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a cis-acting acting element in the promoter

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https://www.readbyqxmd.com/read/29330296/tumor-progression-is-mediated-by-thymosin-%C3%A3-4-through-a-tgf%C3%A3-mrtf-signaling-axis
#1
Tsuyoshi Morita, Kenichiro Hayashi
Although enhanced thymosin beta-ß4 (TMSBX4/Tß4) expression is associated with tumor progression and metastasis, its tumor-promoting functions remain largely unknown. Here it is demonstrated that transforming growth factor beta (TGFß) facilitates Tß4 expression and leads to the activation of myocardin-related transcription factors (MRTFs), which are co-activators of serum response factor (SRF) and regulate the expression of genes critical for the epithelial-mesenchymal transition (EMT) and tumor metastasis...
January 12, 2018: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29304382/transcriptional-regulation-of-chickpea-ferritin-cafer1-influences-its-role-in-iron-homeostasis-and-stress-response
#2
Shaista Parveen, Aarti Pandey, Neha Jameel, Subhra Chakraborty, Niranjan Chakraborty
Ferritin, ubiquitous among all living organisms except yeast, exhibits iron-regulated expression. In plants, this regulation is applied through transcriptional control. Previous studies established the presence of two types of cis-acting elements in the promoter region: the iron regulatory element (FRE) in soybean and the iron-dependent regulatory sequence (IDRS) in maize and Arabidopsis. Adverse environmental conditions (e.g. water-deficit and oxidative stress) are known to modulate the expression of phytoferritin genes...
December 27, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/29291233/in-silico-comparative-analysis-of-promoters-derived-from-plant-pararetroviruses
#3
Dipinte Gupta, Rajiv Ranjan
Promoters are specific sequence of nucleotides present upstream of gene coding region involved in initiation and regulation of transcription. Multiple cis-acting element forms the architecture of promoter to which trans-acting nucleic binding factors bind and regulates its activity. Since 1980 genome of pararetrovirus, are being exploited for developing efficient promoters. Among all of them Cauliflower mosaic virus is the most widely used promoter for gene expression. The basic rational behind the strength of promoter lies in the sequence of cis elements and the spacer nucleotide elements between them, thereby strength of these promoter fragments can be regulated by altering these nucleotide sequences...
December 2017: Virusdisease
https://www.readbyqxmd.com/read/29279404/zmcct9-enhances-maize-adaptation-to-higher-latitudes
#4
Cheng Huang, Huayue Sun, Dingyi Xu, Qiuyue Chen, Yameng Liang, Xufeng Wang, Guanghui Xu, Jinge Tian, Chenglong Wang, Dan Li, Lishuan Wu, Xiaohong Yang, Weiwei Jin, John F Doebley, Feng Tian
From its tropical origin in southwestern Mexico, maize spread over a wide latitudinal cline in the Americas. This feat defies the rule that crops are inhibited from spreading easily across latitudes. How the widespread latitudinal adaptation of maize was accomplished is largely unknown. Through positional cloning and association mapping, we resolved a flowering-time quantitative trait locus to a Harbinger-like transposable element positioned 57 kb upstream of a CCT transcription factor (ZmCCT9). The Harbinger-like element acts in cis to repress ZmCCT9 expression to promote flowering under long days...
December 26, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29273966/molecular-characterization-of-amic-a-positive-regulator-in-acetamidase-operon-of-mycobacterium-smegmatis
#5
Arunkumar Venkatesan, Kannan Palaniyandi, Sujatha Narayanan
Mycobacterium smegmatis, a rapidly growing non-pathogenic mycobacterium, is currently used as a model organism to study mycobacterial genetics. Acetamidase of M. smegmatis is the highly inducible enzyme of Mycobacteria, which utilizes several amide compounds as sole carbon and nitrogen sources. The acetamidase operon has a complex regulatory mechanism, which involves three regulatory proteins, four promoters, and three operator elements. In our previous study, we showed that over-expression of AmiA leads to a negative regulation of acetamidase by blocking the P2 promoter...
December 22, 2017: Cell Stress & Chaperones
https://www.readbyqxmd.com/read/29250931/cis-acting-dna-elements-flanking-the-variable-major-protein-expression-site-of-borrelia-hermsii-are-required-for-murine-persistence
#6
Allison E James, Artem S Rogovskyy, Michael A Crowley, Troy Bankhead
In Borrelia hermsii, antigenic variation occurs as a result of a nonreciprocal gene conversion event that places one of ~60 silent variable major protein genes downstream of a single, transcriptionally active promoter. The upstream homology sequence (UHS) and downstream homology sequence (DHS) are two putative cis-acting DNA elements that have been predicted to serve as crossover points for homologous recombination. In this report, a targeted deletion/in cis complementation technique was used to directly evaluate the role for these elements in antigenic switching...
December 17, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/29241563/two-metallocarboxypeptidase-inhibitors-are-implicated-in-tomato-fruit-development-and-regulated-by-the-inner-no-outer-transcription-factor
#7
B Molesini, G L Rotino, V Dusi, R Chignola, T Sala, G Mennella, G Francese, T Pandolfini
The TCMP-1 and TCMP-2 genes of tomato code for metallocarboxypeptidase inhibitors and show sequential, tightly regulated expression patterns during flower and fruit development. In particular, TCMP-1 is highly expressed in flower buds before anthesis, while TCMP-2 in ripe fruits. Their expression pattern suggests that they might play a role in fruit development. Here, to investigate their function, we altered their endogenous levels by generating transgenic plants harbouring a chimeric gene expressing the TCMP-1 coding sequence under the control of the TCMP-2 promoter...
January 2018: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/29240782/conservation-and-divergence-of-starch-synthase-iii-genes-of-monocots-and-dicots
#8
Bhavya Priyadarshini Mishra, Rajeev Kumar, Amita Mohan, Kulvinder S Gill
Starch Synthase (SS) plays an important role in extending the α-1,4 glucan chains during starch biosynthesis by catalyzing the transfer of the glucosyl moiety from ADP-glucose to the non-reducing end of a pre-existing glucan chain. SS has five distinct isoforms of which SSIII is involved in the formation of longer glucan chain length. Here we report identification and detailed characterization of 'true' orthologs of the well-characterized maize SSIII (ZmSSIII), among six monocots and two dicot species. ZmSSIII orthologs have nucleotide sequence similarity ranging from 56-81%...
2017: PloS One
https://www.readbyqxmd.com/read/29213259/characterization-of-a-suppressive-cis-acting-element-in-the-epstein-barr-virus-lmp1-promoter
#9
Masahiro Yoshida, Takayuki Murata, Keiji Ashio, Yohei Narita, Takahiro Watanabe, H M Abdullah Al Masud, Yoshitaka Sato, Fumi Goshima, Hiroshi Kimura
Latent membrane protein 1 (LMP1) is a major oncogene encoded by Epstein-Barr virus (EBV) and is essential for immortalization of B cells by the virus. Previous studies suggested that several transcription factors, such as PU.1, RBP-Jκ, NFκB, EBF1, AP-2 and STAT, are involved in LMP1 induction; however, the means by which the oncogene is negatively regulated remains unclear. Here, we introduced short mutations into the proximal LMP1 promoter that includes recognition sites for the E-box and Ikaros transcription factors in the context of EBV-bacterial artificial chromosome...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29163393/the-5bsl3-2-functional-rna-domain-connects-distant-regions-in-the-hepatitis-c-virus-genome
#10
REVIEW
Cristina Romero-López, Alfredo Berzal-Herranz
Viral genomes are complexly folded entities that carry all the information required for the infective cycle. The nucleotide sequence of the RNA virus genome encodes proteins and functional information contained in discrete, highly conserved structural units. These so-called functional RNA domains play essential roles in the progression of infection, which requires their preservation from one generation to the next. Numerous functional RNA domains exist in the genome of the hepatitis C virus (HCV). Among them, the 5BSL3...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29148171/identification-and-expression-profiling-of-pht1-phosphate-transporters-in-wheat-in-controlled-environments-and-in-the-field
#11
A Grün, P Buchner, M R Broadley, M J Hawkesford
Phosphorus (P) is an important macronutrient with critical functions in plants. Phosphate (Pi) transporters which mediate Pi acquisition and Pi translocation within the plant are key factors in Pi deficiency responses. However, their relevance for adaptation to long-term Pi limitation under agronomic conditions, particularly in wheat, remains unknown. Here, we describe the identification of the complete Pi transporter gene family (Pht1) in wheat (Triticum aestivum). Gene expression profiles were compared for hydroponic and field-grown plant tissues of wheat at multiple developmental stages...
November 17, 2017: Plant Biology
https://www.readbyqxmd.com/read/29145496/insights-into-soybean-transcriptome-reconfiguration-under-hypoxic-stress-functional-regulatory-structural-and-compositional-characterization
#12
Thiago J Nakayama, Fabiana A Rodrigues, Norman Neumaier, Juliana Marcolino-Gomes, Hugo B C Molinari, Thaís R Santiago, Eduardo F Formighieri, Marcos F Basso, José R B Farias, Beatriz M Emygdio, Ana C B de Oliveira, Ângela D Campos, Aluízio Borém, Frank G Harmon, Liliane M Mertz-Henning, Alexandre L Nepomuceno
Soybean (Glycine max) is one of the major crops worldwide and flooding stress affects the production and expansion of cultivated areas. Oxygen is essential for mitochondrial aerobic respiration to supply the energy demand of plant cells. Because oxygen diffusion in water is 10,000 times lower than in air, partial (hypoxic) or total (anoxic) oxygen deficiency is important component of flooding. Even when oxygen is externally available, oxygen deficiency frequently occurs in bulky, dense or metabolically active tissues such as phloem, meristems, seeds, and fruits...
2017: PloS One
https://www.readbyqxmd.com/read/29142228/genome-wide-mapping-of-genetic-determinants-influencing-dna-methylation-and-gene-expression-in-human-hippocampus
#13
Herbert Schulz, Ann-Kathrin Ruppert, Stefan Herms, Christiane Wolf, Nazanin Mirza-Schreiber, Oliver Stegle, Darina Czamara, Andreas J Forstner, Sugirthan Sivalingam, Susanne Schoch, Susanne Moebus, Benno Pütz, Axel Hillmer, Nadine Fricker, Hartmut Vatter, Bertram Müller-Myhsok, Markus M Nöthen, Albert J Becker, Per Hoffmann, Thomas Sander, Sven Cichon
Emerging evidence emphasizes the strong impact of regulatory genomic elements in neurodevelopmental processes and the complex pathways of brain disorders. The present genome-wide quantitative trait loci analyses explore the cis-regulatory effects of single-nucleotide polymorphisms (SNPs) on DNA methylation (meQTL) and gene expression (eQTL) in 110 human hippocampal biopsies. We identify cis-meQTLs at 14,118 CpG methylation sites and cis-eQTLs for 302 3'-mRNA transcripts of 288 genes. Hippocampal cis-meQTL-CpGs are enriched in flanking regions of active promoters, CpG island shores, binding sites of the transcription factor CTCF and brain eQTLs...
November 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/29133016/dynamic-transcriptional-control-of-macrophage-mirna-signature-via-inflammation-responsive-enhancers-revealed-using-a-combination-of-next-generation-sequencing-based-approaches
#14
Zsolt Czimmerer, Attila Horvath, Bence Daniel, Gergely Nagy, Ixchelt Cuaranta-Monroy, Mate Kiss, Zsuzsanna Kolostyak, Szilard Poliska, Laszlo Steiner, Nikolas Giannakis, Tamas Varga, Laszlo Nagy
MicroRNAs are important components of the post-transcriptional fine-tuning of macrophage gene expression in physiological and pathological conditions. However, the mechanistic underpinnings and the cis-acting genomic factors of how macrophage polarizing signals induce miRNA expression changes are not well characterized. Therefore, we systematically evaluated the transcriptional basis underlying the inflammation-mediated regulation of macrophage microRNome using the combination of different next generation sequencing datasets...
November 10, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29123541/rice-seed-germination-underwater-morpho-physiological-responses-and-the-bases-of-differential-expression-of-alcoholic-fermentation-enzymes
#15
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/29121951/increasing-the-cpg-dinucleotide-abundance-in-the-hiv-1-genomic-rna-inhibits-viral-replication
#16
Irati Antzin-Anduetza, Charlotte Mahiet, Luke A Granger, Charlotte Odendall, Chad M Swanson
BACKGROUND: The human immunodeficiency virus type 1 (HIV-1) structural protein Gag is necessary and sufficient to form viral particles. In addition to encoding the amino acid sequence for Gag, the underlying RNA sequence could encode cis-acting elements or nucleotide biases that are necessary for viral replication. Furthermore, RNA sequences that inhibit viral replication could be suppressed in gag. However, the functional relevance of RNA elements and nucleotide biases that promote or repress HIV-1 replication remain poorly understood...
November 9, 2017: Retrovirology
https://www.readbyqxmd.com/read/29090330/characterization-of-promoter-of-egpal1-a-novel-pal-gene-from-the-oil-palm-elaeis-guineensis-jacq
#17
Chong Yu Lok Yusuf, Janna Ong Abdullah, Noor Azmi Shaharuddin, Idris Abu Seman, Mohd Puad Abdullah
The oil palm EgPAL1 gene promoter and its regulatory region were functional as a promoter in the heterologous system of Arabidopsis according to the cis-acting elements present in that region. The promoter was developmentally regulated, vascular tissue specific and responsive to water stress agents. Phenylalanine ammonia lyase (PAL, EC 4.3.1.24) is the key enzyme of the phenylpropanoid pathway which plays important roles in plant development and adaptation. To date, there is no report on the study of PAL from oil palm (Elaeis guineensis), an economically important oil crop...
October 31, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/29066306/sfrp5-is-a-target-gene-transcriptionally-regulated-by-ppar%C3%AE-in-3t3-l1-adipocytes
#18
Jun Zeng, Jiongyu Hu, Yu Lian, Youzhao Jiang, Bing Chen
Secreted frizzled-related protein 5 (SFRP5) is a newly identified adipokine. SFRP5 expression increases during the differentiation and maturation of adipocytes, but the factors regulating SFRP5 expression during this process remain unclear. This study showed that peroxisome proliferator-activated receptor γ (PPARγ) adenovirus transfection could enhance the SFRP5 expression of 3T3-L1 adipocytes. Three potential binding sites of PPARγ in the SFRP5 promoter domain were found by bioinformatics analysis. Luciferase reporter gene assay demonstrated that PPARγ regulated the activity of the SFRP5 promoter through cis-acting elements at -2,284--1,500bp...
October 21, 2017: Gene
https://www.readbyqxmd.com/read/29063961/genome-wide-identification-and-expression-analysis-of-the-b-box-gene-family-in-the-apple-malus-domestica-borkh-genome
#19
Xin Liu, Rong Li, Yaqing Dai, Xuesen Chen, Xiaoyun Wang
The B-box proteins (BBXs) are a family of zinc finger proteins containing one/two B-box domain(s). Compared with intensive studies of animal BBXs, investigations of the plant BBX family are limited, though some specific plant BBXs have been demonstrated to act as transcription factors in the regulation of flowering and photomorphogenesis. In this study, using a global search of the apple (Malus domestica Borkh.) genome, a total of 64 members of BBX (MdBBX) were identified. All the MdBBXs were divided into five groups based on the phylogenetic relationship, numbers of B-boxes contained and whether there was with an additional CCT domain...
October 24, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29023561/expression-patterns-and-promoter-analyses-of-aluminum-responsive-nac-genes-suggest-a-possible-growth-regulation-of-rice-mediated-by-aluminum-hormones-and-nac-transcription-factors
#20
Hugo Fernando Escobar-Sepúlveda, Libia Iris Trejo-Téllez, Soledad García-Morales, Fernando Carlos Gómez-Merino
In acid soils, the solubilized form of aluminum, Al+3, decreases root growth and affects the development of most crops. However, like other toxic elements, Al can have hormetic effects on plant metabolism. Rice (Oryza sativa) is one of the most tolerant species to Al toxicity, and when this element is supplied at low doses, growth stimulation has been observed, which could be due to combined mechanisms that are partly triggered by NAC transcription factors. This protein family can regulate vital processes in plants, including growth, development, and response to environmental stimuli, whether biotic or abiotic...
2017: PloS One
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