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dna transcription

Luciana L Ferreira, Teresa Cunha-Oliveira, Caroline D Veloso, Cláudio F Costa, Kendall B Wallace, Paulo J Oliveira
Dose-dependent and cumulative cardiotoxicity associated with doxorubicin (DOX) is the main limitation of anticancer therapy. Pediatric cancer survivors are particularly vulnerable, and no effective prevention measures are available. The aim of the present study was to investigate the persistent effects of nanomolar DOX concentrations and determine whether a pretreatment would induce mitochondrial adaptations in H9c2 cardiomyoblasts. H9c2 cells were incubated with DOX (10 and 25 nM) for 24 h, followed by 9 days of recovery in drug-free medium...
December 14, 2018: Food and Chemical Toxicology
Rocío Barroso, Sofía M García-Mauriño, Laura Tomás-Gallardo, Eloísa Andújar, Mónica Pérez-Alegre, Eduardo Santero, Inés Canosa
CbrAB is a high ranked global regulatory system exclusive of the Pseudomonads that responds to carbon limiting conditions. It has become necessary to define the particular regulon of CbrB and discriminate it from the downstream cascades through other regulatory components. We have performed in vivo binding analysis of CbrB in P. putida and determined that it directly controls the expression of at least 61 genes; 20% involved in regulatory functions, including the previously identified CrcZ and CrcY small regulatory RNAs...
2018: PloS One
Gary Wilk, Rosemary Braun
Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) associated with trait diversity and disease susceptibility, yet their functional properties often remain unclear. It has been hypothesized that SNPs in microRNA binding sites may disrupt gene regulation by microRNAs (miRNAs), short non-coding RNAs that bind to mRNA and downregulate the target gene. While several studies have predicted the location of SNPs in miRNA binding sites, to date there has been no comprehensive analysis of their impact on miRNA regulation...
December 17, 2018: PLoS Genetics
Samuel Bowerman, Robert J Hickok, Jeff Wereszczynski
The fundamental unit of eukaryotic chromatin is the nucleosome core particle, a protein/DNA complex that binds ~147 base pairs of DNA to a histone octamer. These histones --- H3, H4, H2A, H2B --- form the nucleosome core through a stacked interaction in which two H2A-H2B dimers flank the (H3-H4)2 tetramer. In vivo, genetic accessibility can be modulated by the substitution of canonical histones with variant proteins that contain the same structural motif but a different amino acid sequence, such as the transcriptional repression-associated macroH2A variant...
December 17, 2018: Journal of Physical Chemistry. B
Tito Candelli, Julien Gros, Domenico Libri
RNA polymerase (RNAPII) transcription occurs pervasively, raising the important question of its functional impact on other DNA-associated processes, including replication. In budding yeast, replication originates from Autonomously Replicating Sequences (ARSs), generally located in intergenic regions. The influence of transcription on ARSs function has been studied for decades, but these earlier studies have neglected the role of non-annotated transcription. We studied the relationships between pervasive transcription and replication origin activity using high-resolution transcription maps...
December 17, 2018: ELife
Yan Zhang, Jiang Wu, Hong Jing, Gui Huang, Zhulei Sun, Shouming Xu
Long noncoding RNA (lncRNA) maternally expressed 3 (MEG3) has been implicated as a tumor suppressor gene in several human cancer types. However, little is known regarding its involvement and potential mechanism in human breast cancer. In this study, we explored the effect of MEG3 on the growth of human breast cancer cell line MDA-MB-231 in vitro and in vivo, and sought to elucidate the potential signaling mechanisms. Ectopic overexpression of MEG3 using a lentiviral vector Lv-MEG3 significantly inhibited breast cancer cell growth in vitro and a cancer xenograft growth in vivo...
December 16, 2018: Journal of Cellular Biochemistry
Daniël O Warmerdam, Rob M F Wolthuis
More than half of the human genome consists of repetitive sequences, with the ribosomal DNA (rDNA) representing two of the largest repeats. Repetitive rDNA sequences may form a threat to genomic integrity and cellular homeostasis due to the challenging aspects of their transcription, replication, and repair. Predisposition to cancer, premature aging, and neurological impairment in ataxia-telangiectasia and Bloom syndrome, for instance, coincide with increased cellular rDNA repeat instability. However, the mechanisms by which rDNA instability contributes to these hereditary syndromes and tumorigenesis remain unknown...
December 17, 2018: Chromosome Research
Oriol Juanola, Paula Piñero, Isabel Gómez-Hurtado, Esther Caparrós, Rocío García-Villalba, Alicia Marín, Pedro Zapater, Fabián Tarín, José M González-Navajas, Francisco A Tomás-Barberán, Rubén Francés
Intestinal permeability to translocation of bacterial products is increased in cirrhosis. Regulatory T cells (Tregs) remain central to the interplay between the host and microbial milieu. We propose that Tregs are involved in promoting gut barrier integrity and a balanced interaction with gut microbiota-derived short-chain fatty acids (SCFAs). Carbon tetrachloride cirrhosis was induced in wild-type and recombination activating gene 1 ( Rag1 )-/- mice. Naive T cells and Treg cells were transferred into Rag1 -/- mice...
December 2018: Hepatology Communications
Zheng Liu, Jing Yang, Chao Ge, Fangyu Zhao, Hong Li, Ming Yao, Jinjun Li, Hua Tian
Inhibitor of DNA binding/differentiation (Id2) is an important regulator involved in the initiation and progression of cancer. However, the function and mechanism of the regulation of Id2 in hepatocellular carcinoma (HCC) was unclear. In the present study, we found that the overexpression of Id2 increased HCC cell proliferation in vitro and in vivo . Knockdown of Id2 inhibited HCC cell proliferation in vitro and in vivo . Furthermore, knockdown of Id2 enhanced sorafenib-induced apoptosis in HCC. Conversely, overexpression of Id2 weakened sorafenib-induced apoptosis in HCC...
2018: American Journal of Cancer Research
Samuel G Towarnicki, J William O Ballard
Mitochondrial DNA (mtDNA) and the dietary macronutrient ratio are known to influence a wide range of phenotypic traits including longevity, fitness and energy production. Commonly mtDNA mutations are posited to be selectively neutral or reduce fitness and, to date, no selectively advantageous mtDNA mutations have been experimentally demonstrated in adult female Drosophila . Here we propose that a ND V161L mutation interacted with diets differing in their macronutrient ratios to influence organismal physiology and mitochondrial traits, but further studies are required to definitively show no linked mtDNA mutations are functionally significant...
2018: Frontiers in Genetics
Evangelia G Chronopoulou, Anastassios C Papageorgiou, Farid Ataya, Irini Nianiou-Obeidat, Panagiotis Madesis, Nikolaos E Labrou
Glutathione transferases (GSTs, EC. are inducible multifunctional enzymes that are essential in the detoxification and degradation of toxic compounds. GSTs have considerable biotechnological potential. In the present work, a new method for the generation of synthetic GSTs was developed. Abiotic stress treatment of Phaseolus vulgaris and Glycine max plants led to the induction of total GST activity and allowed the creation of a GST-enriched cDNA library using degenerated GST-specific primers and reverse transcription-PCR...
2018: Frontiers in Plant Science
Zhaoyong Liu, Ying Zhang, Yelong Chen, Youbin Lin, Zhen Lin, Hu Wang
Background: Signal transducer and activator of transcription (STAT) 1 is an important transcription factor and has been reported to be a tumor suppressor in many types of cancer. However, another STAT family member, STAT3, is considered to be an oncogene. The cross-talk between STAT1 and STAT3 in cancer has not been fully demonstrated. Materials and methods: Esophageal squamous cell carcinoma (ESCC) was used as a model to examine STAT1-STAT3 cross-regulation in cancer...
2018: Cancer Management and Research
Sherif M Shawky, Ahmed M Awad, Arwa A Abugable, Sherif F El-Khamisy
Purpose: The objective of this study is to develop a facile tool for the absolute detection and quantification of nucleic acid transcripts, using a gold nanoparticle-based optical biosensor. Topoisomerase 1 (TOP1) and tyrosyl DNA phosphodiesterase 2 (TDP2) were among the nucleic acid transcripts of choice due to their role as genomic instability biomarkers and their implication in various cancers and neurologic disorders. This opens the door to develop a simple tool that can be used for diagnosing and monitoring treatment response for such diseases, overcoming the requirements for high cost, time, and complexity of the existing technologies for the absolute quantification of transcripts of interest...
2018: International Journal of Nanomedicine
Alexander Idnurm
A DNA region in the mitochondrial genome of the fungus Phycomyces blakesleeanus (Mucorales, Mucoromycota) was characterized in a population of wild-type strains. The region encodes a predicted protein similar to the reverse transcriptases encoded by mitochondrial retroplasmids of Neurospora species and other Sordariomycetes (Ascomycota), but is uncommon in other fungi. DNA sequences of this element, named mystique , are highly variable between the strains, having greater than 2.5% divergence, yet most of the nucleotide differences fall in codon positions that do not change the amino acid sequence...
December 2018: Journal of Genetics
Asaf Zviran, Nofar Mor, Yoach Rais, Hila Gingold, Shani Peles, Elad Chomsky, Sergey Viukov, Jason D Buenrostro, Roberta Scognamiglio, Leehee Weinberger, Yair S Manor, Vladislav Krupalnik, Mirie Zerbib, Hadas Hezroni, Diego Adhemar Jaitin, David Larastiaso, Shlomit Gilad, Sima Benjamin, Ohad Gafni, Awni Mousa, Muneef Ayyash, Daoud Sheban, Jonathan Bayerl, Alejandro Aguilera-Castrejon, Rada Massarwa, Itay Maza, Suhair Hanna, Yonatan Stelzer, Igor Ulitsky, William J Greenleaf, Amos Tanay, Andreas Trumpp, Ido Amit, Yitzhak Pilpel, Noa Novershtern, Jacob H Hanna
The epigenetic dynamics of induced pluripotent stem cell (iPSC) reprogramming in correctly reprogrammed cells at high resolution and throughout the entire process remain largely undefined. Here, we characterize conversion of mouse fibroblasts into iPSCs using Gatad2a-Mbd3/NuRD-depleted and highly efficient reprogramming systems. Unbiased high-resolution profiling of dynamic changes in levels of gene expression, chromatin engagement, DNA accessibility, and DNA methylation were obtained. We identified two distinct and synergistic transcriptional modules that dominate successful reprogramming, which are associated with cell identity and biosynthetic genes...
December 10, 2018: Cell Stem Cell
Stefan Frank, Gaurav Ahuja, Deniz Bartsch, Nicole Russ, Wenjie Yao, Joseph Chao-Chung Kuo, Jens-Peter Derks, Vijay Suresh Akhade, Yulia Kargapolova, Theodore Georgomanolis, Jan-Erik Messling, Marie Gramm, Lilija Brant, Rizwan Rehimi, Natalia Emilse Vargas, Alina Kuroczik, Tsun-Po Yang, Raja Ghazanfar Ali Sahito, Julia Franzen, Juergen Hescheler, Agapios Sachinidis, Martin Peifer, Alvaro Rada-Iglesias, Meena Kanduri, Ivan G Costa, Chandrasekhar Kanduri, Argyris Papantonis, Leo Kurian
Human protein-coding genes are often accompanied by divergently transcribed non-coding RNAs whose functions, especially in cell fate decisions, are poorly understood. Using an hESC-based cardiac differentiation model, we define a class of divergent lncRNAs, termed yin yang lncRNAs (yylncRNAs), that mirror the cell-type-specific expression pattern of their protein-coding counterparts. yylncRNAs are preferentially encoded from the genomic loci of key developmental cell fate regulators. Most yylncRNAs are spliced polyadenylated transcripts showing comparable expression patterns in vivo in mouse and in human embryos...
November 21, 2018: Cell Stem Cell
Cornelia Meisenberg, Sarah I Pinder, Suzanna R Hopkins, Sarah K Wooller, Graeme Benstead-Hume, Frances M G Pearl, Penny A Jeggo, Jessica A Downs
Cohesin subunits are frequently mutated in cancer, but how they function as tumor suppressors is unknown. Cohesin mediates sister chromatid cohesion, but this is not always perturbed in cancer cells. Here, we identify a previously unknown role for cohesin. We find that cohesin is required to repress transcription at DNA double-strand breaks (DSBs). Notably, cohesin represses transcription at DSBs throughout interphase, indicating that this is distinct from its known role in mediating DNA repair through sister chromatid cohesion...
November 28, 2018: Molecular Cell
Xuan Lin, Hedan Chen, Ying Xie, Zhu Zeng, Zuquan Hu, Yi Jia, Yun Wang, Chengjian Tan, Lina Liu
Objective To obtain in vitro transcription of mouse mucin 1(MUC1) mRNA and express it in NIH/3T3 cells. Methods The MUC1 gene was amplified from mouse 4T1 cells by reverse transcription PCR (RT-PCR), and then inserted into the eukaryotic expression vector pcDNA3.1(+) to construct the recombinant vector pcDNA3.1(+)-MUC1. After identification by restriction enzyme cutting, the recombinant plasmid was used as a PCR template for the amplification of the MUC1-HA TAG fusion gene fragment with the reverse primer containing hemagglutinin tag (HA TAG) sequence...
October 2018: Xi Bao Yu Fen Zi Mian Yi Xue za Zhi, Chinese Journal of Cellular and Molecular Immunology
Tae Ho Ryu, Young Sam Go, Seung Hee Choi, Jeong-Il Kim, Byung Yeoup Chung, Jin-Hong Kim
The plant-specific transcription factor (TF) NAC103 was previously reported to modulate the unfolded protein response in Arabidopsis under endoplasmic reticulum (ER) stress. Alternatively, we here report that the NAC103 is involved in the downstream signaling of SOG1, a master regulator for expression of DNA damage response (DDR) genes induced by genotoxic stress. Arabidopsis NAC103 expression was strongly induced by genotoxic stress and nac103 mutants displayed substantial inhibition of DDR gene expression after gamma radiation or radiomimetic zeocin treatment...
December 15, 2018: Plant Journal: for Cell and Molecular Biology
Husile Gong, Ding Yang, Yunxia Qi, Jianghong Wu, Wenguang Zhang
The skin is the primary barrier between the internal organs of an organism and the environment, and it provides protection from ultraviolet (UV) radiation. According to the nocturnal bottleneck hypothesis, ungulates might have traversed to the grasslands and were exposed to UV radiation subsequent to the reduction in predation pressure. UV light exposure might have increased the S100A7 expression. In order to test whether the UV radiation is associated with the selection pressure on S100A7, we acquired the complete S100A7 DNA sequences from each of 42 vertebrate species...
December 15, 2018: Biochemical Genetics
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