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TATA Box

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https://www.readbyqxmd.com/read/28338110/frequency-of-the-ugt1a1-28-polymorphism-in-a-romanian-cohort-of-gilbert-syndrome-individuals
#1
Viorica E Radoi, Radu I Ursu, Elena Poenaru, Cosmin Arsene, Camil L Bohiltea, Roxana Bohiltea
BACKGROUND AND AIMS: Gilbert syndrome (GS) is characterized by unconjugated hyperbilirubinemia without liver disease or overt hemolysis and it is found in 3-10% of the general population. Inherited hyperbilirubinaemia is attributable to a reduced UGT1A1 activity. The UGT1A1 promoter (TA) repeats variants are documented of being involved in abnormally elevated bilirubin levels. The aim of the present study is to analyze the impact of UGT1A1 promoter variants on bilirubin levels in Romanian patients clinically supected with GS...
March 2017: Journal of Gastrointestinal and Liver Diseases: JGLD
https://www.readbyqxmd.com/read/28286728/dna-structural-features-of-eukaryotic-tata-containing-and-tata-less-promoters
#2
Venkata Rajesh Yella, Manju Bansal
Eukaryotic genes can be broadly classified as TATA-containing and TATA-less based on the presence of TATA box in their promoters. Experiments on both classes of genes have revealed a disparity in the regulation of gene expression and cellular functions between the two classes. In this study, we report characteristic differences in promoter sequences and associated structural properties of the two categories of genes in six different eukaryotes. We have analyzed three structural features, DNA duplex stability, bendability, and curvature along with the distribution of A-tracts, G-quadruplex motifs, and CpG islands...
March 2017: FEBS Open Bio
https://www.readbyqxmd.com/read/28273089/drosophila-trf2-and-taf9-regulate-lipid-droplet-size-and-phospholipid-fatty-acid-composition
#3
Wei Fan, Sin Man Lam, Jingxue Xin, Xiao Yang, Zhonghua Liu, Yuan Liu, Yong Wang, Guanghou Shui, Xun Huang
The general transcription factor TBP (TATA-box binding protein) and its associated factors (TAFs) together form the TFIID complex, which directs transcription initiation. Through RNAi and mutant analysis, we identified a specific TBP family protein, TRF2, and a set of TAFs that regulate lipid droplet (LD) size in the Drosophila larval fat body. Among the three Drosophila TBP genes, trf2, tbp and trf1, only loss of function of trf2 results in increased LD size. Moreover, TRF2 and TAF9 regulate fatty acid composition of several classes of phospholipids...
March 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28262749/identification-of-stable-housekeeping-genes-in-response-to-ionizing-radiation-in-cancer-research
#4
Gopal Iyer, Albert R Wang, Sean R Brennan, Shay Bourgeois, Eric Armstrong, Pari Shah, Paul M Harari
Housekeeping genes (HKGs) are essential for basic maintenance of a variety of cellular processes. They ideally maintain uniform expression independent of experimental conditions. However, the effects of ionizing radiation (IR) on HKG expression is unclear. Statistical algorithms, geNorm and Normfinder were used for estimating the stability of HKGs as raw quantification cycle (Cq) values were not a reliable factor for normalization. Head and neck, non-small lung and pancreas cells were exposed to 2, 4 and 6 Gy IR doses and expression of fourteen HKGs was measured at 5 min to 48 h post-irradiation within a given tissue...
March 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28257693/hypomorphic-pathogenic-variants-in-taf13-are-associated-with-autosomal-recessive-intellectual-disability-and-microcephaly
#5
Hasan Tawamie, Igor Martianov, Natalie Wohlfahrt, Rebecca Buchert, Gabrielle Mengus, Steffen Uebe, Luigi Janiri, Franz Wolfgang Hirsch, Johannes Schumacher, Fulvia Ferrazzi, Heinrich Sticht, André Reis, Irwin Davidson, Roberto Colombo, Rami Abou Jamra
In two independent consanguineous families each with two children affected by mild intellectual disability and microcephaly, we identified two homozygous missense variants (c.119T>A [p.Met40Lys] and c.92T>A [p.Leu31His]) in TATA-box-binding-protein-associated factor 13 (TAF13). Molecular modeling suggested a pathogenic effect of both variants through disruption of the interaction between TAF13 and TAF11. These two proteins form a histone-like heterodimer that is essential for their recruitment into the general RNA polymerase II transcription factor IID (TFIID) complex...
March 2, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28250581/genome-wide-comparative-analysis-of-leafy-promoter-sequence-in-angiosperms
#6
Zhichao Sun, Zheng Li, Jianqin Huang, Bingsong Zheng, Liangsheng Zhang, Zhengjia Wang
Regulation of the flowering mechanism is influenced by many environmental factors. Dissecting the regulatory processes upstream of the LFY (LEAFY) gene will help us to understand the molecular mechanisms of floral induction. In total, 53 LFY sequences were identified in 37 species. Among the 53 selected LFY promoters and after eliminating the short sequences, 47 LFY promoters were analyzed. Comparative genome studies for LFY promoters among plants showed that TATA-box existed in all herbaceous plants. The 1345-bp promoter sequence upstream to hickory LFY gene was cloned and analyzed, together with functional studies...
January 2017: Physiology and Molecular Biology of Plants: An International Journal of Functional Plant Biology
https://www.readbyqxmd.com/read/28216628/genome-wide-primary-transcriptome-analysis-of-h2-producing-archaeon-thermococcus-onnurineus-na1
#7
Suhyung Cho, Min-Sik Kim, Yujin Jeong, Bo-Rahm Lee, Jung-Hyun Lee, Sung Gyun Kang, Byung-Kwan Cho
In spite of their pivotal roles in transcriptional and post-transcriptional processes, the regulatory elements of archaeal genomes are not yet fully understood. Here, we determine the primary transcriptome of the H2-producing archaeon Thermococcus onnurineus NA1. We identified 1,082 purine-rich transcription initiation sites along with well-conserved TATA box, A-rich B recognition element (BRE), and promoter proximal element (PPE) motif in promoter regions, a high pyrimidine nucleotide content (T/C) at the -1 position, and Shine-Dalgarno (SD) motifs (GGDGRD) in 5' untranslated regions (5' UTRs)...
February 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28186172/appropriateness-of-reference-genes-for-normalizing-messenger-rna-in-mouse-2-4-dinitrobenzene-sulfonic-acid-dnbs-induced-colitis-using-quantitative-real-time-pcr
#8
Nour Eissa, Laëtitia Kermarrec, Hayam Hussein, Charles N Bernstein, Jean-Eric Ghia
2,4-Dinitrobenzene sulfonic acid (DNBS)-induced colitis is an experimental model that mimics Crohn's disease. Appropriateness of reference genes is crucial for RT-qPCR. This is the first study to determine the stability of reference gene expression (RGE) in mice treated with DNBS. DNBS experimental Colitis was induced in male C57BL/6 mice. RNA was extracted from colon tissue and comprehensive analysis of 13 RGE was performed according to predefined criteria. Relative colonic TNF-α and IL-1β mRNA levels were calculated...
February 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28153533/dysregulation-of-gene-expression-in-the-striatum-of-bachd-rats-expressing-full-length-mutant-huntingtin-and-associated-abnormalities-on-molecular-and-protein-levels
#9
Libo Yu-Taeger, Michael Bonin, Janice Stricker-Shaver, Olaf Riess, Hoa Huu Phuc Nguyen
Huntington disease (HD) is an autosomal dominantly inherited neurodegenerative disorder caused by a CAG repeat expansion in the gene coding for the huntingtin protein (HTT). Mutant HTT (mHTT) has been proposed to cause neuronal dysfunction and neuronal loss through multiple mechanisms. Transcriptional changes may be a core pathogenic feature of HD. Utilizing the Affymetrix platform we performed a genome-wide RNA expression analysis in two BACHD transgenic rat lines (TG5 and TG9) at 12 months of age, both of which carry full-length human mHTT but with different expression levels...
January 30, 2017: Neuropharmacology
https://www.readbyqxmd.com/read/28137832/chromatin-potentiates-transcription
#10
Shigeki Nagai, Ralph E Davis, Pierre Jean Mattei, Kyle Patrick Eagen, Roger D Kornberg
Chromatin isolated from the chromosomal locus of the PHO5 gene of yeast in a transcriptionally repressed state was transcribed with 12 pure proteins (80 polypeptides): RNA polymerase II, six general transcription factors, TFIIS, the Pho4 gene activator protein, and the SAGA, SWI/SNF, and Mediator complexes. Contrary to expectation, a nucleosome occluding the TATA box and transcription start sites did not impede transcription but rather, enhanced it: the level of chromatin transcription was at least sevenfold greater than that of naked DNA, and chromatin gave patterns of transcription start sites closely similar to those occurring in vivo, whereas naked DNA gave many aberrant transcripts...
February 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28134789/mrpl10-and-tbp-are-suitable-reference-genes-for-peripheral-nerve-crush-injury
#11
Yaxian Wang, Qianqian Shan, Yali Meng, Jiacheng Pan, Sheng Yi
Peripheral nerve injury triggers the dysregulation of a large number of genes at multiple sites, including neurons, peripheral nerve stump, and the target organ. Housekeeping genes were frequently used as reference genes to normalize the expression values of target genes. Suitable selection of housekeeping genes that are stably expressed after nerve injury minimizes bias elicited by reference genes and thus helps to better and more sensitively reflect gene expression changes. However, many housekeeping genes have been used as reference genes without testing the expression patterns of themselves...
January 27, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28131821/the-fate-of-retrotransposed-processed-genes-in-arabidopsis-thaliana
#12
Basma T M Abdelkarim, Vincent Maranda, Guy Drouin
Processed genes are functional genes that have arisen as a result of the retrotransposition of mRNA molecules. We found 6 genes that generated processed genes in the common ancestor of five Brassicaceae species (Arabidopsis thaliana, Arabidopsis lyrata, Capsella rubella, Brassica rapa and Thellungiella parvula). These processed genes have therefore been kept for at least 30millionyears. Analyses of the Ka/Ks ratio of these genes, and of those having given rise to them, show that they evolve relatively slowly and suggest that the processed genes maintained the same function as that of their parental gene...
April 20, 2017: Gene
https://www.readbyqxmd.com/read/28124143/molecular-characterization-of-previously-elusive-badnaviruses-associated-with-symptomatic-cacao-in-the-new-world
#13
Nomatter Chingandu, Muhammad Zia-Ur-Rehman, Thyail N Sreenivasan, Surendra Surujdeo-Maharaj, Pathmanathan Umaharan, Osman A Gutierrez, Judith K Brown
Suspected virus-like symptoms were observed in cacao plants in Trinidad during 1943, and the viruses associated with these symptoms were designated as strains A and B of cacao Trinidad virus (CTV). However, viral etiology has not been demonstrated for either phenotype. Total DNA was isolated from symptomatic cacao leaves exhibiting the CTV A and B phenotypes and subjected to Illumina HiSeq and Sanger DNA sequencing. Based on de novo assembly, two apparently full-length badnavirus genomes of 7,533 and 7,454 nucleotides (nt) were associated with CTV strain A and B, respectively...
January 25, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28077637/role-of-litopenaeus-vannamei-yin-yang-1-in-the-regulation-of-the-white-spot-syndrome-virus-immediate-early-gene-ie1
#14
Ping-Han Huang, Ting-Yi Huang, Pei-Si Cai, Li-Kwan Chang
Yin Yang 1 (YY1) is a multifunctional zinc finger transcription factor that regulates many key cellular processes. In this study, we report the cloning of YY1 from Litopenaeus vannamei shrimp (LvYY1). This study shows that LvYY1 is ubiquitously expressed in shrimp tissues, and knockdown of LvYY1 expression by double-stranded RNA (dsRNA) injection in white spot syndrome virus (WSSV)-infected shrimp reduced both mRNA levels of the WSSV immediate early gene ie1 as well as overall copy numbers of the WSSV genome...
March 15, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28071726/the-ppe2-protein-of-mycobacterium-tuberculosis-translocates-to-host-nucleus-and-inhibits-nitric-oxide-production
#15
Khalid Hussain Bhat, Shruti Srivastava, Sandeep Kumar Kotturu, Sudip Ghosh, Sangita Mukhopadhyay
Mycobacterium tuberculosis, the bacterium that causes tuberculosis, is one of the most successful pathogens of humans. It has evolved several adaptive skills and evasion mechanisms to hijack the immunologically educated host to suit its intracellular lifestyle. Here, we show that one of the unique PPE family member proteins of M. tuberculosis, PPE2, can limit nitric oxide (NO) production by inhibiting inos gene transcription. PPE2 protein has a leucine zipper DNA-binding motif and a functional nuclear localization signal...
January 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28062307/transcriptional-regulation-of-follicle-stimulating-hormone-%C3%AE-subunit-in-marmoset-by-an-alternate-distal-promoter
#16
Susha S Kutteyil, Bhakti R Pathak, Smita D Mahale
Follicle-Stimulating Hormone (FSH) is essential for mammalian folliculogenesis and spermatogenesis. Common marmoset (Callithrix jacchus) is a New World primate which exhibits an unusual FSH profile across the ovarian cycle with a mid-follicular FSH peak that is not observed in Catarrhini primates like humans. Since transcription of FSH β-subunit gene (FSHβ) is a rate-limiting step in the production of mature FSH, this study aimed to investigate the regulation of marmoset FSHβ gene expression in comparison to human...
January 3, 2017: General and Comparative Endocrinology
https://www.readbyqxmd.com/read/28060464/rna-polymerase-ii-components-and-rrn7-form-a-preinitiation-complex-on-the-homold-box-to-promote-ribosomal-protein-gene-expression-in-schizosaccharomyces-pombe
#17
Matías Montes, Sandra Moreira-Ramos, Diego A Rojas, Fabiola Urbina, Norbert F Käufer, Edio Maldonado
In Schizosaccharomyces pombe, ribosomal protein gene (RPG) promoters contain a TATA box analog, the HomolD box, which is bound by the Rrn7 protein. Despite the importance of ribosome biogenesis for cell survival, the mechanisms underlying RPG transcription remain unknown. In this study, we found that components of the RNA polymerase II (RNAPII) system, consisting of the initiation or general transcription factors (GTFs) TFIIA, IIB, IIE, TATA-binding protein (TBP) and the RNAPII holoenzyme, interacted directly with Rrn7 in vitro, and were able to form a preinitiation complex (PIC) on the HomolD box...
January 6, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28057501/cloning-and-characterization-of-pyruvate-carboxylase-gene-responsible-for-calcium-malate-overproduction-in-penicillium-viticola-152-and-its-expression-analysis
#18
Ibrar Khan, Sadia Qayyum, Shehzad Ahmed, Farhana Maqbool, Isfahan Tauseef, Kashif Syed Haleem, Zhen-Ming Chi
In this study, a pyruvate carboxylase gene (PYC) from a marine fungus Penicillium viticola 152 isolated from marine algae was cloned and characterized by using Genome Walking method. An open reading frame (ORF) of The PYC gene (accession number: KM593097) had 3582bp encoding 1193 amino acid protein (isoelectric point: 5.01) with a calculated molecular weight of 131.2757kDa. A putative promoter (intronless) of the gene was located at -666bp and contained a TATA box, several CAAT boxes, the 5'-SYGGRG-3' and a 5'-HGATAR-3' sequences...
March 20, 2017: Gene
https://www.readbyqxmd.com/read/28049897/expression-and-regulation-of-tal2-during-neuronal-differentiation-in-p19-cells
#19
Takanobu Kobayashi
 T-cell acute lymphocytic leukemia 2 (Tal2) is a gene encoding a member of the basic helix-loop-helix transcription factor family, which is essential for the normal development of the mouse brain. We found that Tal2 was induced during neural differentiation in P19 cells, which are pluripotent mouse embryonal carcinoma cells that differentiate into the neural lineage upon both exposure to all-trans retinoic acid (atRA) and the formation of cell aggregation. Tal2 expression during neural differentiation in P19 cells was detected within 3 h after induction with atRA and retinoic acid receptor α (RARα)...
2017: Yakugaku Zasshi: Journal of the Pharmaceutical Society of Japan
https://www.readbyqxmd.com/read/28018483/can-terminators-be-used-as-insulators-into-yeast-synthetic-gene-circuits
#20
Wenjiang Song, Jing Li, Qiang Liang, Mario Andrea Marchisio
BACKGROUND: In bacteria, transcription units can be insulated by placing a terminator in front of a promoter. In this way promoter leakage due to the read-through from an upstream gene or RNA polymerase unspecific binding to the DNA is, in principle, removed. Differently from bacterial terminators, yeast S. cerevisiae terminators contain a hexamer sequence, the efficiency element, that strongly resembles the eukaryotic TATA box i.e. the promoter sequence recognized and bound by RNA polymerase II...
2016: Journal of Biological Engineering
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