4) which acts as a receptor for lipopolysaccharide (LPS) has been reported to be involved in carcinogenesis. However, the regulatory mechanism of it has not been elucidated. Herein, we demonstrate that TLR4 promotes the malignant growth of liver cancer stem cells. Mechanistically, TLR4 promotes the expression of histone-lysine N-methyltransferase (SUV39 h2) and increases the formation of trimethyl histone H3 lysine 9-heterochromatin protein 1-telomere repeat binding factor 2 (H3K9me3-HP1-TRF2) complex at the telomeric locus under mediation by long non coding RNA urothelial cancer-associated 1 (CUDR)...
March 30, 2018: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/29599472/examination-of-csr-regulatory-circuitry-using-epistasis-analysis-with-rna-seq-epi-seq-confirms-that-csrd-affects-gene-expression-via-csra-csrb-and-csrc
#16
Anastasia H Potts, Yuanyuan Leng, Paul Babitzke, Tony Romeo
The Csr global regulatory system coordinates gene expression in response to metabolic status. This system utilizes the RNA binding protein CsrA to regulate gene expression by binding to transcripts of structural and regulatory genes, thus affecting their structure, stability, translation, and/or transcription elongation. CsrA activity is controlled by sRNAs, CsrB and CsrC, which sequester CsrA away from other transcripts. CsrB/C levels are partly determined by their rates of turnover, which requires CsrD to render them susceptible to RNase E cleavage...
March 29, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29596841/mir-206-is-required-for-changes-in-cell-adhesion-that-drive-muscle-cell-morphogenesis-in-xenopus-laevis
#17
Hernando Martínez Vergara, Julio Ramirez, Trista Rosing, Ceazar Nave, Rebecca Blandino, Daniel Saw, Parag Saraf, Gabriel Piexoto, Coohleen Coombes, Melissa Adams, Carmen R Domingo
MicroRNAs (miRNAs) are highly conserved small non-coding RNA molecules that post-transcriptionally regulate gene expression in multicellular organisms. Within the set of muscle-specific miRNAs, miR-206 expression is largely restricted to skeletal muscle and is found exclusively within the bony fish lineage. Although many studies have implicated miR-206 in muscle maintenance and disease, its role in skeletal muscle development remains largely unknown. Here, we examine the role of miR-206 during Xenopus laevis somitogenesis...
March 26, 2018: Developmental Biology
https://www.readbyqxmd.com/read/29593215/a-licensing-step-links-aid-to-transcription-elongation-for-mutagenesis-in-b-cells
#18
Stephen P Methot, Ludivine C Litzler, Poorani Ganesh Subramani, Anil K Eranki, Heather Fifield, Anne-Marie Patenaude, Julian C Gilmore, Gabriel E Santiago, Halil Bagci, Jean-François Côté, Mani Larijani, Ramiro E Verdun, Javier M Di Noia
Activation-induced deaminase (AID) mutates the immunoglobulin (Ig) genes to initiate somatic hypermutation (SHM) and class switch recombination (CSR) in B cells, thus underpinning antibody responses. AID mutates a few hundred other loci, but most AID-occupied genes are spared. The mechanisms underlying productive deamination versus non-productive AID targeting are unclear. Here we show that three clustered arginine residues define a functional AID domain required for SHM, CSR, and off-target activity in B cells without affecting AID deaminase activity or Escherichia coli mutagenesis...
March 28, 2018: Nature Communications
https://www.readbyqxmd.com/read/29588524/sumo-suppresses-and-myc-amplifies-transcription-globally-by-regulating-cdk9-sumoylation
#19
Fang Yu, Guang Shi, Shimeng Cheng, Jiwei Chen, Shwu-Yuan Wu, Zhiqiang Wang, Nansong Xia, Yunhao Zhai, Zhenxing Wang, Yu Peng, Dong Wang, James X Du, Lujian Liao, Sheng-Zhong Duan, Tieliu Shi, Jinke Cheng, Cheng-Ming Chiang, Jiwen Li, Jiemin Wong
Regulation of transcription is fundamental to the control of cellular gene expression and function. Although recent studies have revealed a role for the oncoprotein MYC in amplifying global transcription, little is known as to how the global transcription is suppressed. Here we report that SUMO and MYC mediate opposite effects upon global transcription by controlling the level of CDK9 sumoylation. On one hand, SUMO suppresses global transcription via sumoylation of CDK9, the catalytic subunit of P-TEFb kinase essential for productive transcriptional elongation...
March 27, 2018: Cell Research
https://www.readbyqxmd.com/read/29588400/hiv-1-uncoating-and-reverse-transcription-require-eef1a-binding-to-surface-exposed-acidic-residues-of-the-reverse-transcriptase-thumb-domain
#20
Daniel J Rawle, Dongsheng Li, Joakim E Swedberg, Lu Wang, Dinesh C Soares, David Harrich
Once HIV-1 enters a cell, the viral core is uncoated by a poorly understood mechanism and the HIV-1 genomic RNA is reverse transcribed into DNA. Host cell factors are essential for these processes, although very few reverse transcription complex binding host cell factors have been convincingly shown to affect uncoating or reverse transcription. We previously reported that cellular eukaryotic translation elongation factor 1A (eEF1A) interacts tightly and directly with HIV-1 reverse transcriptase (RT) for more efficient reverse transcription...
March 27, 2018: MBio
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