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A Tuğşen Aydemir, Meltem Alper, Feray Köçkar
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...
March 5, 2018: Gene
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
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
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...
February 23, 2018: Computational Biology and Chemistry
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
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 irreplaceable for human disease researches, rhesus macaque IL-22 (rhIL-22) was cloned and expressed, and its biological activity and in vivo distribution were examined. It was found that rhIL-22 gene consists of 5 introns and 6 exons, including a short non-coding exon starting 22bp downstream of a putative TATA box. The amino acid sequence of rhIL-22 showed 95...
February 21, 2018: Immunology
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...
February 21, 2018: New Phytologist
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
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
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
Chisa Shukunami, Aki Takimoto, Yuriko Nishizaki, Yuki Yoshimoto, Seima Tanaka, Shigenori Miura, Hitomi Watanabe, Tetsushi Sakuma, Takashi Yamamoto, Gen Kondoh, Yuji Hiraki
Tenomodulin (Tnmd) is a type II transmembrane glycoprotein predominantly expressed in tendons and ligaments. We found that scleraxis (Scx), a member of the Twist-family of basic helix-loop-helix transcription factors, is a transcriptional activator of Tnmd expression in tenocytes. During embryonic development, Scx expression preceded that of Tnmd. Tnmd expression was nearly absent in tendons and ligaments of Scx-deficient mice generated by transcription activator-like effector nucleases-mediated gene disruption...
February 16, 2018: Scientific Reports
Angad Garg, Ana M Sanchez, Stewart Shuman, Beate Schwer
The expression of the phosphate transporter Pho84 in fission yeast Schizosaccharomyces pombe is repressed in phosphate-rich medium and induced during phosphate starvation. Two other phosphate-responsive genes in S. pombe (pho1 and tgp1) had been shown to be repressed in cis by transcription of a long noncoding (lnc) RNA from the upstream flanking gene, but whether pho84 expression is regulated in this manner is unclear. Here we show that repression of pho84 is enforced by transcription of the SPBC8E4.02c locus upstream of pho84 to produce a lncRNA that we name prt2 (pho-repressive transcript 2) We identify two essential elements of the prt2 promoter: HomolD box and TATA box, mutations of which inactivate the prt2 promoter and derepress the downstream pho84 promoter under phosphate-replete conditions...
February 2, 2018: Journal of Biological Chemistry
Che-Min Lo, Yi-Shing Ma, Yau-Huei Wei, Benjamin Y T Hsieh, Mingli Hsieh
Myoclonic epilepsy with ragged-red fibers (MERRF) is a maternally inherited mitochondrial neuromuscular disease. We previously reported a significant decrease of mRNA and protein levels of nuclear DNA-encoded carbonic anhydrase VIII (CA8) in MERRF cybrids harboring A8344G mutation in mitochondrial DNA (mtDNA). In this study, we established a reporter construct of luciferase gene-carrying hCA8 promoter containing several putative transcription factor-binding sites, including GC-box, AP-2 and TATA-binding element in the 5'flanking region of the hCA8 gene...
January 31, 2018: Archives of Biochemistry and Biophysics
Irina Gogolevskaya, Danil Stasenko, Karina Tatosyan, Dmitri Kramerov
Short nuclear 4.5SI RNA can be found in three related rodent families. Its function remains unknown. The genes of 4.5SI RNA contain an internal promoter of RNA polymerase III composed of the boxes A and B. Here, the effect of the sequence immediately upstream of the mouse 4.5SI RNA on its transcription was studied. The gene with deletions and substitutions in the 5'-flanking sequence was used to transfect HeLa cells and its transcriptional activity was evaluated from the cellular level of 4.5SI RNA. Single-nucleotide substitutions in the region adjacent to the transcription start site (positions -2 to -8) decreased the expression activity of the gene down to 40-60% of the control...
February 2, 2018: Genome Génome / Conseil National de Recherches Canada
Jifeng Guo, Yiting Cui, Qiong Liu, Yang Yang, Yujing Li, Ling Weng, Beisha Tang, Peng Jin, Xiao-Jiang Li, Su Yang, Shihua Li
BACKGROUND: Spinocerebellar ataxia 17 (SCA17) belongs to the family of neurodegenerative diseases caused by polyglutamine (polyQ) expansion. In SCA17, polyQ expansion occurs in the TATA box binding protein (TBP) and leads to the misfolding of TBP and the preferential degeneration in the cerebellar Purkinje neurons. Currently there is no effective treatment for SCA17. Mesencephalic astrocyte-derived neurotrophic factor (MANF) is a recently identified neurotrophic factor, and increasing MANF expression ameliorated SCA17 neuropathology in TBP-105Q knock-in (KI) mouse model, indicating that MANF could be a therapeutic target for treating SCA17...
January 30, 2018: Molecular Neurodegeneration
Mei-Qin Zhuo, Zhi Luo, Yi-Huan Xu, Dan-Dan Li, Ya-Xiong Pan, Kun Wu
In the present study, the length of 360, 1848 and 367 bp sequences of promoters from three subtypes of PI3K family (PI3KCa, PI3KC2b and PI3KC3) of yellow catfish Pelteobagrus fulvidraco were cloned and characterized. Bioinformatics analysis revealed that PI3KCa, PI3KC2b and PI3KC3 had different structures in their core promoter regions. The promoter regions of PI3KCa and PI3KC2b had CpG islands but no CAAT and TATA box. In contrast, the promoter of PI3KC3 had the canonical TATA and CAAT box but no CpG island...
January 16, 2018: International Journal of Molecular Sciences
Zayneb Chaâbene, Agnieszka Rorat, Imen Rekik Hakim, Fabien Bernard, Grubb C Douglas, Amine Elleuch, Franck Vandenbulcke, Hafedh Mejdoub
Phytochelatin synthase and metallothionein gene expressions were monitored via qPCR in order to investigate the molecular mechanisms involved in Cd and Cr detoxification in date palm (Phoenix dactylifera). A specific reference gene validation procedure using BestKeeper, NormFinder and geNorm programs allowed selection of the three most stable reference genes in a context of Cd or Cr contamination among six reference gene candidates, namely elongation factor α1, actin, aldehyde dehydrogenase, SAND family, tubulin 6 and TaTa box binding protein...
December 28, 2017: Chemosphere
Jorge Gutiérrez-Flores, Estrella Ramos, Carlos I Mendoza, Enrique Hernández-Lemus
DNA is one of the most important biomolecules since it contains all the genetic information about an organism. The tridimensional structure of DNA is a determinant factor that influences the physiological and biochemical mechanisms by which this molecule carries out its biological functions. It is believed that hydrogen bonds and π-π stacking are the most relevant non-covalent interactions regarding DNA stability. Due to its importance, several theoretical works have been made to describe these interactions, however, most of them often consider only the presence of two nitrogenous bases, having a limited overview of the participation of these in B-DNA stabilization...
December 12, 2017: Biophysical Chemistry
Yiwen Zhang, Weiwei Liu, Yingshi Chen, Jun Liu, Kang Wu, Lishi Su, Wanying Zhang, Yawen Jiang, Xu Zhang, Yijun Zhang, Chao Liu, Liang Tao, Bingfeng Liu, Hui Zhang
The CD4+CD25+FOXP3+ regulatory T cells (Tregs) mediate immunological self-tolerance and suppress various immune responses. FOXP3 is a key transcriptional factor for the generation and development of Tregs. Its expression is regulated by various cytokines including TGF-β, IL-2, and IL-10. It is important to further identify the regulatory factors for Tregs. Given that many microRNAs (miRNAs) could specifically interact with the core promoter region and specifically enhance the transcription of many target genes, we searched for any possible miRNA(s) targeting the core promoter region of the FOXP3 gene...
December 27, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
Eiryo Kawakami, Naruhiko Adachi, Toshiya Senda, Masami Horikoshi
While both archaeal and eukaryotic transcription initiation systems utilize TBP (TATA box-binding protein) and TFIIB (transcription factor IIB), eukaryotic systems include larger numbers of initiation factors. It remains uncertain how eukaryotic transcription initiation systems have evolved. Here, we investigate the evolutionary development of TBP and TFIIB, each of which has an intramolecular direct repeat, using two evolutionary indicators. Inter-repeat sequence dissimilarity (dDR, distance between direct repeats) indicates that the asymmetry of two repeats in TBP and TFIIB has gradually increased during evolution...
December 26, 2017: Cell Reports
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