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https://www.readbyqxmd.com/read/29785964/mechanism-of-selective-recruitment-of-rna-polymerases-ii-and-iii-to-snrna-gene-promoters
#1
Oleksandr Dergai, Pascal Cousin, Jerome Gouge, Karishma Satia, Viviane Praz, Tracy Kuhlman, Philippe Lhôte, Alessandro Vannini, Nouria Hernandez
RNA polymerase II (Pol II) small nuclear RNA (snRNA) promoters and type 3 Pol III promoters have highly similar structures; both contain an interchangeable enhancer and "proximal sequence element" (PSE), which recruits the SNAP complex (SNAPc). The main distinguishing feature is the presence, in the type 3 promoters only, of a TATA box, which determines Pol III specificity. To understand the mechanism by which the absence or presence of a TATA box results in specific Pol recruitment, we examined how SNAPc and general transcription factors required for Pol II or Pol III transcription of SNAPc-dependent genes (i...
May 21, 2018: Genes & Development
https://www.readbyqxmd.com/read/29778844/identification-of-micrornas-with-heat-stress-responsive-and-immune-properties-in-marsupenaeus-japonicus-based-on-next-generation-sequencing-and-bioinformatics-analysis-essential-regulators-in-the-heat-stress-host-interactions
#2
Jinbin Zheng, Jiawen Cao, Yong Mao, Yongquan Su, Jun Wang
Summer mortality syndrome is one of the most serious issue for Marsupenaeus japonicus aquaculture in China. Since it causes massive economic loss and threatens sustainability of M. japonicus aquaculture industry, thus, there is an urgent desire to reveal the heat stress-host interactions mechanisms that lead to mass mortalities of M. japonicus in hot summer months. MicroRNAs (miRNAs) are small noncoding RNAs that involved in regulation of diverse biological processes, including stress and immune response, and might serve as potential regulators in the heat stress-host interactions...
May 17, 2018: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29778840/identification-of-a-novel-promoter-from-banana-aquaporin-family-gene-matip1-2-which-responses-to-drought-and-salt-stress-in-transgenic-arabidopsis-thaliana
#3
Shun Song, Yi Xu, Dongmei Huang, Hongxia Miao, Juhua Liu, Caihong Jia, Wei Hu, Ana Valeria Valarezo, Biyu Xu, Zhiqiang Jin
Drought and salt stresses often affect plant growth and crop yields. Identification of promoters involved in drought and salt stress responses is of great significance for genetic improvement of crop resistance. Our previous studies showed that aquaporin can respond to drought and salt stresses, but its promoter has not yet been reported in plants. In the present study, cis-acting elements of MaAQP family member promoters were systematically analyzed in banana. Expression of MaTIP1; 2 was induced by drought and salt stresses but not sensitive to cold stress, waterlogging stress, or mechanical damage, and its promoter contained five stress-related cis-acting elements...
May 17, 2018: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29773009/cloning-and-characterization-of-promoters-of-the-fungal-immunomodulatory-protein-genes-from-ganoderma-spp-agaricomycetes-and-their-response-to-methyl-jasmonate-and-salicylic-acid
#4
Qi-Zhang Li, Yu-Zhou Chang, Kai-Qi Su, Xiao-Lei Wang, Xiao-Hui Bai, Xuan-Wei Zhou
Ganoderma mushrooms for medicinal use contain various bioactive compounds, but the genetic elements available for these medicinal mushrooms are still limited. In this study we cloned and analyzed the promoters of fungal immunomodulatory protein (FIP) genes from G. lucidum and G. atrum. FIP gene expression was induced by different concentrations of methyl jasmonate (MeJA) and salicylic acid (SA), and messenger RNA expression was detected by quantitative reverse-transcription polymerase chain reaction. The results provided 5' upstream sequences of FIP genes from G...
2018: International Journal of Medicinal Mushrooms
https://www.readbyqxmd.com/read/29721644/morphology-oriented-epigenetic-research
#5
REVIEW
Sohei Kitazawa, Ryuma Haraguchi, Riko Kitazawa
Cytosine methylation plays a major role in the regulation of sequential and tissue-specific expression of genes. De novo aberrant DNA methylation and demethylation are also crucial processes in tumorigenesis and tumor progression. The mechanisms of how and when such aberrant methylation and demethylation occur in tumor cells are still obscure, however. To evaluate subtle epigenetic alteration among minor subclonal populations, morphology-oriented epigenetic analysis is requisite, especially where heterogeneity and flexibility are as notable as in the process of cancer progression and cellular differentiation at critical stages...
May 2, 2018: Histochemistry and Cell Biology
https://www.readbyqxmd.com/read/29720520/herpes-simplex-virus-2-latency-associated-transcript-lat-region-mutations-do-not-identify-a-role-for-lat-associated-micro-rnas-in-viral-reactivation-in-the-guinea-pig-genital-model
#6
Yoshiki Kawamura, Marta Bosch-Marce, Shuang Tang, Amita Patel, Philip R Krause
Despite the long-standing observation that herpes simplex virus (HSV) Latency-Associated Transcript (LAT) promoter-deletion viruses show impaired recurrence phenotypes in relevant animal models, the mechanism by which these sequences exert this phenotypic effect is unknown. We constructed and evaluated four mutant HSV-2 viruses with targeted mutations in the LAT promoter and LAT-associated miRNAs affecting (1) the LAT TATA box, (2) the LAT ICP4-binding site, (3) miR-I and miR-II (miR-I/II), which both target ICP34...
May 2, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29681080/identification-and-characterisation-of-a-previously-unknown-drought-tolerance-associated-microrna-in-barley
#7
Hui Zhou, Syed Sarfraz Hussain, Michael Hackenberg, Natalia Bazanova, Omid Eini, Jie Li, Perry Gustafson, Bujun Shi
Drought is the most serious abiotic stress, which causes crop losses on worldwide scale. The present study identified a previously unknown microRNA (designated as hvu-miRX) of 21 nucleotides (nt) in barley. Its precursor (designated pre-miRX) and primary transcript (designated pri-miRX) were also identified, with lengths of 73 nt and 559 nt, respectively. The identified upstream sequence of pri-miRX contains both the TATA box and the CAAT box, which are both required for transcription initiation. Transient promoter activation assays showed that the core promoter region of pri-miRX ranged 500 nt from the transcription start site...
April 22, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29657132/structure-of-radical-induced-cell-death1-hub-domain-reveals-a-common-%C3%AE-%C3%AE-scaffold-for-disorder-in-transcriptional-networks
#8
Katrine Bugge, Lasse Staby, Katherine R Kemplen, Charlotte O'Shea, Sidsel K Bendsen, Mikael K Jensen, Johan G Olsen, Karen Skriver, Birthe B Kragelund
Communication within cells relies on a few protein nodes called hubs, which organize vast interactomes with many partners. Frequently, hub proteins are intrinsically disordered conferring multi-specificity and dynamic communication. Conversely, folded hub proteins may organize networks using disordered partners. In this work, the structure of the RST domain, a unique folded hub, is solved by nuclear magnetic resonance spectroscopy and small-angle X-ray scattering, and its complex with a region of the transcription factor DREB2A is provided through data-driven HADDOCK modeling and mutagenesis analysis...
April 12, 2018: Structure
https://www.readbyqxmd.com/read/29608728/insights-into-an-extensively-fragmented-eukaryotic-genome-de-novo-genome-sequencing-of-the-multinuclear-ciliate-uroleptopsis-citrina
#9
Weibo Zheng, Chundi Wang, Ying Yan, Feng Gao, Thomas G Doak, Weibo Song
Ciliated protists are a large group of single-celled eukaryotes with separate germline and somatic nuclei in each cell. The somatic genome is developed from the zygotic nucleus through a series of chromosomal rearrangements, including fragmentation, DNA elimination, de novo telomere addition, and DNA amplification. This unique feature makes them perfect models for research in genome biology and evolution. However, genomic research of ciliates has been limited to a few species, owing to problems with DNA contamination and obstacles in cultivation...
March 1, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29556921/complex-regulation-of-the-tamyc1-gene-expression-in-wheat-grain-synthesizing-anthocyanin-pigments
#10
Olesya Yu Shoeva
The wheat TaMyc1 gene encodes for transcriptional factor (TF) with bHLH domain. The gene is expressed in purple wheat grains and activates transcription of the anthocyanin biosynthesis structural genes. To reveal the features of TaMyc1 regulation in wheat pericarp transcription start sites (TSS) were identified by 5' RACE mean and translation efficiency was predicted by in silico methods. Three alternative transcript variants of TaMyc1 differing by 5' leader sequence only were identified in purple pericarp...
March 19, 2018: Molecular Biology Reports
https://www.readbyqxmd.com/read/29518549/sp1-mediated-downregulation-of-adamts3-gene-expression-in-osteosarcoma-models
#11
A Tuğşen Aydemir, Meltem Alper, Feray Kockar
ADAMTS3 is a member of procollagen N-proteinase subfamily of ADAMTS (a disintegrin and metalloproteinase with thrombospondin motifs) gene family. It has an important function in the procollagen maturation process. The removal of N-peptidases is required for the accurate processing of fibrillar collagens. Otherwise, several disorders can occur that is related with the collagenous tissues. ADAMTS3 mainly maturates type II collagen molecule which is the main component of the bone and cartilage. There are several expression studies about ADAMTS3 gene however its transcriptional regulation has not been lightened up, yet...
June 15, 2018: Gene
https://www.readbyqxmd.com/read/29514716/the-entamoeba-histolytica-tbp-and-trf1-transcription-factors-are-gaac-box-binding-proteins-which-display-differential-gene-expression-under-different-stress-stimuli-and-during-the-interaction-with-mammalian-cells
#12
Ravi Kumar Narayanasamy, Carlos Alberto Castañón-Sanchez, Juan Pedro Luna-Arias, Guillermina García-Rivera, Bartolo Avendaño-Borromeo, María Luisa Labra-Barrios, Jesús Valdés, María Esther Herrera-Aguirre, Esther Orozco
BACKGROUND: Entamoeba histolytica is the protozoan parasite responsible for human amebiasis. It causes up to 100,000 deaths worldwide each year. This parasite has two closely related basal transcription factors, the TATA-box binding protein (EhTBP) and the TBP-related factor 1 (EhTRF1). TBP binds to the canonical TATTTAAA-box, as well as to different TATA variants. TRF1 also binds to the TATTTAAA-box. However, their binding capacity to diverse core promoter elements, including the GAAC-element, and their role in gene regulation in this parasite remains unknown...
March 7, 2018: Parasites & Vectors
https://www.readbyqxmd.com/read/29504899/candidate-snp-markers-of-reproductive-potential-are-predicted-by-a-significant-change-in-the-affinity-of-tata-binding-protein-for-human-gene-promoters
#13
Irina V Chadaeva, Petr M Ponomarenko, Dmitry A Rasskazov, Ekaterina B Sharypova, Elena V Kashina, Dmitry A Zhechev, Irina A Drachkova, Olga V Arkova, Ludmila K Savinkova, Mikhail P Ponomarenko, Nikolay A Kolchanov, Ludmila V Osadchuk, Alexandr V Osadchuk
BACKGROUND: The progress of medicine, science, technology, education, and culture improves, year by year, quality of life and life expectancy of the populace. The modern human has a chance to further improve the quality and duration of his/her life and the lives of his/her loved ones by bringing their lifestyle in line with their sequenced individual genomes. With this in mind, one of genome-based developments at the junction of personalized medicine and bioinformatics will be considered in this work, where we used two Web services: (i) SNP_TATA_Comparator to search for alleles with a single nucleotide polymorphism (SNP) that alters the affinity of TATA-binding protein (TBP) for the TATA boxes of human gene promoters and (ii) PubMed to look for retrospective clinical reviews on changes in physiological indicators of reproductive potential in carriers of these alleles...
February 9, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29501997/characterization-of-regulatory-elements-in-osrglp2-gene-promoter-from-different-rice-accessions-through-sequencing-and-in-silico-evaluation
#14
Tariq Mahmood, Tamkeen Tahir, Faiza Munir, Zabta Khan Shinwari
Germins and germin-like proteins from cupin superfamily contribute resistance to heat denaturation, chemical degradation and against plant pathogens, further functions in plant growth and development. In this study, from three different Oryza sativa accessions KS-282 and Pak 7178 and Pak 7865, OsRGLP2 gene promoter region was amplified, sequenced and analyzed. Sequencing data was evaluated via different computational tools. The regulatory elements were predicted by Consite tool and mapping was done. Many transcription factors binding sites were discovered in OsRGLP2 gene promoter; among these factors, HFH-1 having a significant role in germination was picked for further investigation...
April 2018: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29482522/distinct-core-promoter-codes-drive-transcription-initiation-at-key-developmental-transitions-in-a-marine-chordate
#15
Gemma B Danks, Pavla Navratilova, Boris Lenhard, Eric M Thompson
BACKGROUND: Development is largely driven by transitions between transcriptional programs. The initiation of transcription at appropriate sites in the genome is a key component of this and yet few rules governing selection are known. Here, we used cap analysis of gene expression (CAGE) to generate bp-resolution maps of transcription start sites (TSSs) across the genome of Oikopleura dioica, a member of the closest living relatives to vertebrates. RESULTS: Our TSS maps revealed promoter features in common with vertebrates, as well as striking differences, and uncovered key roles for core promoter elements in the regulation of development...
February 26, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29465767/molecular-characteristics-of-rhesus-macaque-interleukin-22-cloning-in-vitro-expression-and-biological-activities
#16
Lei Yu, Feng-Jie Wang, Yan-Fang Cui, Dong Li, Wen-Rong Yao, Gui-Bo Yang
Interleukin-22 (IL-22) is a potential therapeutic agent for diseases driven by epithelial injury. To characterize the IL-22 expressed by rhesus macaques, animals that are irreplaceable for human disease research, rhesus macaque IL-22 (rhIL-22) was cloned and expressed, and its biological activity and in vivo distribution were examined. It was found that the rhIL-22 gene consists of five introns and six exons, including a short non-coding exon starting 22 bp downstream of a putative TATA box. The amino acid sequence of rhIL-22 showed 95·5% identity to that of humans, and it shared two conserved disulphide bonds, three N-glycosylation sites and all the critical residues for binding to IL-22R1...
February 21, 2018: Immunology
https://www.readbyqxmd.com/read/29465754/core-cis-element-variation-confers-subgenome-biased-expression-of-a-transcription-factor-that-functions-in-cotton-fiber-elongation
#17
Bo Zhao, Jun-Feng Cao, Guan-Jing Hu, Zhi-Wen Chen, Lu-Yao Wang, Xiao-Xia Shangguan, Ling-Jian Wang, Ying-Bo Mao, Tian-Zhen Zhang, Jonathan F Wendel, Xiao-Ya Chen
Cotton cultivars have evolved to produce extensive, long, seed-born fibers important for the textile industry, but we know little about the molecular mechanism underlying spinnable fiber formation. Here, we report how PACLOBUTRAZOL RESISTANCE 1 (PRE1) in cotton, which encodes a basic helix-loop-helix (bHLH) transcription factor, is a target gene of spinnable fiber evolution. Differential expression of homoeologous genes in polyploids is thought to be important to plant adaptation and novel phenotypes. PRE1 expression is specific to cotton fiber cells, upregulated during their rapid elongation stage and A-homoeologous biased in allotetraploid cultivars...
May 2018: New Phytologist
https://www.readbyqxmd.com/read/29464457/cloning-and-characterization-of-the-human-lactoferrin-receptor-gene-promoter
#18
Rulan Jiang, Bo Lönnerdal
Lactoferrin (Lf) is a major protein in human milk. Multiple biological functions of Lf are postulated to be mediated by a Lf receptor (LfR). The Lf receptor (LfR) plays an important role in absorption of Lf and Lf-bound iron by intestinal epithelial cells. Here, we cloned and characterized the promoter from a ~ 3.1 kb 5'-flanking region of the human LfR gene. Neither a TATA box nor a CCAAT box is found at the typical positions. The transcription start site was identified as 298 bp upstream of the translation start codon (+ 1) by 5' RLM-RACE...
February 20, 2018: Biometals: An International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine
https://www.readbyqxmd.com/read/29458534/specific-transcriptional-and-post-transcriptional-regulation-of-the-major-immediate-early-icp4-gene-of-gahv-2-during-the-lytic-latent-and-reactivation-phases
#19
Perrine Rasschaert, Isabelle Gennart, Imane Boumart, Ginette Dambrine, Benoit Muylkens, Denis Rasschaert, Sylvie Laurent
Transcriptional and post-transcriptional mechanisms are involved in the switch between the lytic, latent and reactivation phases of the viral cycle in herpesviruses. During the productive phases, herpesvirus gene expression is characterized by a temporally regulated cascade of immediate early (IE), early (E) and late (L) genes. In alphaherpesviruses, the major product of the IE ICP4 gene is a transcriptional regulator that initiates the cascade of gene expression that is essential for viral replication. In this study, we redefine the infected cell protein 4 (ICP4) gene of the oncogenic Marek's disease virus (MDV or gallid herpesvirus 2) as a 9438 nt gene ended with four alternative poly(A) signals and controlled by two alternative promoters containing essentially ubiquitous functional response elements (GC, TATA and CCAAT boxes)...
January 22, 2018: Journal of General Virology
https://www.readbyqxmd.com/read/29458530/sumoylation-of-ie2p86-is-required-for-efficient-autorepression-of-the-human-cytomegalovirus-major-immediate-early-promoter
#20
Nina Reuter, Anna Reichel, Anne-Charlotte Stilp, Myriam Scherer, Thomas Stamminger
The human cytomegalovirus (HCMV) IE2p86 protein is pivotal for coordinated regulation of viral gene expression. Besides functioning as a promiscuous transactivator, IE2p86 is also known to negatively regulate its own transcription. This occurs via direct binding of IE2p86 to a 14-bp palindromic DNA element located between the TATA box and the transcription start site of the major immediate-early promoter (MIEP), which is referred to as the cis repression signal (CRS). However, the exact mechanism of IE2p86-based autorepression is still unclear...
February 8, 2018: Journal of General Virology
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