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a cis-acting acting element in the promoter

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https://www.readbyqxmd.com/read/28208770/splicing-and-polyadenylation-of-human-papillomavirus-type-16-mrnas
#1
REVIEW
Chengjun Wu, Naoko Kajitani, Stefan Schwartz
The human papillomavirus type 16 (HPV16) life cycle can be divided into an early stage in which the HPV16 genomic DNA is replicated, and a late stage in which the HPV16 structural proteins are synthesized and virions are produced. A strong coupling between the viral life cycle and the differentiation state of the infected cell is highly characteristic of all HPVs. The switch from the HPV16 early gene expression program to the late requires a promoter switch, a polyadenylation signal switch and a shift in alternative splicing...
February 9, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28174683/post-translational-modifications-of-annexin-a2-are-linked-to-its-association-with-perinuclear-nonpolysomal-mrnp-complexes
#2
Ingvild Aukrust, Linn Andersen Rosenberg, Mia Madeleine Ankerud, Vibeke Bertelsen, Hanne Hollås, Jaakko Saraste, Ann Kari Grindheim, Anni Vedeler
Various post-translational modifications (PTMs) regulate the localisation and function of the multifunctional protein Annexin A2 (AnxA2). In addition to its various tasks as a cytoskeletal- and membrane-associated protein, AnxA2 can function as a trans-acting protein binding to cis-acting sequences of specific mRNAs. In the present study, we have examined the role of Ser25 phosphorylation in subcellular localisation of AnxA2 and its interaction with mRNP complexes. Subcellular fractionation and confocal microscopy of rat neuroendocrine PC12 cells showed that Ser25-phosphorylated AnxA2 (pSer25AnxA2) is absent from the nucleus and mainly localised to the perinuclear region, evidently associating with both membranes and cytoskeletal elements...
February 2017: FEBS Open Bio
https://www.readbyqxmd.com/read/28174576/comparative-analysis-of-agpase-genes-and-encoded-proteins-in-eight-monocots-and-three-dicots-with-emphasis-on-wheat
#3
Ritu Batra, Gautam Saripalli, Amita Mohan, Saurabh Gupta, Kulvinder S Gill, Pritish K Varadwaj, Harindra S Balyan, Pushpendra K Gupta
ADP-glucose pyrophosphorylase (AGPase) is a heterotetrameric enzyme with two large subunits (LS) and two small subunits (SS). It plays a critical role in starch biosynthesis. We are reporting here detailed structure, function and evolution of the genes encoding the LS and the SS among monocots and dicots. "True" orthologs of maize Sh2 (AGPase LS) and Bt2 (AGPase SS) were identified in seven other monocots and three dicots; structure of the enzyme at protein level was also studied. Novel findings of the current study include the following: (i) at the DNA level, the genes controlling the SS are more conserved than those controlling the LS; the variation in both is mainly due to intron number, intron length and intron phase distribution; (ii) at protein level, the SS genes are more conserved relative to those for LS; (iii) "QTCL" motif present in SS showed evolutionary differences in AGPase belonging to wheat 7BS, T...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28174238/functional-characterisation-of-cis-regulatory-elements-governing-dynamic-eomes-expression-in-the-early-mouse-embryo
#4
Claire S Simon, Damien J Downes, Matthew E Gosden, Jelena Telenius, Douglas R Higgs, Jim R Hughes, Ita Costello, Elizabeth K Bikoff, Elizabeth J Robertson
The T-box transcription factor (TF) Eomes is a key regulator of cell fate decisions during early mouse development. The cis-acting regulatory elements that direct expression in the anterior visceral endoderm (AVE), primitive streak (PS) and definitive endoderm (DE) have yet to be defined. Here, we identified three gene-proximal enhancer-like sequences (PSE_a, PSE_b and VPE) that faithfully activate tissue specific expression in transgenic embryos. However, targeted deletion experiments demonstrate that PSE_a and PSE_b are dispensable and only the VPE is required for optimal Eomes expression in vivo Embryos lacking this enhancer display variably penetrant defects in anterior-posterior axis orientation and DE formation...
February 7, 2017: Development
https://www.readbyqxmd.com/read/28168220/the-structurally-disordered-paramyxovirus-nucleocapsid-protein-tail-domain-is-a-regulator-of-the-mrna-transcription-gradient
#5
Robert M Cox, Stefanie A Krumm, Vidhi D Thakkar, Maximilian Sohn, Richard K Plemper
The paramyxovirus RNA-dependent RNA-polymerase (RdRp) complex loads onto the nucleocapsid protein (N)-encapsidated viral N:RNA genome for RNA synthesis. Binding of the RdRp of measles virus (MeV), a paramyxovirus archetype, is mediated through interaction with a molecular recognition element (MoRE) located near the end of the carboxyl-terminal Ntail domain. The structurally disordered central Ntail section is thought to add positional flexibility to MoRE, but the functional importance of this Ntail region for RNA polymerization is unclear...
February 2017: Science Advances
https://www.readbyqxmd.com/read/28167039/apple-autophagy-related-protein-mdatg3s-afford-tolerance-to-multiple-abiotic-stresses
#6
Ping Wang, Xun Sun, Xin Jia, Fengwang Ma
The efficient degradation system of autophagy in plant cells has important roles in removing and recycling intracellular components during normal development or under environmental stresses. Formation of autophagosomes requires the conjugation of ubiquitin-like protein ATG8 to phosphatidylethanolamine (PE). We isolated two ubiquitin-conjugating enzyme E2-like ATG3 homologues from Malus domestica - MdATG3a and MdATG3b - that are crucial for ATG8-PE conjugation. Both share a conserved N-terminal, as well as the catalytic and C-terminal domains of ATG3 with HPC and FLKF motifs...
March 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/28166800/a-purine-rich-element-in-foamy-virus-pol-regulates-env-splicing-and-gag-pol-expression
#7
Rebecca Moschall, Sarah Denk, Steffen Erkelenz, Christian Schenk, Heiner Schaal, Jochen Bodem
BACKGROUND: The foamy viral genome encodes four central purine-rich elements localized in the integrase-coding region of pol. Previously, we have shown that the first two of these RNA elements (A and B) are required for protease dimerization and activation. The D element functions as internal polypurine tract during reverse transcription. Peters et al., described the third element (C) as essential for gag expression suggesting that it might serve as an RNA export element for the unspliced genomic transcript...
February 6, 2017: Retrovirology
https://www.readbyqxmd.com/read/28163300/identification-of-two-novel-rhizoctonia-solani-inducible-cis-acting-elements-in-the-promoter-of-the-maize-gene-grmzm2g315431
#8
Ning Li, Jing Chen, Fangfang Yang, Shutong Wei, Lingguang Kong, Xinhua Ding, Zhaohui Chu
Plants are continuously exposed to myriad pathogen stresses. However, the molecular mechanisms by which these stress signals are perceived and transduced are poorly understood. In this study, the maize gene GRMZM2G315431 was identified to be highly inducible by Rhizoctonia solani infection, suggesting that the promoter of GRMZM2G315431 (pGRMZM2G315431) might contain a specific cis-acting element responsive to R. solani attack. To identify the R. solani-responsive element in pGRMZM2G315431, a series of binary plant transformation vectors were constructed by fusing pGRMZM2G315431 or its deletion-derivatives with the reporter genes...
February 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28161858/wheat-drought-responsive-wxpl-transcription-factors-regulate-cuticle-biosynthesis-genes
#9
Huihui Bi, Sukanya Luang, Yuan Li, Natalia Bazanova, Nikolai Borisjuk, Maria Hrmova, Sergiy Lopato
The cuticle forms a hydrophobic waxy layer that covers plant organs and provides protection from biotic and abiotic stresses. Transcription of genes responsible for cuticle formation is regulated by several types of transcription factors (TFs). Five orthologous to WAX PRODUCTION (WXP1 and WXP2) genes from Medicago truncatula were isolated from a cDNA library prepared from flag leaves and spikes of drought tolerant wheat (Triticum aestivum, breeding line RAC875) and designated TaWXP-like (TaWXPL) genes. Tissue-specific and drought-responsive expression of TaWXPL1D and TaWXPL2B was investigated by quantitative RT-PCR in two Australian wheat genotypes, RAC875 and Kukri, with contrasting glaucousness and drought tolerance...
February 4, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28128303/analysis-of-carotenogenic-genes-promoters-and-wrky-transcription-factors-in-response-to-salt-stress-in-dunaliella-bardawil
#10
Ming-Hua Liang, Jian-Guo Jiang
The unicellular alga Dunaliella bardawil is a highly salt-tolerant organism, capable of accumulating glycerol, glycine betaine and β-carotene under salt stress, and has been considered as an excellent model organism to investigate the molecular mechanisms of salt stress responses. In this study, several carotenogenic genes (DbCRTISO, DbZISO, DbLycE and DbChyB), DbBADH genes involved in glycine betaine synthesis and genes encoding probable WRKY transcription factors from D. bardawil were isolated, and promoters of DbCRTISO and DbChyB were cloned...
January 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28119417/in-vivo-evidence-that-eif3-stays-bound-to-ribosomes-elongating-and-terminating-on-short-upstream-orfs-to-promote-reinitiation
#11
Mahabub Pasha Mohammad, Vanda Munzarová Pondělíčková, Jakub Zeman, Stanislava Gunišová, Leoš Shivaya Valášek
Translation reinitiation is a gene-specific translational control mechanism characterized by the ability of some short upstream ORFs to prevent recycling of the post-termination 40S subunit in order to resume scanning for reinitiation downstream. Its efficiency decreases with the increasing uORF length, or by the presence of secondary structures, suggesting that the time taken to translate a uORF is more critical than its length. This led to a hypothesis that some initiation factors needed for reinitiation are preserved on the 80S ribosome during early elongation...
January 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28119334/genome-wide-analysis-of-cis-regulatory-element-structure-and-discovery-of-motif-driven-gene-co-expression-networks-in-grapevine
#12
Darren Chern Jan Wong, Rodrigo Lopez Gutierrez, Gregory Alan Gambetta, Simone Diego Castellarin
Coordinated transcriptional and metabolic reprogramming ensures a plant's continued growth and survival under adverse environmental conditions. Transcription factors (TFs) act to modulate gene expression through complex cis-regulatory element (CRE) interactions. Genome-wide analysis of known plant CREs was performed for all currently predicted protein-coding gene promoters in grapevine (Vitis vinifera L.). Many CREs such as abscisic acid (ABA)-responsive, drought-responsive, auxin-responsive, and evening elements, exhibit bona fide CRE properties such as strong position bias towards the transcription start site (TSS) and over-representation when compared with random promoters...
January 24, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28106824/identification-of-the-muc2-promoter-as-a-strong-promoter-for-intestinal-gene-expression-through-generation-of-transgenic-quail-expressing-gfp-in-gut-epithelial-cells
#13
Rachel M Woodfint, Paula R Chen, Jinsoo Ahn, Yeunsu Suh, Seongsoo Hwang, Sang Suk Lee, Kichoon Lee
Identification of tissue- and stage-specific gene promoters is valuable for delineating the functional roles of specific genes in genetically engineered animals. Here, through the comparison of gene expression in different tissues by analysis of a microarray database, the intestinal specificity of mucin 2 (MUC2) expression was identified in mice and humans, and further confirmed in chickens by RT-PCR (reverse transcription-PCR) analysis. An analysis of cis-acting elements in avian MUC2 gene promoters revealed conservation of binding sites, within a 2...
January 19, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28096402/establishment-of-expression-state-boundaries-by-rif1-and-taz1-in-fission-yeast
#14
Tea Toteva, Bethany Mason, Yutaka Kanoh, Peter Brøgger, Daniel Green, Janne Verhein-Hansen, Hisao Masai, Geneviève Thon
The Shelterin component Rif1 has emerged as a global regulator of the replication-timing program in all eukaryotes examined to date, possibly by modulating the 3D-organization of the genome. In fission yeast a second Shelterin component, Taz1, might share similar functions. Here, we identified unexpected properties for Rif1 and Taz1 by conducting high-throughput genetic screens designed to identify cis- and trans-acting factors capable of creating heterochromatin-euchromatin boundaries in fission yeast. The preponderance of cis-acting elements identified in the screens originated from genomic loci bound by Taz1 and associated with origins of replication whose firing is repressed by Taz1 and Rif1...
January 31, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28057216/histone-acetylation-and-the-regulation-of-major-histocompatibility-class-ii-gene-expression
#15
K Suzuki, Y Luo
Major histocompatibility complex (MHC) class II molecules are essential for processing and presenting exogenous pathogen antigens to activate CD4(+) T cells. Given their central role in adaptive immune responses, MHC class II genes are tightly regulated in a tissue- and activation-specific manner. The regulation of MHC class II gene expression involves various transcription factors that interact with conserved proximal cis-acting regulatory promoter elements, as well as MHC class II transactivator that interacts with a variety of chromatin remodeling machineries...
2017: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/28031366/the-autographa-californica-nucleopolyhedrovirus-ac83-gene-contains-a-cis-acting-element-that-is-essential-for-nucleocapsid-assembly
#16
Zhihong Huang, Mengjia Pan, Silei Zhu, Hao Zhang, Wenbi Wu, Meijin Yuan, Kai Yang
: Baculoviridae is a family of insect-specific viruses that have a circular double-stranded DNA genome packaged within a rod-shaped capsid. The mechanism of baculovirus nucleocapsid assembly remains unclear. Previous studies have shown that deletion of the ac83 gene of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) blocks viral nucleocapsid assembly. Interestingly, the ac83-encoded protein Ac83 is not a component of the nucleocapsid, implying a particular role for ac83 in nucleocapsid assembly that may be independent of its protein product...
December 28, 2016: Journal of Virology
https://www.readbyqxmd.com/read/28018410/molecular-evolution-and-expression-divergence-of-the-aconitase-aco-gene-family-in-land-plants
#17
Yi-Ming Wang, Qi Yang, Yan-Jing Liu, Hai-Ling Yang
Aconitase (ACO) is a key enzyme that catalyzes the isomerization of citrate to isocitrate in the tricarboxylic acid (TCA) and glyoxylate cycles. The function of ACOs has been well studied in model plants, such as Arabidopsis. In contrast, the evolutionary patterns of the ACO family in land plants are poorly understood. In this study, we systematically examined the molecular evolution and expression divergence of the ACO gene family in 12 land plant species. Thirty-six ACO genes were identified from the 12 land plant species representing the four major land plant lineages: Bryophytes, lycophytes, gymnosperms, and angiosperms...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28011694/wind1-promotes-shoot-regeneration-through-transcriptional-activation-of-enhancer-of-shoot-regeneration1-in-arabidopsis
#18
Akira Iwase, Hirofumi Harashima, Momoko Ikeuchi, Bart Rymen, Mariko Ohnuma, Shinichiro Komaki, Kengo Morohashi, Tetsuya Kurata, Masaru Nakata, Masaru Ohme-Takagi, Erich Grotewold, Keiko Sugimoto
Many plant species display remarkable developmental plasticity and regenerate new organs after injury. Local signals produced by wounding are thought to trigger organ regeneration but molecular mechanisms underlying this control remain largely unknown. We previously identified an AP2/ERF transcription factor WOUND INDUCED DEDIFFERENTIATION 1 (WIND1) as a central regulator of wound-induced cellular reprogramming in plants. In this study, we demonstrate that WIND1 promotes callus formation and shoot regeneration by up-regulating the expression of the ENHANCER OF SHOOT REGENERATION1 (ESR1) gene, which encodes another AP2/ERF transcription factor in Arabidopsis...
December 23, 2016: Plant Cell
https://www.readbyqxmd.com/read/27979739/genetic-variants-in-sirt3-transcriptional-regulatory-region-affect-promoter-activity-and-fat-deposition-in-three-cattle-breeds
#19
Linsheng Gui, Jieyun Hong, Sayed Haidar Abbas Raza, Linsen Zan
Sirtuin 3 (SIRT3) is a mitochondrial nicotinamide adenine dinucleotide (NAD)-dependent deacetylase. It has crucial roles in regulating the respiratory chain, in adenosine triphosphate (ATP) production, and in both the citric acid and urea cycles. The aim of this study was to investigate whether SIRT3 could be used as a candidate gene in the breeding of cattle. Expression analysis by quantitative real-time polymerase chain reactions (qPCR) indicated that expression levels of SIRT3 were highest in the kidney, rumen, liver, omasum and muscle...
December 12, 2016: Molecular and Cellular Probes
https://www.readbyqxmd.com/read/27965700/genome-wide-analysis-of-the-aquaporin-gene-family-in-chickpea-cicer-arietinum-l
#20
Amit A Deokar, Bunyamin Tar'an
Aquaporins (AQPs) are essential membrane proteins that play critical role in the transport of water and many other solutes across cell membranes. In this study, a comprehensive genome-wide analysis identified 40 AQP genes in chickpea (Cicer arietinum L.). A complete overview of the chickpea AQP (CaAQP) gene family is presented, including their chromosomal locations, gene structure, phylogeny, gene duplication, conserved functional motifs, gene expression, and conserved promoter motifs. To understand AQP's evolution, a comparative analysis of chickpea AQPs with AQP orthologs from soybean, Medicago, common bean, and Arabidopsis was performed...
2016: Frontiers in Plant Science
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