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Transcriptional elongation

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https://www.readbyqxmd.com/read/27920256/a-transcription-factor-pulse-can-prime-chromatin-for-heritable-transcriptional-memory
#1
Aimee Iberg-Badeaux, Samuel Collombet, Benoit Laurent, Chris van Oevelen, Kuo-Kai Chin, Denis Thieffry, Thomas Graf, Shi Yang
Short-term and long-term transcriptional memory is the phenomenon whereby the kinetics or magnitude of gene induction is enhanced following a prior induction period. Short-term memory persists within one cell generation or in post-mitotic cells, while long-term memory can survive multiple rounds of cell division. We have developed a tissue culture model to study the epigenetic basis for long-term transcriptional memory (LTTM), and subsequently used this model to better understand the epigenetic mechanisms that enable heritable memory of temporary stimuli...
December 5, 2016: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/27920087/structural-visualization-of-the-p53-rna-polymerase-ii-assembly
#2
Sameer K Singh, Zhen Qiao, Lihua Song, Vijay Jani, William Rice, Edward Eng, Robert A Coleman, Wei-Li Liu
The master tumor suppressor p53 activates transcription in response to various cellular stresses in part by facilitating recruitment of the transcription machinery to DNA. Recent studies have documented a direct yet poorly characterized interaction between p53 and RNA polymerase II (Pol II). Therefore, we dissected the human p53/Pol II interaction via single-particle cryo-electron microscopy, structural docking, and biochemical analyses. This study reveals that p53 binds Pol II via the Rpb1 and Rpb2 subunits, bridging the DNA-binding cleft of Pol II proximal to the upstream DNA entry site...
December 5, 2016: Genes & Development
https://www.readbyqxmd.com/read/27917184/studying-secondary-growth-and-bast-fiber-development-the-hemp-hypocotyl-peeks-behind-the-wall
#3
Marc Behr, Sylvain Legay, Eva Žižková, Václav Motyka, Petre I Dobrev, Jean-Francois Hausman, Stanley Lutts, Gea Guerriero
Cannabis sativa L. is an annual herbaceous crop grown for the production of long extraxylary fibers, the bast fibers, rich in cellulose and used both in the textile and biocomposite sectors. Despite being herbaceous, hemp undergoes secondary growth and this is well exemplified by the hypocotyl. The hypocotyl was already shown to be a suitable model to study secondary growth in other herbaceous species, namely Arabidopsis thaliana and it shows an important practical advantage, i.e., elongation and radial thickening are temporally separated...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27916935/genome-wide-survey-reveals-transcriptional-differences-underlying-the-contrasting-trichome-phenotypes-of-two-sister-desert-poplars
#4
Jianchao Ma, Xiaodong He, Xiaotao Bai, Zhimin Niu, Bingbing Duan, Ningning Chen, Xuemin Shao, Dongshi Wan
Trichomes, which are widely used as an important diagnostic characteristic in plant species delimitation, play important roles in plant defense and adaptation to adverse environments. In this study, we used two sister poplar species, Populus pruinosa and Populus euphratica-which have, respectively, dense and sparse trichomes-to examine the genetic differences associated with these contrasting phenotypes. The results showed that 42 and 45 genes could be identified as candidate genes related to trichomes in P...
December 1, 2016: Genes
https://www.readbyqxmd.com/read/27916794/a-jacalin-related-lectin-regulated-the-formation-of-aerial-mycelium-and-fruiting-body-in-flammulina-velutipes
#5
Yuan-Ping Lu, Ren-Liang Chen, Ying Long, Xiao Li, Yu-Ji Jiang, Bao-Gui Xie
Flammulina velutipes, one of the most popular mushroom species in the world, has been recognized as a useful model system to study the biochemical and physiological aspects of the formation and elongation of fruit body. However, few reports have been published on the regulation of fruiting body formation in F. velutipes at the molecular level. In this study, a jacalin-related lectin gene from F. velutipes was characterized. The phylogenetic tree revealed that Fv-JRL1 clustered with other basidiomycete jacalin-like lectins...
November 28, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27915455/overexpression-of-atedt1-promotes-root-elongation-and-affects-medicinal-secondary-metabolite-biosynthesis-in-roots-of-transgenic-salvia-miltiorrhiza
#6
Yu Liu, Geng Sun, Zhaohui Zhong, Linyi Ji, Yong Zhang, Jianping Zhou, Xuelian Zheng, Kejun Deng
Medicinal secondary metabolites (salvianolic acids and tanshinones) are valuable natural bioactive compounds in Salvia miltiorrhiza and have widespread applications. Improvement of medicinal secondary metabolite accumulation through biotechnology is necessary and urgent to satisfy their increasing demand. Herein, it was demonstrated that the overexpression of the transcription factor Arabidopsis thaliana-enhanced drought tolerance 1 (AtEDT1) could affect medicinal secondary metabolite accumulation. In this study, we observed that the transgenic lines significantly conferred drought tolerance phenotype...
December 3, 2016: Protoplasma
https://www.readbyqxmd.com/read/27912083/robust-root-growth-in-altered-hydrotropic-response1-ahr1-mutant-of-arabidopsis-is-maintained-by-high-rate-of-cell-production-at-low-water-potential-gradient
#7
Amed Salazar-Blas, Laura Noriega-Calixto, María E Campos, Delfeena Eapen, Tania Cruz-Vázquez, Luis Castillo-Olamendi, Gabriela Sepulveda-Jiménez, Helena Porta, Joseph G Dubrovsky, Gladys I Cassab
Hydrotropism is the directional root growth response determined by water stimulus. In a water potential gradient system (WPGS) the roots of the Arabidopsis wild type have a diminished root growth compared to normal medium (NM). In contrast, the altered hydrotropic response1 (ahr1) mutant roots maintain their robust growth in the same WPGS. The aims of this work were to ascertain how ahr1 roots could sustain growth in the WPGS, with a special focus on the integration of cellular processes involved in the signaling that determines root growth during abiotic stress and their relation to hydrotropism...
November 17, 2016: Journal of Plant Physiology
https://www.readbyqxmd.com/read/27911610/successful-consecutive-expansion-of-limbal-explants-using-a-biosafe-culture-medium-under-feeder-layer-free-conditions
#8
Marina López-Paniagua, Teresa Nieto-Miguel, Ana de la Mata, Sara Galindo, José M Herreras, Rosa M Corrales, Margarita Calonge
PURPOSE: Transplantation of in vitro cultured limbal epithelial stem cells (LESCs) is a treatment widely used for LESC deficiency. However, the number of limbal tissue donors is limited, and protocols for LESC cultivation often include compounds and/or feeder layers that can induce side effects and/or increase the cost of the culture procedure. We investigated the feasibility of obtaining more than one limbal primary culture (LPC) from the same biopsy using a culture medium in which several potentially harmful compounds were replaced at the same time by biosafe supplements, allowing the LESC cultivation without feeder layers...
December 2, 2016: Current Eye Research
https://www.readbyqxmd.com/read/27908735/unr-csde1-drives-a-post-transcriptional-program-to-promote-melanoma-invasion-and-metastasis
#9
Laurence Wurth, Panagiotis Papasaikas, David Olmeda, Nadine Bley, Guadalupe T Calvo, Santiago Guerrero, Daniela Cerezo-Wallis, Javier Martinez-Useros, María García-Fernández, Stefan Hüttelmaier, Maria S Soengas, Fátima Gebauer
RNA binding proteins (RBPs) modulate cancer progression through poorly understood mechanisms. Here we show that the RBP UNR/CSDE1 is overexpressed in melanoma tumors and promotes invasion and metastasis. iCLIP sequencing, RNA sequencing, and ribosome profiling combined with in silico studies unveiled sets of pro-metastatic factors coordinately regulated by UNR as part of RNA regulons. In addition to RNA steady-state levels, UNR was found to control many of its targets at the level of translation elongation/termination...
November 14, 2016: Cancer Cell
https://www.readbyqxmd.com/read/27906160/mechanistic-insights-into-the-alternative-translation-termination-by-arfa-and-rf2
#10
Chengying Ma, Daisuke Kurita, Ningning Li, Yan Chen, Hyouta Himeno, Ning Gao
During cellular translation of mRNAs by ribosomes, various situations that would result in the pausing or stalling of translation apparatus at elongation and termination steps often occur(1-6). Except for programmed stalling, which is usually utilized by the cells to exert regulatory purposes(5,7,8), ribosomes stalled on mRNAs need to be terminated and recycled to maintain adequate cellular translation capacity(9). A large source of ribosome stalling originates in aberrant mRNAs that lack a stop codon. Transcriptional errors and misprocessing of primary transcripts, as well as undesired mRNA cleavage, all contribute to the formation of non-stop mRNAs...
December 1, 2016: Nature
https://www.readbyqxmd.com/read/27899647/spliceosomal-protein-eftud2-mutation-leads-to-p53-dependent-apoptosis-in-zebrafish-neural-progenitors
#11
Lei Lei, Shou-Yu Yan, Ran Yang, Jia-Yu Chen, Yumei Li, Ye Bu, Nannan Chang, Qinchao Zhou, Xiaojun Zhu, Chuan-Yun Li, Jing-Wei Xiong
Haploinsufficiency of EFTUD2 (Elongation Factor Tu GTP Binding Domain Containing 2) is linked to human mandibulofacial dysostosis, Guion-Almeida type (MFDGA), but the underlying cellular and molecular mechanisms remain to be addressed. We report here the isolation, cloning and functional analysis of the mutated eftud2 (snu114) in a novel neuronal mutant fn10a in zebrafish. This mutant displayed abnormal brain development with evident neuronal apoptosis while the development of other organs appeared less affected...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899640/structural-insights-into-nusg-regulating-transcription-elongation
#12
Bin Liu, Thomas A Steitz
NusG is an essential transcription factor that plays multiple key regulatory roles in transcription elongation, termination and coupling translation and transcription. The core role of NusG is to enhance transcription elongation and RNA polymerase processivity. Here, we present the structure of Escherichia coli RNA polymerase complexed with NusG. The structure shows that the NusG N-terminal domain (NGN) binds at the central cleft of RNA polymerase surrounded by the β' clamp helices, the β protrusion, and the β lobe domains to close the promoter DNA binding channel and constrain the β' clamp domain, but with an orientation that is different from the one observed in the archaeal β' clamp-Spt4/5 complex...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899597/thermotoga-maritima-nusg-domain-interaction-mediates-autoinhibition-and-thermostability
#13
Johanna Drögemüller, Christin Schneider, Kristian Schweimer, Martin Strauß, Birgitta M Wöhrl, Paul Rösch, Stefan H Knauer
NusG, the only universally conserved transcription factor, comprises an N- and a C-terminal domain (NTD, CTD) that are flexibly connected and move independently in Escherichia coli and other organisms. In NusG from the hyperthermophilic bacterium Thermotoga maritima (tmNusG), however, NTD and CTD interact tightly. This closed state stabilizes the CTD, but masks the binding sites for the interaction partners Rho, NusE and RNA polymerase (RNAP), suggesting that tmNusG is autoinhibited. Furthermore, tmNusG and some other bacterial NusGs have an additional domain, DII, of unknown function...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27898830/endoplasmic-reticulum-body-related-gene-expression-in-different-root-zones-of-arabidopsis-isolated-by-laser-assisted-microdissection
#14
Maxime Gotté, Magalie Bénard, Marie-Christine Kiefer-Meyer, Rim Jaber, John P Moore, Maïté Vicré-Gibouin, Azeddine Driouich
Endoplasmic reticulum (ER) bodies are important organelles for root defense. However, little is known regarding the genetic control of their formation in root tissues. In the present study, (L.) Heynh. roots were dissected using laser-assisted microdissection (LAM) with minimal sample preparation (no fixation or embedding steps) and the expression of genes associated with ER body formation and function was assessed by real-time quantitative reverse-transcription polymerase chain reaction (RT-qRT-PCR) in the presence and absence of the defense phytohormone methyl jasmonate (MeJA)...
July 2016: Plant Genome
https://www.readbyqxmd.com/read/27895724/expression-profile-of-spaca5-spaca5-in-spermatogenesis-and-transitional-cell-carcinoma-of-the-bladder
#15
Xiao-Yue Zhang, Qiu-Xia Yan, Xiao-Yan Guo, Cai-Rong Chen, Run-Qiang Chen, Zhi-Ming Cai, Ai-Fa Tang
The majority of bladder cancer-associated mortalities are due to transitional cell carcinoma (TCC), which is the most prevalent and chemoresistant malignancy of the bladder. Sperm acrosome associated 5 (SPACA5)/Spaca5 is a sperm acrosome-associated, c-type lysozyme-like protein that has been recently identified, and has been designated as an attractive candidate antigen for cancer testis. In the present study, the expression profile of SPACA5/Spaca5 was analyzed in spermatogenesis and TCC of the bladder using diverse molecular and cellular biology methods...
November 2016: Oncology Letters
https://www.readbyqxmd.com/read/27892458/modulation-of-mrna-and-lncrna-expression-dynamics-by-the-set2-rpd3s-pathway
#16
Ji Hyun Kim, Bo Bae Lee, Young Mi Oh, Chenchen Zhu, Lars M Steinmetz, Yookyeong Lee, Wan Kyu Kim, Sung Bae Lee, Stephen Buratowski, TaeSoo Kim
H3K36 methylation by Set2 targets Rpd3S histone deacetylase to transcribed regions of mRNA genes, repressing internal cryptic promoters and slowing elongation. Here we explore the function of this pathway by analysing transcription in yeast undergoing a series of carbon source shifts. Approximately 80 mRNA genes show increased induction upon SET2 deletion. A majority of these promoters have overlapping lncRNA transcription that targets H3K36me3 and deacetylation by Rpd3S to the mRNA promoter. We previously reported a similar mechanism for H3K4me2-mediated repression via recruitment of the Set3C histone deacetylase...
November 28, 2016: Nature Communications
https://www.readbyqxmd.com/read/27890635/hos1-facilitates-the-phytochrome-b-mediated-inhibition-of-pif4-function-during-hypocotyl-growth-in-arabidopsis
#17
Ju-Heon Kim, Hyo-Jun Lee, Jae-Hoon Jung, Sangmin Lee, Chung-Mo Park
Upon exposure to light, developing seedlings undergo photomorphogenesis, as illustrated by inhibition of hypocotyl elongation, cotyledon opening, and leaf greening. Hypocotyl growth is a well-established model for photomorphogenesis studies. During hypocotyl photomorphogenesis, light signals are sensed by multiple photoreceptors, among which the red/far-red light-sensing phytochromes have been extensively studied. However, it is not fully understood how the phytochromes modulate hypocotyl growth. Here, we demonstrated that HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES 1 (HOS1), which is known to either act as E3 ubiquitin ligase or affect chromatin organization, inhibits the transcriptional activation activity of PHYTOCHROME INTERACTING FACTOR 4 (PIF4) that promotes hypocotyl growth...
November 24, 2016: Molecular Plant
https://www.readbyqxmd.com/read/27889523/identification-of-target-genes-and-processes-involved-in-erucic-acid-accumulation-during-seed-development-in-the-biodiesel-feedstock-pennycress-thlaspi-arvense-l
#18
Ana Claver, Raquel Rey, M Victoria López, Rafael Picorel, Miguel Alfonso
We studied erucic acid accumulation in the biodiesel feedstock Pennycress (Thlaspi arvense L.) as a first step towards the development of a sustainable strategy for biofuel production in the EU territory. To that end, two inbred Pennycress lines of European origin, "NASC" and "French," were cultivated in a controlled chamber and in experimental field plots, and their growth, seed production and seed oil characteristics analyzed. Differences in some agronomical traits like vernalization (winter-French versus spring-NASC), flowering time (delayed in the French line) and seed production (higher in the French line) were detected...
November 18, 2016: Journal of Plant Physiology
https://www.readbyqxmd.com/read/27889295/novel-t7-like-expression-systems-used-for-halomonas
#19
Han Zhao, Haoqian M Zhang, Xiangbin Chen, Teng Li, Qiong Wu, Qi Ouyang, Guo-Qiang Chen
To engineer non-model organisms, suitable genetic parts must be available. However, biological parts are often host strain sensitive. It is therefore necessary to develop genetic parts that are functional regardless of host strains. Here we report several novel phage-derived expression systems used for transcriptional control in non-model bacteria. Novel T7-like RNA polymerase-promoter pairs were obtained by mining phage genomes, followed by in vivo characterization in non-model strains Halomonas spp TD01 and Pseudomonas entomophila...
November 24, 2016: Metabolic Engineering
https://www.readbyqxmd.com/read/27889265/integration-of-phytochrome-and-cryptochrome-signals-determines-plant-growth-during-competition-for-light
#20
Mieke de Wit, Diederik H Keuskamp, Franca J Bongers, Patricia Hornitschek, Charlotte M M Gommers, Emilie Reinen, Carmen Martínez-Cerón, Christian Fankhauser, Ronald Pierik
Plants in dense vegetation perceive their neighbors primarily through changes in light quality. Initially, the ratio between red (R) and far-red (FR) light decreases due to reflection of FR by plant tissue well before shading occurs. Perception of low R:FR by the phytochrome photoreceptors induces the shade avoidance response [1], of which accelerated elongation growth of leaf-bearing organs is an important feature. Low R:FR-induced phytochrome inactivation leads to the accumulation and activation of the transcription factors PHYTOCHROME-INTERACTING FACTORs (PIFs) 4, 5, and 7 and subsequent expression of their growth-mediating targets [2, 3]...
November 17, 2016: Current Biology: CB
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