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dna transcription

Jolanta Kamińska, Paulina Langa, Milena Deptuła, Jacek Zieliński, Paweł Sachadyn, Anna Wardowska, Michał Pikuła
PURPOSE: In vitro expansion is an invaluable method to obtain keratinocytes in amounts necessary for effective transplantation therapies. In vitro cell culturing provokes questions concerning potential epigenetic alterations occurring in expanded cells in the context of usefulness for transplantation and safety. The purpose of this study was to investigate as to whether keratinocyte expansion is associated with changes in the activity of genes responsible for the maintenance of epigenetic stability...
March 19, 2019: Advances in Medical Sciences
Anna Lewinska, Jolanta Klukowska-Rötzler, Anna Deregowska, Jagoda Adamczyk-Grochala, Maciej Wnuk
Medulloblastoma (MB) is a common and highly aggressive pediatric brain tumor of a heterogeneous nature. According to transcriptome-based profiling, four molecular subgroups of MB have been revealed, namely WNT, SHH, Group 3 and Group 4. High MYC mRNA expression and MYC gene amplification in MB have been considered as indicators of poor prognosis. However, the role of c-Myc in MB biology is still not well established. In the present study, the effects of c-Myc activation in UW228-MycER MB cell line were investigated using 4-hydroxytamoxifen (4-OHT) induction system...
March 13, 2019: Redox Biology
Abel Gonzalez-Perez, Radhakrishnan Sabarinathan, Nuria Lopez-Bigas
Large-scale chromatin features, such as replication time and accessibility influence the rate of somatic and germline mutations at the megabase scale. This article reviews how local chromatin structures -e.g., DNA wrapped around nucleosomes, transcription factors bound to DNA- affect the mutation rate at a local scale. It dissects how the interaction of some mutagenic agents and/or DNA repair systems with these local structures influence the generation of mutations. We discuss how this local mutation rate variability affects our understanding of the evolution of the genomic sequence, and the study of the evolution of organisms and tumors...
March 21, 2019: Cell
Pengfei Guo, Chang-Hyun Lee, Huiyan Lei, Yonggang Zheng, Katiuska Daniela Pulgar Prieto, Duojia Pan
The Hippo tumor suppressor pathway regulates tissue growth in Drosophila by restricting the activity of the transcriptional coactivator Yorkie (Yki), which normally complexes with the TEF/TEAD family DNA-binding transcription factor Scalloped (Sd) to drive the expression of growth-promoting genes. Given its pivotal role as a central hub in mediating the transcriptional output of Hippo signaling, there is great interest in understanding the molecular regulation of the Sd-Yki complex. In this study, we identify Nerfin-1 as a transcriptional repressor that antagonizes the activity of the Sd-Yki complex by binding to the TEA DNA-binding domain of Sd...
March 22, 2019: ELife
Sebastian P Sacharowski, Tomasz J Sarnowski
Genomic DNA is highly packaged in eukaryotic cells and occurs in the form of nucleoprotein complex called chromatin. Although high DNA compaction allows to store large amount of genomic information in the cell nuclei, it also restricts the access to DNA regulatory sequences. Therefore, to overcome this issue, chromatin must be subjected to various alterations which are dependent on few interrelated factors: DNA modification, histones variants and modifications, ncRNA, chromatin remodeling complexes and chromatin architecture in nuclei...
March 22, 2019: Postepy Biochemii
Helena C Reinardy, Kristine B Pedersen, Jasmine Nahrgang, Marianne Frantzen
In Norway, mine tailings waste can be deposited by coastal submarine dispersal. Mine tailings slurry include fine particles <10 µm with elevated levels of metals (e.g. copper, iron) from residual mineral ore. Prolonged suspension of small particles in the water column may bring them into contact with locally spawned pelagic fish eggs, including Atlantic cod, Gadus morhua. Newly-fertilised cod embryos were exposed to suspended mine tailings particles up to 3.2 mg/L in flow-through aquaria for a total of 21 days...
March 22, 2019: Environmental Toxicology and Chemistry
Raquel Cabrera-Pérez, Ferran Vila-Julia, Michio Hirano, Federico Mingozzi, Javier Torres-Torronteras, Ramon Marti
MNGIE (mitochondrial neurogastrointestinal encephalomyopathy) is a devastating disease caused by mutations in TYMP, encoding thymidine phosphorylase (TP). In MNGIE patients, TP dysfunction results in systemic thymidine and deoxyuridine overload, which interferes with mitochondrial DNA replication. Preclinical studies have shown that gene therapy using a lentiviral vector targeted to hematopoietic stem cells or an adeno-associated vector (AAV) transcriptionally targeted to liver are feasible approaches to treat MNGIE...
March 22, 2019: Human Gene Therapy
David Garenne, Chase L Beisel, Vincent Noireaux
RATIONALE: Cell-free transcription-translation (TXTL) is becoming a popular technology to prototype and engineer biological systems outside living organisms. TXTL relies commonly to a cytoplasmic extract that provides the molecular components necessary to recapitulate gene expression in vitro, where most of the available systems are derived from E. coli. The proteinic and enzymatic composition of lysates, however, is typically unknown. In this work, we analyzed by mass spectrometry the molecular constituents of the all-E...
March 22, 2019: Rapid Communications in Mass Spectrometry: RCM
Silvina Epsztejn-Litman, Rachel Eiges
The vast majority of fragile X affected patients do not transcribe FMR1 due to a CGG repeat expansion in the 5'-untranslated region of the FMR1 gene. When the CGGs considerably expand, it elicits abnormal DNA methylation and histone modifications, which are responsible for FMR1 transcriptional silencing. In this chapter, we describe in detail two commonly used protocols for monitoring the epigenetic state of the FMR1 gene that bypass the difficulty in directly analyzing the CGGs. One protocol is for accurately measuring DNA methylation levels and the other is for profiling histone modifications...
2019: Methods in Molecular Biology
Ravindra Donde, Manoj Kumar Gupta, Gayatri Gouda, Jitendra Kumar, Ramakrishna Vadde, Khirod Kumar Sahoo, Sushanta Kumar Dash, Lambodar Behera
Rice serves as the major food for almost half of the world population. Because of its origin in the tropical and subtropical area, rice is more sensitive towards cold stress. Three homologs of DREB1, namely DREB1A, DREB1B and DREB1C are induced Queryduring cold stress and after binding with GCC-box in the promoter region of the target gene, they enhance cold tolerance in rice plants. Though the majority of DREBs bind GCC-box, the degree of activation varies among DREBs. The protein encoded via these three transcription factors contains a common domain, namely AP2/ERF...
March 21, 2019: Amino Acids
Luciano Procópio, Marcelo Pádula, Jan Dirk van Elsas, Lucy Seldin
The oxidative stress response of the highly resistant actinomycete Dietzia cinnamea P4 after treatment with hydrogen peroxide (H2 O2 ) was assessed in order to depict the possible mechanisms underlying its intrinsic high resistance to DNA damaging agents. We used transcriptional profiling to monitor the magnitude and kinetics of changes in the mRNA levels after exposure to different concentrations of H2 O2 at 10 min and 1 h following the addition of the stressor. Catalase and superoxide dismutase genes were induced in different ways, according to the condition applied...
March 21, 2019: World Journal of Microbiology & Biotechnology
Mengya Chen, Meng Wu, Xingxing Hu, Jiajia Yang, Renfang Han, Yubo Ma, Xu Zhang, Yaping Yuan, Rui Liu, Guangming Jiang, Shengqian Xu, Jianhua Xu, Zongwen Shuai, Faming Pan
OBJECTIVES: To investigate the role of methylation levels of the IFN regulatory factor 8 (IRF8) gene promoter in the development of ankylosing spondylitis (AS). METHODS: In this study, we compared the methylation levels of the IRF8 gene promoter between 99 AS patients and 99 healthy controls using MethylTarget approach. Quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) was performed to compare the mRNA levels of the IRF8 gene in the other 19 AS patients and 19 healthy controls...
March 21, 2019: Clinical Rheumatology
Emily R Theisen, Kyle R Miller, Iftekhar A Showpnil, Cenny Taslim, Kathleen I Pishas, Stephen L Lessnick
EWS/FLI is the pathognomic fusion oncoprotein that drives Ewing sarcoma. The amino-terminal EWS portion coordinates transcriptional regulation and the carboxy-terminal FLI portion contains an ETS DNA-binding domain. EWS/FLI acts as an aberrant transcription factor, orchestrating a complex mix of gene activation and repression, from both high affinity ETS motifs and repetitive GGAA-microsatellites. Our overarching hypothesis is that executing multi-faceted transcriptional regulation requires EWS/FLI to use distinct molecular mechanisms at different loci...
February 2019: Genes & Cancer
Xian Wang, Hua Wang, Bo Xu, Dongrui Jiang, Shan Huang, Hongzhen Yu, Zhengsheng Wu, Qiang Wu
DOT1-like protein (Dot1L) is the sole methyltransferase for methylation of lysine 79 in histone H3. Dot1L-dependent H3K79 methylation is involved in many biological processes, including telomeric silencing, cell cycle regulation, transcriptional activation and DNA repair. Genome-wide sequencing studies have revealed recurrent deletion and mutations of Dot1L gene in many types of human malignancies including ovarian cancer, however the role of Dot1L in ovarian cancer are largely unknown. To demonstrate the role of Dot1L in ovarian cancer, the expression of Dot1L was knocked out in ovarian cancer cells using CRISPR/Cas9 technology in the present study...
2019: American Journal of Translational Research
Bernat Blasco-Moreno, Leire de Campos-Mata, René Böttcher, José García-Martínez, Jennifer Jungfleisch, Danny D Nedialkova, Shiladitya Chattopadhyay, María-Eugenia Gas, Baldomero Oliva, José E Pérez-Ortín, Sebastian A Leidel, Mordechai Choder, Juana Díez
The highly conserved 5'-3' exonuclease Xrn1 regulates gene expression in eukaryotes by coupling nuclear DNA transcription to cytosolic mRNA decay. By integrating transcriptome-wide analyses of translation with biochemical and functional studies, we demonstrate an unanticipated regulatory role of Xrn1 in protein synthesis. Xrn1 promotes translation of a specific group of transcripts encoding membrane proteins. Xrn1-dependence for translation is linked to poor structural RNA contexts for translation initiation, is mediated by interactions with components of the translation initiation machinery and correlates with an Xrn1-dependence for mRNA localization at the endoplasmic reticulum, the translation compartment of membrane proteins...
March 21, 2019: Nature Communications
Lei Huang, Zhaoyun Liu, Huijuan Jiang, Lijuan Li, Rong Fu
Most of the International Prognostic Scoring System (IPSS) high-risk patients with myelodysplastic syndrome partly responded to hypomethylating therapy even with transient remission, while arsenic trioxide (ATO) had partial effect in patients with MDS. Therefore, we sought to investigate the effects and possible mechanisms of the combination of ATO and decitabine (DAC) in MDS cells. In our study, the MUTZ-1 and SKM-1 cells were treated with ATO, DAC or both. Cell viability, cell apoptosis, levels of reactive oxygen species (ROS) and expressions of the endoplasmicreticulum (ER) stress-associated genes and proteins were examined...
March 20, 2019: Journal of Investigative Medicine: the Official Publication of the American Federation for Clinical Research
Karine Choquet, Diane Forget, Elisabeth Meloche, Marie-Josée Dicaire, Geneviève Bernard, Adeline Vanderver, Raphael Schiffmann, Marc R Fabian, Martin Teichmann, Benoit Coulombe, Bernard Brais, Claudia L Kleinman
RNA polymerase III (Pol III) is an essential enzyme responsible for the synthesis of several small non-coding RNAs, a number of which are involved in mRNA translation. Recessive mutations in POLR3A , encoding the largest subunit of Pol III, cause POLR3-related hypomyelinating leukodystrophy (POLR3-HLD), characterized by deficient central nervous system myelination. Identification of the downstream effectors of pathogenic POLR3A mutations has been so far elusive. Here, we used CRISPR-Cas9 to introduce the POLR3A mutation c...
March 21, 2019: Journal of Biological Chemistry
John B Wojcik, Dylan M Marchione, Simone Sidoli, Anissa Djedid, Amanda Lisby, Jacek Majewski, Benjamin A Garcia
Malignant peripheral nerve sheath tumor (MPNST) is an aggressive sarcoma with recurrent loss of function alterations in polycomb-repressive complex 2 (PRC2), a histone-modifying complex involved in transcriptional silencing.To understand the role of PRC2 loss in pathogenesis and identify therapeutic targets, we conducted parallel global epigenomic and proteomic analysis of archival formalin-fixed, paraffin-embedded human MPNST with and without PRC2 loss (MPNSTLOSS vs. MPNSTRET). Loss of PRC2 resulted in increased histone post-translational modifications (PTMs) associated with active transcription, most notably H3K27Ac and H3K36me2, whereas repressive H3K27 di- and trimethylation (H3K27me2/3) marks were globally lost without a compensatory gain in other repressive PTMs...
March 21, 2019: Cancer Research
Zhaokun Wang, Xin Wang, GuiyuLou, LitaoQin, ShashaBian, Xia Tang, HongjieZhu, ShengranWang, BingtaoHao, ShixiuLiao
INTRODUCTION: Adams-Oliver syndrome (AOS) is a rare developmental disorder characterized by the combination of aplasia cutis congenita of the scalp vertex and terminal transverse limb defects. DOCK6 (Dedicator of cytokinesis 6) is one of the six identified AOS genes. METHODS: We performed targeted next-generation sequencing (NGS) of a child with an AOS phenotype. Sanger DNA sequencing further validated her lineal consanguinity. To explore the pathological features of the mutation, a minigene assay was used to investigate the effects of the mutation on splicing...
March 18, 2019: Gene
Gabriela Nestal de Moraes, Luciana da Torre Carneiro, Raquel Ciuvalschi Maia, Eric Wing-Fai Lam, Andrew David Sharrocks
Forkhead box (FOX) transcription factors compose a large family of regulators of key biological processes within a cell. FOXK2 is a member of FOX family, whose biological functions remain relatively unexplored, despite its description in the early nineties. More recently, growing evidence has been pointing towards a role of FOXK2 in cancer, which is likely to be context-dependent and tumour-specific. Here, we provide an overview of important aspects concerning the mechanisms of regulation of FOXK2 expression and function, as well as its complex interactions at the chromatin level, which orchestrate how it differentially regulates the expression of gene targets in pathophysiology...
March 20, 2019: Cancers
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