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Transcriptional regulation

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https://www.readbyqxmd.com/read/29454261/frequency-of-somatic-tp53-mutations-in-combination-with-known-pathogenic-mutations-in-colon-adenocarcinoma-non-small-cell-lung-carcinoma-and-gliomas-as-identified-by-next-generation-sequencing
#1
Zahra Shajani-Yi, Francine B de Abreu, Jason D Peterson, Gregory J Tsongalis
The tumor suppressor gene TP53 is the most frequently mutated gene in human cancer. It encodes p53, a DNA-binding transcription factor that regulates multiple genes involved in DNA repair, metabolism, cell cycle arrest, apoptosis, and senescence. TP53 is associated with human cancer by mutations that lead to a loss of wild-type p53 function as well as mutations that confer alternate oncogenic functions that enable them to promote invasion, metastasis, proliferation, and cell survival. Identifying the discrete TP53 mutations in tumor cells may help direct therapies that are more effective...
February 13, 2018: Neoplasia: An International Journal for Oncology Research
https://www.readbyqxmd.com/read/29454161/physiological-low-dose-oestrogen-promotes-the-development-of-experimental-autoimmune-thyroiditis-through-the-up-regulation-of-th1-th17-responses
#2
Yang Xiang, Qian Jin, Li Li, Yali Yang, Hongmei Zhang, Miao Liu, Chenling Fan, Jing Li, Zhongyan Shan, Weiping Teng
Previous studies have reported a preponderance of autoimmune thyroiditis (AIT) in females, but the detailed mechanisms have not been elucidated. In this study, we explored the effects of oestrogen on experimental AIT (EAT) and its potential mechanisms in an ovariectomised mouse model through the supplementation of high (equivalent to the level during pregnancy) or low (equivalent to the level at the oestrus stage) doses of oestradiol (E2). We found that EAT incidence, the intrathyroidal inflammatory score, serum anti-thyroglobulin IgG2b levels, splenic mRNA expression of Th1- and Th17-specific transcription factors and typical cytokines and the proportion of IL-12-producing dendritic cells were significantly increased in EAT mice treated with low-dose E2 compared with those in the control group...
February 7, 2018: Journal of Reproductive Immunology
https://www.readbyqxmd.com/read/29454089/genome-wide-gene-expression-analysis-of-45-days-pregnant-fetal-cotyledons-vis-a-vis-non-pregnant-caruncles-in-buffalo-bubalus-bubalis
#3
Masoud Lotfan, Syed Azmal Ali, Munnalal Yadav, Suman Chuadhary, Manoj Kumar Jena, Sudarshan Kumar, Ashok Kumar Mohanty
The crosstalk between fetus and mother starts with the onset of placental attachment to the uterus. The cotyledons and caruncles are the two anatomically distinct structures that play a crucial role in this physiological communication. Using Agilent Gene Chip Genome microarray, we measured the expression profile of pregnancy cotyledons in comparison to caruncular reminiscence of the uteri in non-pregnant buffalo (Bubalus bubalis) for the detection of the early post-pregnancy rapid changes in cellular expression of mRNA transcripts...
February 14, 2018: Gene
https://www.readbyqxmd.com/read/29454088/hsf4-transcriptional-regulates-hmox-1-expression-in-hlecs
#4
Shengjie Liao, Zhen Qu, Linqiang Li, Benwen Zhou, Meng Gao, Mi Huang, Duanzhuo Li
The major causes for cataract formation are free radicals, which are neutralized by the endogenous antioxidants. However, how the human lens clean these harmful free radicals is still unclear. Transcriptional factor heat shock factor 4 (HSF4) is a cataract-causing gene and plays important roles during lens development. Here we show that HMOX-1, an anti-oxidase, is a bona fide transcriptional target gene of HSF4 in HLECs (human lens epithelial cells). HSF4 directly binds to the HSE element in HMOX-1 promoter to mediate its mRNA transcription and protein accumulation...
February 14, 2018: Gene
https://www.readbyqxmd.com/read/29454087/multi-step-splicing-of-sphingomyelin-synthase-linear-and-circular-rnas
#5
Ivan B Filippenkov, Olga Yu Sudarkina, Svetlana A Limborska, Lyudmila V Dergunova
The SGMS1 gene encodes the enzyme sphingomyelin synthase 1 (SMS1), which is involved in the regulation of lipid metabolism, apoptosis, intracellular vesicular transport and other significant processes. The SGMS1 gene is located on chromosome 10 and has a size of 320 kb. Previously, we showed that dozens of alternative transcripts of the SGMS1 gene are present in various human tissues. In addition to mRNAs that provide synthesis of the SMS1 protein, this gene participates in the synthesis of non-coding transcripts, including circular RNAs (circRNAs), which include exons of the 5'-untranslated region (5'-UTR) and are highly represented in the brain...
February 14, 2018: Gene
https://www.readbyqxmd.com/read/29453995/changes-of-lipid-peroxidation-and-glutathione-redox-system-and-expression-of-glutathione-peroxidase-regulatory-genes-as-effect-of-short-term-aflatoxin-b-1-exposure-in-common-carp
#6
Benjamin Kövesi, Csilla Pelyhe, Erika Zándoki, Miklós Mézes, Krisztián Balogh
Lipid peroxidation, glutathione content, glutathione peroxidase activity and gene expression of transcription factors, glutathione peroxidase, glutathione synthetase and glutathione reductase was investigated in common carp liver. Short term (24 h) exposure of aflatoxin B 1 at different doses (100, 200 and 400 μg AFB 1 kg -1 feed) was used. It was found that conjugated dienes and trienes elevated after 16 h, while thiobarbituric acid reactive substances content increased only at the lowest dose after 16 and 24 h of exposure...
February 14, 2018: Toxicon: Official Journal of the International Society on Toxinology
https://www.readbyqxmd.com/read/29453983/aldolase-a-overexpression-is-associated-with-poor-prognosis-and-promotes-tumor-progression-by-the-epithelial-mesenchymal-transition-in-colon-cancer
#7
Feng Ye, Yixing Chen, Lu Xia, Jiabian Lian, Shuyu Yang
There is increasing evidence that glycolysis is involved in cancer progression. Aldolase is a glycolytic enzyme that catalyzes the reversible conversion of fructose-1,6-bisphosphate to glyceraldehyde-3-phosphate and dihydroxyacetone phosphate. Disruption of the aldolase genes also plays a role in the progression of multiple types of cancer. However, the underlying mechanism of the action of aldolases in colon cancer progression remains elusive. In this study, aldolase A expression was investigated and found to be upregulated along with human colon cancer progression and metastasis at both the mRNA and protein levels in human colon cancer tissues...
February 14, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29453918/high-dose-of-histone-deacetylase-inhibitors-affects-insulin-secretory-mechanism-of-pancreatic-beta-cell-line
#8
Eiji Yamato
OBJECTIVE: Histone deacytylase inhibitors (HDACis) inhibit the deacetylation of the lysine residue of proteins, including histones, and regulate the transcription of a variety of genes. Recently, HDACis have been used clinically as anti-cancer drugs and possible anti-diabetic drugs. Even though HDACis have been proven to protect the cytokine-induced damage of pancreatic beta cells, evidence also shows that high doses of HDACis are cytotoxic. In the present study, we, therefore, investigated the eff ect of HDACis on insulin secretion in a pancreatic beta cell line...
January 1, 2018: Endocrine Regulations
https://www.readbyqxmd.com/read/29453862/insights-into-transcriptional-silencing-and-anti-silencing-in-shigella-flexneri-a-detailed-molecular-analysis-of-the-icsp-virulence-locus
#9
Natasha Weatherspoon-Griffin, Michael A Picker, Krystle L Pew, Hiromichi S Park, Daren Ginete, Monika M Karney, Pashtana Usufzy, Maria I Castellanos, Juan Carlos Duhart, Dustin J Harrison, Jillian N Socea, Alexander D Karabachev, Christopher T Hensley, Amber J Howerton, Rosa Ojeda-Daulo, Joy A Immak, Helen J Wing
Transcriptional silencing and anti-silencing mechanisms modulate bacterial physiology and virulence in many human pathogens. In Shigella species, many virulence plasmid genes are silenced by the histone-like nucleoid structuring protein H-NS and anti-silenced by the virulence gene regulator VirB. Despite the key role that these regulatory proteins play in Shigella virulence, their mechanisms of transcriptional control remain poorly understood. Here, we characterize the regulatory elements and their relative spacing requirements needed for the transcriptional silencing and anti-silencing of icsP, a locus that requires remotely located regulatory elements for both types of transcriptional control...
February 17, 2018: Molecular Microbiology
https://www.readbyqxmd.com/read/29453757/localization-of-epithelial-sodium-channel-enac-and-cftr-in-the-germinal-epithelium-of-the-testis-sertoli-cells-and-spermatozoa
#10
Sachin Sharma, Aaron Hanukoglu, Israel Hanukoglu
Spermatogenesis starts within the seminiferous tubules of the testis by mitotic division of spermatogonia that produces spermatocytes. Meiotic division of these spermatocytes produces haploid spermatids that differentiate into spermatozoa. In this study, we examined the expression of ENaC and CFTR (a Cl - channel) in rat testicular sections using confocal microscopic immunofluorescence. The structural integrity of the seminiferous tubule sections was verified by precise phalloidin staining of the actin fibers located abundantly at both basal and adluminal tight junctions...
February 16, 2018: Journal of Molecular Histology
https://www.readbyqxmd.com/read/29453573/gene-silencing-of-human-sertoli-cells-utilizing-small-interfering-rnas
#11
Hong Wang, Qingqing Yuan, Minghui Niu, Liping Wen, Hongyong Fu, Fan Zhou, Weihui Zhang, Zuping He
Sertoli cells, as the unique somatic cells within the seminiferous tubules, play essential roles in regulating normal spermatogenesis. In addition, recent studies have demonstrated that Sertoli cells could have significant applications in regenerative medicine due to their great plasticity. However, the roles of genes in controlling the fate determinations of human Sertoli cells remain largely unknown. Silencing genes of human Sertoli cells utilizing small interfering RNAs (siRNAs) is an important method to explore their functions and mechanisms in human Sertoli cells...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29453404/prep1-tumor-suppressor-protects-the-late-replicating-dna-by-controlling-its-replication-timing-and-symmetry
#12
Angela Palmigiano, Francesco Santaniello, Aurora Cerutti, Dmitry Penkov, Divya Purushothaman, Ekta Makhija, Lucilla Luzi, Fabrizio d'Adda di Fagagna, Pier Giuseppe Pelicci, Viveswara Shivashankar, Gaetano Ivan Dellino, Francesco Blasi
The synthesis of middle-to-late-replicating DNA can be affected independently of the rest of the genome by down-regulating the tumor suppressor PREP1 (PKNOX1). Indeed, DNA combing shows that PREP1 down-regulation affects DNA replication rate, increases the number of simultaneously firing origins and the asymmetry of DNA replication, leading to DNA damage. Genome-wide analysis of replication timing by Repli-seq shows that, upon PREP1 down-regulation, 25% of the genome is replicated earlier in the S-phase. The targeted DNA sequences correspond to Lamin-Associated Domains (LADs), and include late-replicating (LRRs) and temporal transition regions (TTRs)...
February 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29453395/the-genes-of-the-sulphoquinovose-catabolism-in-escherichia-coli-are-also-associated-with-a-previously-unknown-pathway-of-lactose-degradation
#13
Anna Kaznadzey, Pavel Shelyakin, Evgeniya Belousova, Aleksandra Eremina, Uliana Shvyreva, Darya Bykova, Vera Emelianenko, Anastasiya Korosteleva, Maria Tutukina, Mikhail S Gelfand
Comparative genomics analysis of conserved gene cassettes demonstrated resemblance between a recently described cassette of genes involved in sulphoquinovose degradation in Escherichia coli K-12 MG1655 and a Bacilli cassette linked with lactose degradation. Six genes from both cassettes had similar functions related to carbohydrate metabolism, namely, hydrolase, aldolase, kinase, isomerase, transporter, and transcription factor. The Escherichia coli sulphoglycolysis cassette was thus predicted to be associated with lactose degradation...
February 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29453387/structural-determinants-of-the-sine-b2-element-embedded-in-the-long-non-coding-rna-activator-of-translation-as-uchl1
#14
Peter Podbevšek, Francesca Fasolo, Carlotta Bon, Laura Cimatti, Sabine Reißer, Piero Carninci, Giovanni Bussi, Silvia Zucchelli, Janez Plavec, Stefano Gustincich
Pervasive transcription of mammalian genomes leads to a previously underestimated level of complexity in gene regulatory networks. Recently, we have identified a new functional class of natural and synthetic antisense long non-coding RNAs (lncRNA) that increases translation of partially overlapping sense mRNAs. These molecules were named SINEUPs, as they require an embedded inverted SINE B2 element for their UP-regulation of translation. Mouse AS Uchl1 is the representative member of natural SINEUPs. It was originally discovered for its role in increasing translation of Uchl1 mRNA, a gene associated with neurodegenerative diseases...
February 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29453355/co-expression-network-analysis-and-cis-regulatory-element-enrichment-determine-putative-functions-and-regulatory-mechanisms-of-grapevine-atl-e3-ubiquitin-ligases
#15
Darren C J Wong, Pietro Ariani, Simone Castellarin, Annalisa Polverari, Elodie Vandelle
Arabidopsis thaliana Toxicos en Levadura (ATL) proteins are a subclass of the RING-H2 zinc finger binding E3 ubiquitin ligases. The grapevine (Vitis vinifera) ATL family was recently characterized, revealing 96 members that are likely to be involved in several physiological processes through protein ubiquitination. However, the final targets and biological functions of most ATL E3 ligases are still unknown. We analyzed the co-expression networks among grapevine ATL genes across a set of transcriptomic data related to defense and abiotic stress, combined with a condition-independent dataset...
February 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29453333/scleraxis-is-a-transcriptional-activator-that-regulates-the-expression-of-tenomodulin-a-marker-of-mature-tenocytes-and-ligamentocytes
#16
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
https://www.readbyqxmd.com/read/29453323/rna-stabilization-factors-in-chloroplasts-of-vascular-plants
#17
REVIEW
Nikolay Manavski, Lisa-Marie Schmid, Jörg Meurer
In contrast to the cyanobacterial ancestor, chloroplast gene expression is predominantly governed on the post-transcriptional level such as modifications of the RNA sequence, decay rates, exo- and endonucleolytic processing as well as translational events. The concerted function of numerous chloroplast RNA-binding proteins plays a fundamental and often essential role in all these processes but our understanding of their impact in regulation of RNA degradation is only at the beginning. Moreover, metabolic processes and post-translational modifications are thought to affect the function of RNA protectors...
February 16, 2018: Essays in Biochemistry
https://www.readbyqxmd.com/read/29453316/brd1-mediated-acetylation-promotes-integrin-%C3%AE-v-gene-expression-via-interaction-with-sulfatide
#18
Qian Qian Cai, Yi Wei Dong, Bing Qi, Xiao-Ting Shao, Rong Wang, Zhong Yi Chen, Bao Mei He, Xing Zhong Wu
Integrin αV (ITGAV) gene expression is often dysregulated in cancers especially in hepatocellular carcinoma (HCC); however, the mechanism of regulation is poorly understood. Here, it is demonstrated that sulfatide activated integrin αV gene transcription, through histone H3K9/14 acetylation at the promoter, and high integrin αV expression are closely associated with poor prognosis. To elucidate the mechanism of regulation of acetylation, sulfatide-bound proteins were screened by mass spectrometry (MS), and BRD1 (bromodomain containing protein 1) was identified as an interacting protein that also co-localized with sulfatide in HCC cells...
February 16, 2018: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29453291/lsd1-inhibition-exerts-its-anti-leukemic-effect-by-recommissioning-pu-1-and-c-ebp%C3%AE-dependent-enhancers-in-aml
#19
Monica Cusan, Sheng F Cai, Helai P Mohammad, Andrei Krivtsov, Alan Chramiec, Evangelia Loizou, Matthew D Witkin, Kimberly N Smitheman, Daniel G Tenen, Min Ye, Britta Will, Ulrich Steidl, Ryan G Kruger, Ross L Levine, Hugh Y Rienhoff, Richard P Koche, Scott A Armstrong
Epigenetic regulators are recurrently mutated and aberrantly expressed in acute myeloid leukemia (AML). Targeted therapies designed to inhibit these chromatin-modifying enzymes, such as the histone demethylase lysine specific demethylase 1 (LSD1) and the histone methyltransferase DOT1L, have been developed as novel treatment modalities for these often refractory diseases. A common feature of many of these targeted agents is their ability to induce myeloid differentiation, suggesting that multiple paths toward a myeloid gene expression program can be engaged to relieve the differentiation blockade that is uniformly seen in AML...
February 16, 2018: Blood
https://www.readbyqxmd.com/read/29453285/the-distal-upstream-region-of-insulin-like-growth-factor-binding-protein-1-enhances-its-expression-in-endometrial-stromal-cells-during-decidualization
#20
Isao Tamura, Kosuke Jozaki, Shun Sato, Yuichiro Shirafuta, Masahiro Shinagawa, Ryo Maekawa, Toshiaki Taketani, Hiromi Asada, Hiroshi Tamura, Norihiro Sugino
We have previously shown that decidualization of human endometrial stromal cells (ESCs) causes a genome-wide increase in the levels of acetylation of histone-H3 Lys-27 (H3K27ac). We also reported that the distal gene regions, more than 3 kb up or downstream of gene transcription start sites have increased H3K27ac levels. Insulin-like growth factor-binding protein-1 (IGFBP-1) is a specific decidualization marker and has increased H3K27ac levels in its distal upstream region (-4701 bp to -7501 bp). Here, using a luciferase reporter gene construct containing this IGFBP-1 upstream region, we tested the hypothesis that it is an IGFBP-1 enhancer...
February 16, 2018: Journal of Biological Chemistry
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