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https://www.readbyqxmd.com/read/29161365/genome-scale-analysis-ofescherichia-coliwith-a-comprehensive-prokaryotic-sequence-based-biophysical-model-of-translation-initiation-and-elongation
#1
Gilad Shaham, Tamir Tuller
Translation initiation in prokaryotes is affected by the mRNA folding and interaction of the ribosome binding site with the ribosomal RNA. The elongation rate is affected, among other factors, by the local biophysical properties of the coding regions, the decoding rates of different codons, and the interactions among ribosomes. Currently, there is no comprehensive biophysical model of translation that enables the prediction of mRNA translation dynamics based only on the transcript sequence and while considering all of these fundamental aspects of translation...
November 17, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29158086/pfn2a-a-new-partner-of-rar%C3%AE-in-the-cytoplasm
#2
Dina Andriamoratsiresy, Aleksandr Piskunov, Regis Lutzing, Cécile Rochette-Egly
Retinoic acid receptors (RARs) are classically considered as nuclear ligand-dependent regulators of transcription. Here we highlighted a novel face of the RARα subtype: RARα is present in low amounts in the cytoplasm of mouse embryonic fibroblasts (MEFs) where it interacts with profilin2a (PFN2A), a small actin-binding protein involved in filaments polymerisation. The interaction involves the N-terminal proline-rich motif (PRM) of RARα and the SH3-like domain of PFN2a. When increased in the cytoplasm, RARα competes with other PFN2a-binding proteins bearing PRMs and involved in actin filaments elongation...
November 17, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29157917/the-mediator-complex-in-genomic-and-non-genomic-signaling-in-cancer
#3
Hannah Weber, Michael J Garabedian
Mediator is a conserved, multi-subunit macromolecular machine divided structurally into head, middle, and tail modules, along with a transiently associating kinase module. Mediator functions as an integrator of transcriptional regulatory activity by interacting with DNA-bound transcription factors and with RNA polymerase II (Pol II) to both activate and repress gene expression. Mediator has been shown to affect multiple steps in transcription, including chromatin looping between enhancers and promoters, pre-initiation complex formation, transcriptional elongation, and mRNA splicing...
November 17, 2017: Steroids
https://www.readbyqxmd.com/read/29156681/the-histone-demethylase-kdm3a-is-required-for-normal-epithelial-proliferation-ductal-elongation-and-tumor-growth-in-the-mouse-mammary-gland
#4
Li Qin, Yixiang Xu, Xiaobin Yu, Michael J Toneff, Dabing Li, Lan Liao, Jarrod D Martinez, Yi Li, Jianming Xu
Histone modification alters chromatin architecture to regulate gene transcription. KDM3A is a histone demethylase in the JmjC domain-containing protein family. It removes di- and mono- methyl residues from di- or mono-methylated lysine 9 of histone H3 (H3K9me2/me1). Recent studies have shown that Kdm3a plays an important role in self-renewal of embryonic stem cells, spermatogenesis, metabolism, sex determination and tumor angiogenesis. However, its role in mammary gland development and breast carcinogenesis remains unclear...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29155810/regulation-of-transcription-elongation-in-response-to-osmostress
#5
Andrea Silva, Santiago Cavero, Victoria Sarah, Carme Solé, René Böttcher, Sebastián Chávez, Francesc Posas, Eulàlia de Nadal
Cells trigger massive changes in gene expression upon environmental fluctuations. The Hog1 stress-activated protein kinase (SAPK) is an important regulator of the transcriptional activation program that maximizes cell fitness when yeast cells are exposed to osmostress. Besides being associated with transcription factors bound at target promoters to stimulate transcriptional initiation, activated Hog1 behaves as a transcriptional elongation factor that is selective for stress-responsive genes. Here, we provide insights into how this signaling kinase functions in transcription elongation...
November 20, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/29155071/structural-rearrangements-of-the-rna-polymerase-iii-machinery-during-trna-transcription-initiation
#6
REVIEW
Ewan Phillip Ramsay, Alessandro Vannini
RNA polymerase III catalyses the synthesis of tRNAs in eukaryotic organisms. Through combined biochemical and structural characterisation, multiple auxiliary factors have been identified alongside RNA Polymerase III as critical in both facilitating and regulating transcription. Together, this machinery forms dynamic multi-protein complexes at tRNA genes which are required for polymerase recruitment, DNA opening and initiation and elongation of the tRNA transcripts. Central to the function of these complexes is their ability to undergo multiple conformational changes and rearrangements that regulate each step...
November 15, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29153392/polycomb-repressive-complex-2-methylates-elongin-a-to-regulate-transcription
#7
M Behfar Ardehali, Anthony Anselmo, Jesse C Cochrane, Sharmistha Kundu, Ruslan I Sadreyev, Robert E Kingston
Polycomb repressive complex 2 (PRC2-EZH2) methylates histone H3 at lysine 27 (H3K27) and is required to maintain gene repression during development. Misregulation of PRC2 is linked to a range of neoplastic malignancies, which is believed to involve methylation of H3K27. However, the full spectrum of non-histone substrates of PRC2 that might also contribute to PRC2 function is not known. We characterized the target recognition specificity of the PRC2 active site and used the resultant data to screen for uncharacterized potential targets...
November 15, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29150605/global-role-of-the-bacterial-post-transcriptional-regulator-csra-revealed-by-integrated-transcriptomics
#8
Anastasia H Potts, Christopher A Vakulskas, Archana Pannuri, Helen Yakhnin, Paul Babitzke, Tony Romeo
CsrA is a post-transcriptional regulatory protein that is widely distributed among bacteria. This protein influences bacterial lifestyle decisions by binding to the 5' untranslated and/or early coding regions of mRNA targets, causing changes in translation initiation, RNA stability, and/or transcription elongation. Here, we assess the contribution of CsrA to gene expression in Escherichia coli on a global scale. UV crosslinking immunoprecipitation and sequencing (CLIP-seq) identify RNAs that interact directly with CsrA in vivo, while ribosome profiling and RNA-seq uncover the impact of CsrA on translation, RNA abundance, and RNA stability...
November 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/29143279/arabidopsis-noncoding-rna-modulates-seedling-greening-during-deetiolation
#9
Yuqiu Wang, Jian Li, Xing-Wang Deng, Danmeng Zhu
Seedling greening is essential for the survival of plants emerging from the soil. The abundance of chlorophyll precursors, including protochlorophyllide (Pchlide), is precisely controlled during the dark-to-light transition, as over-accumulation of Pchlide can lead to cellular photooxidative damage. Previous studies have identified and characterized multiple regulators controlling this important process. HID1 (hidden treasure 1) is the first noncoding RNA (ncRNA) found in photomorphogenesis. Under continuous red light, HID1 has been shown to inhibit hypocotyl elongation by repressing the transcription of PIF3 (phytochrome interacting factor 3)...
October 13, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/29142233/crystal-structure-of-the-n-terminal-domain-of-human-cdc73-and-its-implications-for-the-hyperparathyroidism-jaw-tumor-hpt-jt-syndrome
#10
Wei Sun, Xiao-Lin Kuang, Yan-Ping Liu, Li-Fei Tian, Xiao-Xue Yan, Wenqing Xu
CDC73/Parafibromin is a critical component of the Paf1 complex (PAF1C), which is involved in transcriptional elongation and histone modifications. Mutations of the human CDC73/HRPT2 gene are associated with hyperparathyroidism-jaw tumor (HPT-JT) syndrome, an autosomal dominant disorder. CDC73/parafibromin was initially recognized as a tumor suppressor by inhibiting cell proliferation via repression of cyclin D1 and c-myc genes. In recent years, it has also shown oncogenic features by activating the canonical Wnt/β-catenin signal pathway...
November 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29142123/initiation-elongation-and-realignment-during-influenza-virus-mrna-synthesis
#11
Aartjan J W Te Velthuis, Judith Oymans
The RNA-dependent RNA polymerase (RdRp) of the influenza A virus replicates and transcribes the viral genome segments in the nucleus of the host cell. To transcribe these viral genome segments, the RdRp 'snatches' capped RNA oligonucleotides from nascent host cell mRNAs and aligns these primers to the ultimate or penultimate nucleotide of the segments for the initiation of viral mRNA synthesis. It has been proposed that this initiation process is not processive and that the RdRp uses a prime-realign mechanism during transcription...
November 15, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29138932/soybean-glycine-max-wrinkled1-transcription-factor-gmwri1a-positively-regulates-seed-oil-accumulation
#12
Liang Chen, Yuhong Zheng, Zhimin Dong, Fanfan Meng, Xingmiao Sun, Xuhong Fan, Yunfeng Zhang, Mingliang Wang, Shuming Wang
Soybean is the world's most important leguminous crop producing high-quality protein and oil. Elevating oil accumulation in soybean seed is always many researchers' goal. WRINKLED1 (WRI1) encodes a transcription factor of the APETALA2/ethylene responsive element-binding protein (AP2/EREBP) family that plays important roles during plant seed oil accumulation. In this study, we isolated and characterized three distinct orthologues of WRI1 in soybean (Glycine max) that display different organ-specific expression patterns, among which GmWRI1a was highly expressed in maturing soybean seed...
November 14, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29138433/transcriptomic-analysis-of-the-regulation-of-stalk-development-in-flowering-chinese-cabbage-brassica-campestris-by-rna-sequencing
#13
Xinmin Huang, Yuling Lei, Hongling Guan, Yanwei Hao, Houcheng Liu, Guangwen Sun, Riyuan Chen, Shiwei Song
Flowering Chinese cabbage is a stalk vegetable whose quality and yield are directly related to stalk development. However, no comprehensive investigations on stalk development have been performed. To address this issue, the present study used RNA sequencing to investigate transcriptional regulation at three key stages (seedling, bolting, and flowering) of stalk development in flowering Chinese cabbage. Anatomical analysis revealed that cell division was the main mode of stalk thickening and elongation at all key stages...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29135031/comparative-proteomics-illustrates-the-molecular-mechanism-of-potato-solanum-tuberosum-l-tuberization-inhibited-by-exogenous-gibberellins-in-vitro
#14
Lixiang Cheng, Yuping Wang, Yueshan Liu, Qingquan Zhang, Huihui Gao, Zhang Feng
Among the multiple environmental signals and hormonal factors regulating potato tuberization, gibberellins (GAs) are important components of the signaling pathways in these processes. To understand the GAs-signaling response mechanism of potato tuberization, a comparative proteomics approach was applied to analyze proteome change of potato tuberization in vitro subjected to a range of exogenous GA3 treatments (0, 0.01, 0.1 and 1.0 μΜ) using two-dimensional gel electrophoresis. Quantitative image analyses showed that a total of 37 protein spots have their abundance significantly altered more than 2-fold...
November 14, 2017: Physiologia Plantarum
https://www.readbyqxmd.com/read/29134529/transcriptional-changes-measured-in-rice-roots-after-exposure-to-arsenite-contaminated-sediments
#15
Alexandra Brinke, Georg Reifferscheid, Roland Klein, Ute Feiler, Sebastian Buchinger
Transcriptional analyses are discussed to provide a deeper understanding of the molecular mechanisms underlying toxic effects. Thus, they can complement classic ecotoxicological test methods and potentially allow the identification of biomarkers associated to the exposure of chemical stressors and or adverse biological effects. This feasibility study intended to identify a set of potential gene expression biomarkers for arsenite-exposure in rice roots that could complement the informative value of an existing sediment-contact test with rice...
November 13, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/29133017/rpb5-modulates-the-rna-polymerase-ii-transition-from-initiation-to-elongation-by-influencing-spt5-association-and-backtracking
#16
Verónica Martínez-Fernández, Ana Isabel Garrido-Godino, María Carmen Mirón-García, Victoria Begley, Antonio Fernández-Pévida, Jesús de la Cruz, Sebastián Chávez, Francisco Navarro
Rpb5 is a subunit shared by the three eukaryotic RNA polymerases although its role in transcription remains unclear. It has been proposed that it makes contact with the promoter DNA and to participate in the coordination of the opening/closing of the RNA polymerase II DNA cleft. Here, we report the specific role of Rpb5 in the function of the yeast RNA polymerase II. The rpb5-P151T mutation specifically impairs transcription elongation by RNA polymerase II but does not influence the functions of RNA polymerases I or III...
November 11, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29129639/determinants-of-histone-h3k4-methylation-patterns
#17
Luis M Soares, P Cody He, Yujin Chun, Hyunsuk Suh, TaeSoo Kim, Stephen Buratowski
Various factors differentially recognize trimethylated histone H3 lysine 4 (H3K4me3) near promoters, H3K4me2 just downstream, and promoter-distal H3K4me1 to modulate gene expression. This methylation "gradient" is thought to result from preferential binding of the H3K4 methyltransferase Set1/complex associated with Set1 (COMPASS) to promoter-proximal RNA polymerase II. However, other studies have suggested that location-specific cues allosterically activate Set1. Chromatin immunoprecipitation sequencing (ChIP-seq) experiments show that H3K4 methylation patterns on active genes are not universal or fixed and change in response to both transcription elongation rate and frequency as well as reduced COMPASS activity...
November 16, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29128541/a-pegylated-platelet-free-plasma-hydrogel-based-composite-scaffold-enables-stable-vascularization-and-targeted-cell-delivery-for-volumetric-muscle-loss
#18
Amit Aurora, Nicole Wrice, Thomas J Walters, Robert J Christy, Shanmugasundaram Natesan
Extracellular matrix (ECM) scaffolds are being used for the clinical repair of soft tissue injuries. Although improved functional outcomes have been reported, ECM scaffolds show limited tissue specific remodeling response with concomitant deposition of fibrotic tissue. One plausible explanation is the regression of blood vessels which may be limiting the diffusion of oxygen and nutrients across the scaffold. Herein we develop a composite scaffold as a vasculo-inductive platform by integrating PEGylated platelet free plasma (PFP) hydrogel with a muscle derived ECM scaffold (m-ECM)...
November 8, 2017: Acta Biomaterialia
https://www.readbyqxmd.com/read/29123541/rice-seed-germination-underwater-morpho-physiological-responses-and-the-bases-of-differential-expression-of-alcoholic-fermentation-enzymes
#19
Berta Miro, Toshisangba Longkumer, Frederickson D Entila, Ajay Kohli, Abdelbagi M Ismail
The water-, energy-, and labor-intensive system of transplanted puddled rice (Oryza sativa) is steadily being replaced by direct seeding due to the progressive scarcity of these resources. However, the alternate dry direct seeding leads to competition with weeds and poor establishment when soils are flooded. Direct seeded rice capable of anaerobic germination (germination in flooded soil, AG) is ideal, which under rainfed ecosystems would also overcome waterlogging during germination. AG tolerance is associated with faster germination and faster elongation of coleoptiles, with the activities of alcoholic fermentation enzymes replacing aerobic respiration as a source of energy...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29122985/tsnac1-is-a-key-transcription-factor-in-abiotic-stress-resistance-and-growth
#20
Can Liu, Baomei Wang, Zhaoxia Li, Zhenghua Peng, Juren Zhang
NAC proteins constitute one of the largest families of plant-specific transcription factors, and a number of these proteins participate in the regulation of plant development and responses to abiotic stress. T. HALOPHILA STRESS RELATED NAC1 (TsNAC1) cloned from the halophyte Thellungiella halophila is a NAC transcription factor gene, and its overexpression can improve abiotic stress resistance, especially in the salt stress tolerance, in both T. halophila and Arabidopsis and retard the growth of these plants...
November 9, 2017: Plant Physiology
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