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Transcriptional elongation

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https://www.readbyqxmd.com/read/28078426/calreticulin-is-required-for-calcium-homeostasis-and-proper-pollen-tube-tip-growth-in-petunia
#1
Anna Suwińska, Piotr Wasąg, Przemysław Zakrzewski, Marta Lenartowska, Robert Lenartowski
Calreticulin is involved in stabilization of the tip-focused Ca (2+) gradient and the actin cytoskeleton arrangement and function that is required for several key processes driving Petunia pollen tube tip growth. Although the precise mechanism is unclear, stabilization of a tip-focused calcium (Ca(2+)) gradient seems to be critical for pollen germination and pollen tube growth. We hypothesize that calreticulin (CRT), a Ca(2+)-binding/buffering chaperone typically residing in the lumen of the endoplasmic reticulum (ER) of eukaryotic cells, is an excellent candidate to fulfill this role...
January 11, 2017: Planta
https://www.readbyqxmd.com/read/28077651/bromodomain-containing-4-brd4-couples-nf%C3%AE%C2%BAb-rela-with-airway-inflammation-and-the-irf-rig-i-amplification-loop-in-respiratory-syncytial-virus-infection
#2
Bing Tian, Jun Yang, Yingxin Zhao, Teodora Ivanciuc, Hong Sun, Roberto P Garofalo, Allan R Brasier
: The airway mucosa expresses protective interferon (IFN) and inflammatory cytokines in response to Respiratory Syncytial Virus (RSV) infection. In this study, we examine the role of bromodomain containing 4 (BRD4) in mediating this innate immune response in human small airway epithelial cells. We observe that RSV induces BRD4 to complex with NFκB/RelA. BRD4 is functionally required for expression of the NFκB-dependent inflammatory gene regulatory network (GRN), including the IFN Response Factor (IRFs)-1 and -7 that mediate a cross-talk pathway for RIG-I upregulation...
January 11, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28077274/the-role-and-regulation-of-the-peroxisome-proliferator-activated-receptor-alpha-in-human-liver
#3
REVIEW
Sander Kersten, Rinke Stienstra
The peroxisome proliferator-activated receptor α (PPARα) is a ligand-activated transcription factor that is abundantly expressed in liver. PPARα is activated by fatty acids and various other lipid species, as well as by a class of chemicals referred to as peroxisome proliferators. Studies in mice have shown that PPARα serves as the master regulator of hepatic lipid metabolism during fasting. In addition, PPARα suppresses inflammation and the acute phase response. Comparatively little is known about PPARα in human liver...
January 7, 2017: Biochimie
https://www.readbyqxmd.com/read/28076780/det1-and-hy5-control-pif4-mediated-thermosensory-elongation-growth-through-distinct-mechanisms
#4
Sreeramaiah N Gangappa, S Vinod Kumar
Plant growth and development are defined by environmental cues. The transcription factor PHYTOCHROME INTERACTING FACTOR 4 (PIF4) is the central signaling hub that integrates environmental cues, including light and temperature, to regulate growth and development. The thermosensory mechanisms controlling the PIF4-mediated temperature response, and its integration with other environmental responses, remain poorly understood. DE-ETIOLATED 1 (DET1) and CONSTITUTIVE PHOTOMORPHOGENESIS 1 (COP1), key regulators of light signaling, have been proposed to control thermosensory growth by transcriptional regulation of PIF4, through ELONGATED HYPOCOTYL 5 (HY5)...
January 10, 2017: Cell Reports
https://www.readbyqxmd.com/read/28076366/plum-fruit-development-occurs-via-gibberellin-sensitive-and-insensitive-della-repressors
#5
Islam El-Sharkawy, Sherif Sherif, Mahboob Abdulla, Subramanian Jayasankar
Fruit growth depends on highly coordinated hormonal activities. The phytohormone gibberellin (GA) promotes growth by triggering degradation of the growth-repressing DELLA proteins; however, the extent to which such proteins contribute to GA-mediated fruit development remains to be clarified. Three new plum genes encoding DELLA proteins, PslGAI, PslRGL and PslRGA were isolated and functionally characterized. Analysis of expression profile during fruit development suggested that PslDELLA are transcriptionally regulated during flower and fruit ontogeny with potential positive regulation by GA and ethylene, depending on organ and developmental stage...
2017: PloS One
https://www.readbyqxmd.com/read/28072558/a-link-between-transcription-fidelity-and-pausing-in-vivo
#6
Pamela Gamba, Katherine James, Nikolay Zenkin
Pausing by RNA polymerase is a major mechanism that regulates transcription elongation but can cause conflicts with fellow RNA polymerases and other cellular machineries. Here, we summarize our recent finding that misincorporation could be a major source of transcription pausing in vivo, and discuss the role of misincorporation-induced pausing.
January 10, 2017: Transcription
https://www.readbyqxmd.com/read/28069895/brassinosteroid-induced-transcriptional-repression-and-dephosphorylation-dependent-protein-degradation-negatively-regulate-bin2-interacting-aif2-a-br-signaling-negative-regulator-bhlh-transcription-factor
#7
Yoon Kim, Ji-Hye Song, Seon-U Park, You-Seung Jeong, Soo-Hwan Kim
Brassinosteroids (BRs) are plant polyhydroxy-steroids that play important roles in plant growth and development via extensive signal integration through direct interactions between regulatory components of different signaling pathways. Recent studies have shown that diverse helix-loop-helix/basic helix-loop-helix (HLH/bHLH) family proteins are actively involved in control of BR signaling pathways and interact with other signaling pathways. In this study, we show that ATBS1-INTERACTING FACTOR 2 (AIF2), a nuclear-localized atypical bHLH transcription factor, specifically interacts with BRASSINOSTEROID-INSENSITIVE 2 (BIN2) among other BR-signaling molecules...
January 9, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28067669/targeting-deregulated-ampk-mtorc1-pathways-improves-muscle-function-in-myotonic-dystrophy-type-i
#8
Marielle Brockhoff, Nathalie Rion, Kathrin Chojnowska, Tatiana Wiktorowicz, Christopher Eickhorst, Beat Erne, Stephan Frank, Corrado Angelini, Denis Furling, Markus A Rüegg, Michael Sinnreich, Perrine Castets
Myotonic dystrophy type I (DM1) is a disabling multisystemic disease that predominantly affects skeletal muscle. It is caused by expanded CTG repeats in the 3'-UTR of the dystrophia myotonica protein kinase (DMPK) gene. RNA hairpins formed by elongated DMPK transcripts sequester RNA-binding proteins, leading to mis-splicing of numerous pre-mRNAs. Here, we have investigated whether DM1-associated muscle pathology is related to deregulation of central metabolic pathways, which may identify potential therapeutic targets for the disease...
January 9, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28064320/-interactions-of-the-trex-2-complex-with-mrnp-particle-of-%C3%AE-tubulin-56d-gene
#9
V V Popova, A A Glukhova, S G Georgieva, G P Georgiev, D V Kopytova
mRNA transport from the nucleus to the cytoplasm is an essential step of eukaryotic gene expression. A pre-mRNA molecule undergoes modification, such as 5'-capping, splicing, and 3'-end processing, in the nucleus. The molecule being modified interacts with a large number of proteins and, thus, mRNP particles are formed. The binding of factors involved in nuclear export also occurs during transcription and mRNA processing. We have shown that the functioning of TREX-2, an mRNA export complex, is restricted to the nucleus...
November 2016: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/28064318/-translation-elongation-factor-ef1%C3%AE-1-interacts-with-zad-domains-of-transcription-factors-from-drosophila-melanogaster
#10
N A Zolotarev, O G Maksimenko, Yu V Shidlovskii, P G Georgiev, A N Bonchuk
A large class of arthropod transcription factors is formed by proteins with a characteristic N-terminal Zinc-finger-Associated Domain (ZAD) which contains four cysteine residues that coordinate a zinc ion. The number of putative proteins with ZAD in the Drosophila genome exceeds 90, and the degree of sequence similarity between these domains can be as low as 23%. Efficient binding of ZADs from the proteins Grau, ZIPIC, and Zw5 to the translation elongation factor EF1α1 in nuclear and cytoplasmic extracts has been demonstrated...
November 2016: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/28062044/multiplexed-tethered-particle-microscopy-for-studies-of-dna-enzyme-dynamics
#11
S Ucuncuoglu, D A Schneider, E R Weeks, D Dunlap, L Finzi
DNA is the carrier of genetic information and, as such, is at the center of most essential cellular processes. To regulate its physiological function, specific proteins and motor enzymes constantly change conformational states with well-controlled dynamics. Twenty-five years ago, Schafer, Gelles, Sheetz, and Landick employed the tethered particle motion (TPM) technique for the first time to study transcription by RNA polymerase at the single-molecule level. TPM has since then remained one of the simplest, most affordable, and yet incisive single-molecule techniques available...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28058744/expression-of-the-uvr8-photoreceptor-in-different-tissues-reveals-tissue-autonomous-features-of-uv-b-signalling
#12
Péter Bernula, Carlos Daniel Crocco, Adriana Beatriz Arongaus, Roman Ulm, Ferenc Nagy, András Viczián
The Arabidopsis UV-B photoreceptor UV RESISTANCE LOCUS 8 (UVR8) orchestrates the expression of hundreds of genes, many of which can be associated with UV-B tolerance. UV-B does not efficiently penetrate into tissues, yet UV-B regulates complex growth and developmental responses. To unravel to what extent and how UVR8 located in different tissues contributes to UV-B-induced responses, we expressed UVR8 fused to the YELLOW FLUORESCENT PROTEIN (YFP) under the control of tissue-specific promoters in a uvr8 null mutant background...
January 6, 2017: Plant, Cell & Environment
https://www.readbyqxmd.com/read/28057262/cooperation-between-t-box-factors-regulates-the-continuous-segregation-of-germ-layers-during-vertebrate-embryogenesis
#13
G E Gentsch, R S Monteiro, J C Smith
A wild-type vertebrate embryo first generates its head and then extends its main body axis by successively appending trunk and tail. This rostro-caudal (head-to-tail) development is initiated by a set of morphogenetic movements known as gastrulation that recruits multipotent cells into one of the three morphologically distinct germ layers: ectoderm, endoderm, and mesoderm. These primordial tissues go on to form complementary sets of connective tissues and organs to build the head and at least some of the trunk...
2017: Current Topics in Developmental Biology
https://www.readbyqxmd.com/read/28056486/dynamics-of-bridge-helix-bending-in-rna-polymerase-ii
#14
Zhan-Feng Wang, Yi-Ben Fu, Peng-Ye Wang, Ping Xie
One of critical issues for RNA polymerase is how the enzyme translocates along the DNA substrate during transcription elongation cycle. Comparisons of the structure of RNA polymerase II (Pol II) with that of bacterial enzyme have suggested that the transition of the bridge helix (BH) from straight to flipped-out conformations facilitates the translocation of upstream DNA-RNA hybrid. However, the flipped-out conformation of BH in Pol II has not been observed up to now and the detailed mechanism of how the BH facilitating upstream hybrid translocation still remains obscure...
January 5, 2017: Proteins
https://www.readbyqxmd.com/read/28053118/a-meiosis-specific-spt5-homolog-involved-in-non-coding-transcription
#15
Julita Gruchota, Cyril Denby Wilkes, Olivier Arnaiz, Linda Sperling, Jacek K Nowak
Spt5 is a conserved and essential transcriptional regulator that binds directly to RNA polymerase and is involved in transcription elongation, polymerase pausing and various co-transcriptional processes. To investigate the role of Spt5 in non-coding transcription, we used the unicellular model Paramecium tetraurelia In this ciliate, development is controlled by epigenetic mechanisms that use different classes of non-coding RNAs to target DNA elimination. We identified two SPT5 genes. One (STP5v) is involved in vegetative growth, while the other (SPT5m) is essential for sexual reproduction...
January 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28051102/rna-synthesis-is-associated-with-multiple-tbp-chromatin-binding-events
#16
Hussain A Zaidi, David T Auble, Stefan Bekiranov
Competition ChIP is an experimental method that allows transcription factor (TF) chromatin turnover dynamics to be measured across a genome. We develop and apply a physical model of TF-chromatin competitive binding using chemical reaction rate theory and are able to derive the physical half-life or residence time for TATA-binding protein (TBP) across the yeast genome from competition ChIP data. Using our physical modeling approach where we explicitly include the induction profile of the competitor in the model, we are able to estimate yeast TBP-chromatin residence times as short as 1...
January 4, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28049856/irregular-pollen-exine1-is-a-novel-factor-in-anther-cuticle-and-pollen-exine-formation
#17
Xiaoyang Chen, Hua Zhang, Huayue Sun, Hongbing Luo, Li Zhao, Zhaobin Dong, Shuangshuang Yan, Cheng Zhao, Renyi Liu, Chunyan Xu, Song Li, Huabang Chen, Weiwei Jin
Anther cuticle and pollen exine are protective barriers for pollen development and fertilization. Despite that several regulators have been identified for anther cuticle and pollen exine development in rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana), few genes have been characterized in maize (Zea mays) and the underlying regulatory mechanism remains elusive. Here, we report a novel male-sterile mutant in maize, irregular pollen exine1 (ipe1), which exhibited a glossy outer anther surface, abnormal Ubisch bodies, and defective pollen exine...
January 2017: Plant Physiology
https://www.readbyqxmd.com/read/28045133/calpain-dependent-disruption-of-nucleo-cytoplasmic-transport-in-als-motor-neurons
#18
Takenari Yamashita, Hitoshi Aizawa, Sayaka Teramoto, Megumi Akamatsu, Shin Kwak
Nuclear dysfunction in motor neurons has been hypothesized to be a principal cause of amyotrophic lateral sclerosis (ALS) pathogenesis. Here, we investigated the mechanism by which the nuclear pore complex (NPC) is disrupted in dying motor neurons in a mechanistic ALS mouse model (adenosine deaminase acting on RNA 2 (ADAR2) conditional knockout (AR2) mice) and in ALS patients. We showed that nucleoporins (Nups) that constituted the NPC were cleaved by activated calpain via a Ca(2+)-permeable AMPA receptor-mediated mechanism in dying motor neurons lacking ADAR2 expression in AR2 mice...
January 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28045091/ctcf-interacts-with-the-lytic-hsv-1-genome-to-promote-viral-transcription
#19
Fengchao Lang, Xin Li, Olga Vladimirova, Benxia Hu, Guijun Chen, Yu Xiao, Vikrant Singh, Danfeng Lu, Lihong Li, Hongbo Han, J M A S P Wickramasinghe, Sheryl T Smith, Chunfu Zheng, Qihan Li, Paul M Lieberman, Nigel W Fraser, Jumin Zhou
CTCF is an essential chromatin regulator implicated in important nuclear processes including in nuclear organization and transcription. Herpes Simplex Virus-1 (HSV-1) is a ubiquitous human pathogen, which enters productive infection in human epithelial and many other cell types. CTCF is known to bind several sites in the HSV-1 genome during latency and reactivation, but its function has not been defined. Here, we report that CTCF interacts extensively with the HSV-1 DNA during lytic infection by ChIP-seq, and its knockdown results in the reduction of viral transcription, viral genome copy number and virus yield...
January 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28045055/personalised-proteome-analysis-by-means-of-protein-microarrays-made-from-individual-patient-samples
#20
Syafrizayanti, Smiths S Lueong, Cuixia Di, Jonas V Schaefer, Andreas Plückthun, Jörg D Hoheisel
DNA sequencing has advanced to a state that permits studying the genomes of individual patients as nearly a matter of routine. Towards analysing a tissue's protein content in a similar manner, we established a method for the production of microarrays that represent full-length proteins as they are encoded in individual specimens, exhibiting the particular variations, such as mutations or splice variations, present in these samples. From total RNA isolates, each transcript is copied to a specific location on the array by an on-chip polymerase elongation reaction, followed by in situ cell-free transcription and translation...
January 3, 2017: Scientific Reports
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