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Takumi Takeuchi, Mami Hattori-Kato, Yumiko Okuno, Atsushi Kanatani, Masayoshi Zaitsu, Koji Mikami
Various conditions including distal renal tubular acidosis (dRTA) can induce stone formation in the kidney. dRTA is characterized by an impairment of urine acidification in the distal nephron. dRTA is caused by variations in genes functioning in intercalated cells including SLC4A1/AE1/Band3 transcribing two kinds of mRNAs encoding the Cl(-)/HCO3(-) exchanger in erythrocytes and that expressed in α-intercalated cells (kAE1). With the acid-loading test, 25% of urolithiasis patients were diagnosed with incomplete dRTA...
October 21, 2016: Scientific Reports
Yonggang Zhang, Fang Li, Xiao Xiao, Wu Deng, Chaoran Yin, Ting Zhang, Karnam S Murthy, Wenhui Hu
GATA transcription factors regulate an array of genes important in cell proliferation and differentiation. Here we report the identification of regulator of G protein signaling 4 (RGS4) as a novel target for GATA-6 transcription factor. Although three sites (a, b, c) within the proximal region of rabbit RGS4 promoter for GATA transcription factors were predicted by bioinformatics analysis, only GATA-a site (16 bp from the core TATA box) is essential for RGS4 transcriptional regulation. RT-PCR analysis demonstrated that only GATA-6 was highly expressed in rabbit colonic smooth muscle cells but GATA-4/6 were expressed in cardiac myocytes and GATA-1/2/3 expressed in blood cells...
October 13, 2016: Biochemical and Biophysical Research Communications
Cristina Silva Meira-Strejevitch, Vera Lucia Pereira-Chioccola, Marta Marques Maia, Daise Damaris Carnietto de Hipólito, Hui-Tzu Lin Wang, Gabriela Motoie, Aparecida Helena de Souza Gomes, Cristina Takami Kanamura, Roosecelis Brasil Martines, Cinara Cássia Brandão de Mattos, Fábio Batista Frederico, Luiz Carlos de Mattos, Cinara Cássia Brandão de Mattos, Fábio Batista Frederico, Rubens Camargo Siqueira, Mariana Previato, Amanda Pires Barbosa, Fernando Henrique Antunes Murata
This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at
October 12, 2016: Gene
Amanda L Lumsden, Richard L Young, Nektaria Pezos, Damien J Keating
BACKGROUND: Huntingtin-associated Protein 1 (HAP1) is expressed in neurons and endocrine cells, and is critical for postnatal survival in mice. HAP1 shares a conserved "HAP1_N" domain with TRAfficking Kinesin proteins TRAK1 and TRAK2 (vertebrate), Milton (Drosophila) and T27A3.1 (C. elegans). HAP1, TRAK1 and TRAK2 have a degree of common function, particularly regarding intracellular receptor trafficking. However, TRAK1, TRAK2 and Milton (which have a "Milt/TRAK" domain that is absent in human and rodent HAP1) differ in function to HAP1 in that they are mitochondrial transport proteins, while HAP1 has emerging roles in starvation response...
October 13, 2016: BMC Evolutionary Biology
Huynh Thi Thu Hue, Duong Thi Thu Ha, Nong Van Hai, Le Thi Thu Hien
The most important enzyme of the phenylpropanoid pathway, 4-coumarate:coenzyme A ligase (4CL), is encoded by several homologous genes including 4CL1. The 4CL1 promoter is a tissue-specific gene expression element, particularly active in the secondary xylem or older stems. In this study, the 1127 bp 5'- upstream region of the 4CL1 coding sequence from Eucalyptus camaldulensis, Euc4CL1, was isolated and characterized. Essential putative cis-elements in the Euc4CL1 promoter included: a TATA-box at -22/-28 position, two CCAAT-boxes at -256/-260 and -277/-281 positions, respectively, an AC-element at -328/-336 and A-boxes at -115/-120 and -990/-995 positions...
July 2016: Physiology and Molecular Biology of Plants: An International Journal of Functional Plant Biology
Panagiotis Kotsantis, Lara Marques Silva, Sarah Irmscher, Rebecca M Jones, Lisa Folkes, Natalia Gromak, Eva Petermann
Cancer is a disease associated with genomic instability that often results from oncogene activation. This in turn leads to hyperproliferation and replication stress. However, the molecular mechanisms that underlie oncogene-induced replication stress are still poorly understood. Oncogenes such as HRAS(V12) promote proliferation by upregulating general transcription factors to stimulate RNA synthesis. Here we investigate whether this increase in transcription underlies oncogene-induced replication stress. We show that in cells overexpressing HRAS(V12), elevated expression of the general transcription factor TATA-box binding protein (TBP) leads to increased RNA synthesis, which together with R-loop accumulation results in replication fork slowing and DNA damage...
October 11, 2016: Nature Communications
Elisa Pin, Frauke Henjes, Mun-Gwan Hong, Fredrik Wiklund, Patrik Magnusson, Anders Bjartell, Mathias Uhlén, Peter Nilsson, Jochen M Schwenk
There is a demand for novel targets and approaches to diagnose and treat prostate cancer (PCA). In this context, serum and plasma samples from a total of 609 individuals from two independent patient cohorts were screened for IgG reactivity against a sum of 3,833 human protein fragments. Starting from planar protein arrays with 3,786 protein fragments to screen 80 patients with and without PCA diagnosis, 161 fragments (4%) were chosen for further analysis based on their reactivity profiles. Adding 71 antigens from literature, the selection of antigens were corroborated for their reactivity in a set of 550 samples using suspension bead arrays...
October 4, 2016: Journal of Proteome Research
Srivastav Ranganathan, Samir K Maji, Ranjith Padinhateeri
Self-assembly of proteins into ordered, fibrillar structures is a commonly observed theme in biology. It has been observed that diverse set of proteins (e.g alpha-synuclein, insulin, TATA-box binding protein, Sup35, p53), independent of their sequence, native structure, or function could self-assemble into highly ordered structures known as amyloids. What are the crucial features underlying amyloidogenesis that make it so generic? Using coarse-grained simulations of peptide self-assembly, we argue that variation in two physical parameters- bending-stiffness of the polypeptide and strength of inter-molecular interactions- can give rise to many of the structural features typically associated with amyloid self-assembly...
October 3, 2016: Journal of the American Chemical Society
Geoffrey N Hendy, Lucie Canaff
The human calcium-sensing receptor gene (CASR) has 8 exons, and localizes to chromosome 3q. Exons 1A and 1B encode alternative 5'-untranslated regions (UTRs) that splice to exon 2 encoding the AUG initiation codon. Exons 2-7 encode the CaSR protein of 1078 amino acids. Promoter P1 has TATA and CCAAT boxes upstream of exon 1A, and promoter P2 has Sp1/3 motifs at the start site of exon 1B. Exon 1A transcripts from the P1 promoter are reduced in parathyroid tumors and colon carcinomas. Studies of colon carcinomas and neuroblastomas have emphasized the importance of epigenetic changes-promoter methylation of the GC-rich P2 promoter, histone acetylation-as well as involvement of microRNAs in bringing about CASR gene silencing and reduced CaSR expression...
2016: Frontiers in Physiology
Olga Arkova, Nikita Kuznetsov, Olga Fedorova, Ludmila Savinkova
It is known that only a single-nucleotide substitution (SNP: a single nucleotide polymorphism) in the sequence of a TATA box can influence the affinity of the interaction of TBP with the TATA box and contribute to the pathogenesis of complex hereditary human diseases and sometimes may be a cause of monogenic diseases (for instance, β-thalassemia).. In the present work, we studied the interaction of human TBP with a double-stranded oligodeoxyribonucleotide (ODN) 15 or 26 bp long identical to a TATA box of promoters of a real-life human gene, TPI or LEP, and labeled with fluorophores TAMRA and FAM...
September 25, 2016: Journal of Biomolecular Structure & Dynamics
Jordan T Feigerle, P Anthony Weil
The evolutionarily conserved TFIID complex is composed of TATA-box Binding Protein (TBP) and 13 TBP-associated factors (Tafs). The mechanisms by which many Taf subunits contribute to the essential function of TFIID are only poorly understood. To address this gap in knowledge, we present the results of a molecular genetic dissection of the TFIID subunit Taf2. Through systematic site-directed mutagenesis, we have discovered 12 taf2 temperature sensitive alleles (Ts). Two of these alleles display growth defects that can be strongly suppressed by overexpression of the yeast-specific TFIID subunit TAF14 but not by overexpression of any other TFIID subunit...
September 1, 2016: Journal of Biological Chemistry
Igor Martianov, Amandine Velt, Guillaume Davidson, Mohamed-Amin Choukrallah, Irwin Davidson
Mammalian genomes encode two genes related to the TATA-box binding protein (TBP), TBP-related factors 2 and 3 (TRF2 and TRF3). Male Trf2(-/-) mice are sterile and characterized by arrested spermatogenesis at the transition from late haploid spermatids to early elongating spermatids. Despite this characterization, the molecular function of murine Trf2 remains poorly characterized and no direct evidence exists to show that it acts as a bona fide chromatin-bound transcription factor. We show here that Trf2 forms a stable complex with TFIIA or the testis expressed paralogue ALF chaperoned in the cytoplasm by heat shock proteins...
2016: Scientific Reports
Hye Rim Oh, Chang Hyeok An, Nam Jin Yoo, Sug Hyung Lee
Initiation of transcription by RNA polymerase II requires TATA-box-binding protein (TBP)-associated factors (TAFs). TAF1 is a major scaffold by which TBP and TAFs interact in the basal transcription factor. TAF1L is a TAF1 homologue with 95 % amino acid identity with TAF1. TAF1 is involved in apoptosis induction and cell cycle regulation, but roles of TAF1 and TAF1L in tumorigenesis remain unknown. The aim of this study was to explore whether TAF1 and TAF1L genes were mutated in gastric (GC) and colorectal cancers (CRC)...
August 29, 2016: Pathology Oncology Research: POR
Supipi Duffy, Hok Khim Fam, Yi Kan Wang, Erin B Styles, Jung-Hyun Kim, J Sidney Ang, Tejomayee Singh, Vladimir Larionov, Sohrab P Shah, Brenda Andrews, Cornelius F Boerkoel, Philip Hieter
Somatic copy number amplification and gene overexpression are common features of many cancers. To determine the role of gene overexpression on chromosome instability (CIN), we performed genome-wide screens in the budding yeast for yeast genes that cause CIN when overexpressed, a phenotype we refer to as dosage CIN (dCIN), and identified 245 dCIN genes. This catalog of genes reveals human orthologs known to be recurrently overexpressed and/or amplified in tumors. We show that two genes, TDP1, a tyrosyl-DNA-phosphdiesterase, and TAF12, an RNA polymerase II TATA-box binding factor, cause CIN when overexpressed in human cells...
September 6, 2016: Proceedings of the National Academy of Sciences of the United States of America
Juzer A Kakal, Feras M Ghazawi, Elliott M Faller, Scott M Sugden, Parmvir Parmar, Paul A MacPherson
Interleukin-7 is essential for the development and maintenance of T cells, and the expression of the IL-7 receptor is tightly regulated at every stage of the T cell's lifespan. In mature CD8 T cells, IL-7 plays important roles in cell survival, peripheral homeostasis, and cytolytic function. The IL-7 receptor alpha-chain (CD127) is expressed at high levels on naïve and memory cells, but it is rapidly downregulated upon IL-7 stimulation. In this study, we illustrate the dynamicity of the CD127 promoter and show that it possesses positive as well as negative regulatory sites involved in upregulating and downregulating CD127 expression, respectively...
August 19, 2016: Immunogenetics
Qiusheng Kong, Lingyun Gao, Lei Cao, Yue Liu, Hameed Saba, Yuan Huang, Zhilong Bie
Melon (Cucumis melo L.) is an attractive model plant for investigating fruit development because of its morphological, physiological, and biochemical diversity. Quantification of gene expression by quantitative reverse transcription polymerase chain reaction (qRT-PCR) with stably expressed reference genes for normalization can effectively elucidate the biological functions of genes that regulate fruit development. However, the reference genes for data normalization in melon fruits have not yet been systematically validated...
2016: Frontiers in Plant Science
J H Kim, Y S Go, J K Kim, B Y Chung
MicroRNAs (miRNAs) regulate gene expression in response to biotic and abiotic stress in plants. We investigated gamma-ray-responsive miRNAs in Arabidopsis wild-type and cmt3-11t mutant plants using miRNA microarray analysis. miRNA expression was differentiated between the wild-type and cmt3-11t mutants. miR164a, miR169d, miR169h, miR172b*, and miR403 were identified as repressible in the wild-type and/or cmt3-11t mutant in response to gamma irradiation, while miR827, miR840, and miR850 were strongly inducible...
2016: Genetics and Molecular Research: GMR
Emi Hibino, Rintaro Inoue, Masaaki Sugiyama, Jun Kuwahara, Katsumi Matsuzaki, Masaru Hoshino
The expression of eukaryotic genes is precisely controlled by specific interactions between general transcription initiation factors and gene-specific transcriptional activators. The general transcription factor TFIID, which plays an essential role in mediating transcriptional activation, is a multisubunit complex comprising the TATA box-binding protein (TBP) and multiple TBP-associated factors (TAFs). On the other hand, biochemical and genetic approaches have shown that the promoter-specific transcriptional activator Sp1 has the ability to interact with one of the components of TFIID, the TBP-associated factor TAF4...
August 12, 2016: Protein Science: a Publication of the Protein Society
Gaili Fan, Kai Zhang, Hao Huang, Heng Zhang, Ao Zhao, Libin Chen, Ruiqi Chen, Guangpu Li, Zonghua Wang, Guo-Dong Lu
Multiprotein bridging factor 1 (MBF1) is a transcriptional co-activator that mediates transcriptional activation by bridging sequence-specific activator like proteins and the TATA-box binding protein (TBP). MBF1 has been well-studied in Arabidopsis thaliana, Saccharomyces cerevisiae, Drosophila melanogaster, and Homo sapiens, but it is not well understood in filamentous fungi. In this study, we report the identification and characterization of a MBF1 ortholog (MoMBF1) in the rice blast fungus Magnaporthe oryzae), which causes the devastating rice blast disease and is an ideal model for studying the growth, development and pathogenic mechanisms of filamentous fungi...
August 2, 2016: Current Genetics
Katjana Tantale, Florian Mueller, Alja Kozulic-Pirher, Annick Lesne, Jean-Marc Victor, Marie-Cécile Robert, Serena Capozi, Racha Chouaib, Volker Bäcker, Julio Mateos-Langerak, Xavier Darzacq, Christophe Zimmer, Eugenia Basyuk, Edouard Bertrand
Live-cell imaging has revealed unexpected features of gene expression. Here using improved single-molecule RNA microscopy, we show that synthesis of HIV-1 RNA is achieved by groups of closely spaced polymerases, termed convoys, as opposed to single isolated enzymes. Convoys arise by a Mediator-dependent reinitiation mechanism, which generates a transient but rapid succession of polymerases initiating and escaping the promoter. During elongation, polymerases are spaced by few hundred nucleotides, and physical modelling suggests that DNA torsional stress may maintain polymerase spacing...
2016: Nature Communications
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