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https://www.readbyqxmd.com/read/28428825/comprehensive-evaluation-of-genome-wide-5-hydroxymethylcytosine-profiling-approaches-in-human-dna
#1
Ksenia Skvortsova, Elena Zotenko, Phuc-Loi Luu, Cathryn M Gould, Shalima S Nair, Susan J Clark, Clare Stirzaker
BACKGROUND: The discovery that 5-methylcytosine (5mC) can be oxidized to 5-hydroxymethylcytosine (5hmC) by the ten-eleven translocation (TET) proteins has prompted wide interest in the potential role of 5hmC in reshaping the mammalian DNA methylation landscape. The gold-standard bisulphite conversion technologies to study DNA methylation do not distinguish between 5mC and 5hmC. However, new approaches to mapping 5hmC genome-wide have advanced rapidly, although it is unclear how the different methods compare in accurately calling 5hmC...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28428226/rapid-throughput-analysis-of-gabaa-receptor-subtype-modulators-and-blockers-using-disbac1-3-membrane-potential-red-dye
#2
Atefeh Mousavi Nik, Brandon Pressly, Vikrant Singh, Shane Antrobus, Susan Hulsizer, Michael A Rogawski, Heike Wulff, Isaac N Pessah
Fluorometric Imaging Plate Reader (FLIPR®) membrane potential dye (FMP-Red-Dye) is a proprietary tool for basic discovery and high throughput drug screening for G-protein coupled receptors and ion channels. We optimized and validated this potentiometric probe to assay functional modulators of heterologous expressed GABAA receptor (GABAAR) isoforms (synaptic α1β3γ2, extrasynaptic α4β3δ, and β3 homopentomers). High-resolution mass spectrometry identified FMP-Red-dye as DisSBAC1(3). GABAAR expressing cells equilibrated with FMP-Red-Dye exhibited depolarized equilibrium membrane (Em) potentials compared to GABAAR-null cells...
April 20, 2017: Molecular Pharmacology
https://www.readbyqxmd.com/read/28411375/development-of-tetramethylenedisulfotetramine-tets-hapten-library-synthesis-electrophysiological-studies-and-immune-response-in-rabbits
#3
Bogdan Barnych, Natalia Vasylieva, Tom Joseph, Susan Hulsizer, Hai Nguyen, Tomas Cajka, Isaac Pessah, Heike Wulff, Shirley Gee, Bruce Hammock
There is a need for fast detection methods for the banned rodenticide tetramethylenedisulfotetramine (TETS), a highly potent blocker of the γ-aminobutyric acid (GABAA) receptors. General synthetic approach toward two groups of analogues was developed. Screening of the resulting library of compounds by FLIPR or whole-cell voltage-clamp revealed that despite the structural differences some of the TETS analogues retained GABAA receptor inhibition, however their potency was an order of magnitude lower. Antibodies raised in rabbits against some of the TETS analogues conjugated to protein recognized free TETS and will be used for the development of an immunoassay for TETS...
April 14, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28408905/tet-methylcytosine-oxidases-in-t-cell-and-b-cell-development-and-function
#4
REVIEW
Ageliki Tsagaratou, Chan-Wang J Lio, Xiaojing Yue, Anjana Rao
DNA methylation is established by DNA methyltransferases and is a key epigenetic mark. Ten-eleven translocation (TET) proteins are enzymes that oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) and further oxidization products (oxi-mCs), which indirectly promote DNA demethylation. Here, we provide an overview of the effect of TET proteins and altered DNA modification status in T and B cell development and function. We summarize current advances in our understanding of the role of TET proteins and 5hmC in T and B cells in both physiological and pathological contexts...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28396520/cytosine-modifications-modulate-the-chromatin-architecture-of-transcriptional-enhancers
#5
Elise A Mahé, Thierry Madigou, Aurélien A Sérandour, Maud Bizot, Stéphane Avner, Frédéric Chalmel, Gaëlle Palierne, Raphaël Métivier, Gilles Salbert
Epigenetic mechanisms are believed to play key roles in the establishment of cell-specific transcription programs. Accordingly, the modified bases 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) have been observed in DNA of genomic regulatory regions such as enhancers, and oxidation of 5mC into 5hmC by Ten Eleven Translocation (TET) proteins correlates with enhancer activation. However, the functional relationship between cytosine modifications and the chromatin architecture of enhancers remains elusive...
April 10, 2017: Genome Research
https://www.readbyqxmd.com/read/28393256/tetrandrine-inhibits-the-proliferation-of-human-osteosarcoma-cells-by-upregulating-the-pten-pathway
#6
Dong-Dong Tian, Ran-Xi Zhang, Nian Wu, Wei Yuan, Shuai-Hong Luo, Hou-Qing Chen, Yang Liu, Yang Wang, Bai-Cheng He, Zhong-Liang Deng
Tetrandrine (TET) is a natural product isolated from the Chinese herb Stephania tetrandra S. Moore and has been reported to have antiproliferation and apoptosis-inducing activity in various malignant tumor cells. However, the exact molecular mechanisms underlying these effects remain unclear. In the present study, we tested the antiproliferation effect of TET on osteosarcoma (OS) 143B cells and explored the possible potential molecular mechanism in this process. Using CCK-8 assay and flow cytometry, we found that TET inhibited proliferation, induced apoptosis and arrested the cell cycle of the 143B cells...
April 6, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28390956/the-structure-of-the-amorphous-matrix-of-keratins
#7
Murat Kadir, Xinwei Wang, Bowen Zhu, Jing Liu, Duane Harland, Crisan Popescu
Various keratin fibers, particularly human hairs, were investigated by transmission electron microscopy, TEM, solid-state 1HNMR and Transient Electro-Thermal Technique, TET. The results converge to suggest that the matrix of keratin fiber cortex, far from being amorphous, has a well-defined nano-scale grainy structure, the size of these grains being around 2 - 4 nm. The size of the grains appears to strongly depend on the chemical treatment of the fiber, on the temperature and on the relative humidity of the environment, as well as on the physiological factors at the level of fiber production in follicle...
April 5, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28360820/the-effect-of-tetrandrine-combined-with-cisplatin-on-proliferation-and-apoptosis-of-a549-ddp-cells-and-a549-cells
#8
Ling-Yun Ye, Song Hu, Hua-E Xu, Rong-Rong Xu, Hui Kong, Xiao-Ning Zeng, Wei-Ping Xie, Hong Wang
BACKGROUND: Non-small cell lung cancer comprises the majority of lung cancer cases and is insensitive to chemotherapy. Most patients develop drug resistance. Recently, tetrandrine (TET), a bis-benzylisoquinoline alkaloid, was identified as a novel anti-cancer agent. However, the effect of tetrandrine combined with cisplatin on lung cancer has not yet been studied. We aimed to identify a possible synergistic effect between tetrandrine and cisplatin, besides, to investigate the effects of TET in combination with DDP on proliferation and apoptosis in cisplatin-resistant and cisplatin-sensitive A549 cell lines, and to study the underlying mechanism...
2017: Cancer Cell International
https://www.readbyqxmd.com/read/28357664/generation-of-a-tet-on-expression-system-to-study-transactivation-ability-of-tax-2
#9
Fabio Bignami, Riccardo Alessio Sozzi, Elisabetta Pilotti
HTLV Tax proteins (Tax-1 and Tax-2) are known to be able to transactivate several host cellular genes involved in complex molecular pathways. Here, we describe a stable and regulated high-level expression model based on Tet-On system, to study the capacity of Tax-2 to transactivate host genes. In particular, the Jurkat Tet-On cell line suitable for evaluating the ability of Tax-2 to stimulate transactivation of a specific host gene, CCL3L1 (C-C motif chemokine ligand 3 like 1 gene), was selected. Then, a plasmid expressing tax-2 gene under control of a tetracycline-response element was constructed...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28349832/differential-expression-of-ten-eleven-translocation-genes-in-endometrial-cancers
#10
Piotr Ciesielski, Paweł Jóźwiak, Katarzyna Wójcik-Krowiranda, Ewa Forma, Łukasz Cwonda, Sylwia Szczepaniec, Andrzej Bieńkiewicz, Magdalena Bryś, Anna Krześlak
Ten-eleven translocation proteins are α-ketoglutarate-dependent dioxygenases involved in the conversion of 5-methylcytosines (5-mC) to 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine, and 5-carboxylcytosine that play a significant role in DNA demethylation. Deregulation of TET genes expression and changes in the level of 5-hmC are thought to be associated with the onset and progression of several types of cancer, but there are no such data related to endometrial cancer. The aim of the work was to investigate the messenger RNA expression levels of TET1, TET2, and TET3 in relation to clinicopathological characteristics of endometrial cancer as well as the correlation between expression of TET genes and the level of 5-hmC/5-mC...
March 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28349469/automated-chemical-solid-phase-synthesis-and-deprotection-of-5-hydroxymethylcytosine-containing-rna
#11
Christian Riml, Ronald Micura
5-Hydroxymethylcytosine is an epigenetic base modification that is part of the demethylation pathway of 5-methylcytosine in DNA. 5-Methylcytosine is iteratively oxidized to 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxycytosine by enzymes of the TET protein family. Since the discovery of 5-hydroxymethylcytosine also in RNA its role in regulatory processes and metabolism remains elusive. To gain more insight into the function of RNA containing 5-hydroxymethylcytidine, innovative and interdisciplinary approaches are required...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28346420/hepatic-cyclooxygenase-2-overexpression-induced-spontaneous-hepatocellular-carcinoma-formation-in-mice
#12
H Chen, W Cai, E S H Chu, J Tang, C-C Wong, S H Wong, W Sun, Q Liang, J Fang, Z Sun, J Yu
Cyclooxygenase (COX)-2 is upregulated in hepatocellular carcinoma (HCC). However, the direct causative effect of COX-2 in spontaneous HCC formation remains unknown. We thus investigate the role and molecular pathogenesis of COX-2 in HCC by using liver-specific COX-2 transgenic (TG) mice. We found spontaneous HCC formation with elevated inflammatory infiltrates and neovessels in male TG mice (3/21, 14.3%), but not in any of male WT mice (0/19). Reduced representation bisulfite sequencing (RRBS) and gene expression microarrays were performed in the HCC tumor and non-HCC liver tissues to investigate the molecular mechanisms of COX-2-driven HCC...
March 27, 2017: Oncogene
https://www.readbyqxmd.com/read/28343982/single-cell-5-formylcytosine-landscapes-of-mammalian-early-embryos-and-escs-at-single-base-resolution
#13
Chenxu Zhu, Yun Gao, Hongshan Guo, Bo Xia, Jinghui Song, Xinglong Wu, Hu Zeng, Kehkooi Kee, Fuchou Tang, Chengqi Yi
Active DNA demethylation in mammals involves ten-eleven translocation (TET) family protein-mediated oxidation of 5-methylcytosine (5mC). However, base-resolution landscapes of 5-formylcytosine (5fC) (an oxidized derivative of 5mC) at the single-cell level remain unexplored. Here, we present "CLEVER-seq" (chemical-labeling-enabled C-to-T conversion sequencing), which is a single-cell, single-base resolution 5fC-sequencing technology, based on biocompatible, selective chemical labeling of 5fC and subsequent C-to-T conversion during amplification and sequencing...
March 15, 2017: Cell Stem Cell
https://www.readbyqxmd.com/read/28339104/transferable-antibiotic-resistances-in-marketed-edible-grasshoppers-locusta-migratoria-migratorioides
#14
Andrea Osimani, Cristiana Garofalo, Lucia Aquilanti, Vesna Milanović, Federica Cardinali, Manuela Taccari, Marina Pasquini, Stefano Tavoletti, Francesca Clementi
Grasshoppers are the most commonly eaten insects by humans worldwide, as they are rich in proteins and micronutrients. This study aimed to assess the occurrence of transferable antibiotic resistance genes in commercialized edible grasshoppers. To this end, the prevalence of 12 selected genes [aac(6')-Ie aph(2″)-Ia, blaZ, erm(A), erm(B), erm(C), mecA, tet(M), tet(O), tet(S), tet(K), vanA, vanB] coding for resistance to antibiotics conventionally used in clinical practice was determined. The majority of samples were positive for tet(M) (70...
March 24, 2017: Journal of Food Science
https://www.readbyqxmd.com/read/28335006/a-platform-for-functional-assessment-of-large-variant-libraries-in-mammalian-cells
#15
Kenneth A Matreyek, Jason J Stephany, Douglas M Fowler
Sequencing-based, massively parallel genetic assays have revolutionized our ability to quantify the relationship between many genotypes and a phenotype of interest. Unfortunately, variant library expression platforms in mammalian cells are far from ideal, hindering the study of human gene variants in their physiologically relevant cellular contexts. Here, we describe a platform for phenotyping variant libraries in transfectable mammalian cell lines in two steps. First, a landing pad cell line with a genomically integrated, Tet-inducible cassette containing a Bxb1 recombination site is created...
March 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28333198/a-tetracycline-inducible-integrative-expression-system-for-streptococcus-pneumoniae
#16
Marina Meiers, Anke Laux, Daniela Eichinger, Anne Sexauer, Patrick Marx, Ralph Bertram, Reinhold Brückner
Inducible gene expression systems are very useful to analyze cellular processes. The ability to switch the expression state of genes of interest may even be crucial if essential traits or genetic instability are involved. An integrative plasmid, pTEX2, was designed using the (anhydro)tetracycline-inducible promoter Pxyl/tet from staphylococcal plasmid pRAB11 to control gene expression in Streptococcus pneumoniae. The system was evaluated by expressing genes of the two-component regulatory system ciaRH of S...
February 21, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/28321439/overexpression-of-parkinson-s-disease-associated-mutation-lrrk2-g2019s-in-mouse-forebrain-induces-behavioral-deficits-and-%C3%AE-synuclein-pathology
#17
Yulan Xiong, Stewart Neifert, Senthilkumar S Karuppagounder, Jeannette N Stankowski, Byoung Dae Lee, Jonathan C Grima, Guanxing Chen, Han Seok Ko, Yunjong Lee, Debbie Swing, Lino Tessarollo, Ted M Dawson, Valina L Dawson
Mutations in the leucine-rich repeat kinase 2 (LRRK2) gene have been identified as an unambiguous cause of late-onset, autosomal-dominant familial Parkinson's disease (PD) and LRRK2 mutations are the strongest genetic risk factor for sporadic PD known to date. A number of transgenic mice expressing wild-type or mutant LRRK2 have been described with varying degrees of LRRK2-related abnormalities and modest pathologies. None of these studies directly addressed the role of the kinase domain in the changes observed and none of the mice present with robust features of the human disease...
March 2017: ENeuro
https://www.readbyqxmd.com/read/28288190/tetrandrine-inhibits-migration-and-invasion-of-human-renal-cell-carcinoma-by-regulating-akt-nf-%C3%AE%C2%BAb-mmp-9-signaling
#18
Shurui Chen, Wei Liu, Ke Wang, Yizeng Fan, Jiaqi Chen, Jianbin Ma, Xinyang Wang, Dalin He, Jin Zeng, Lei Li
Renal cell carcinoma (RCC) is known as one of the most lethal malignancies in the urological system because of its high incidence of metastasis. Tetrandrine (Tet), a traditional Chinese herbal medicine, exerts a potent anti-cancer effect in a variety of cancer cells. However, the anti-metastatic effect of Tet and its possible mechanism in RCC is still unclear. The present study revealed that Tet significantly suppressed the migration and invasion of RCC 786-O and 769-P cells in vitro. Mechanistically, the protein levels of matrix metalloproteinases 9 (MMP-9), phosphorylated PI3K, PDK1, Akt and NF-κB were markedly reduced after Tet treatment...
2017: PloS One
https://www.readbyqxmd.com/read/28277978/targeted-dna-demethylation-in-human-cells-by-fusion-of-a-plant-5-methylcytosine-dna-glycosylase-to-a-sequence-specific-dna-binding-domain
#19
Jara Teresa Parrilla-Doblas, Rafael R Ariza, Teresa Roldán-Arjona
DNA methylation is a crucial epigenetic mark associated to gene silencing, and its targeted removal is a major goal of epigenetic editing. In animal cells, DNA demethylation involves iterative 5mC oxidation by TET enzymes followed by replication-dependent dilution and/or replication-independent DNA repair of its oxidized derivatives. In contrast, plants use specific DNA glycosylases that directly excise 5mC and initiate its substitution for unmethylated C in a base excision repair process. In this work, we have fused the catalytic domain of Arabidopsis ROS1 5mC DNA glycosylase (ROS1_CD) to the DNA binding domain of yeast GAL4 (GBD)...
April 3, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28274739/dual-role-of-act1-in-keratinocyte-differentiation-and-host-defense-traf3ip2-silencing-alters-keratinocyte-differentiation-while-inhibiting-il-17-responses
#20
Sylviane Lambert, William R Swindell, Lam C Tsoi, Stefan W Stoll, James T Elder
TRAF3IP2 is a candidate psoriasis susceptibility gene encoding Act1, an adaptor protein with ubiquitin ligase activity that couples the IL-17 receptor to downstream signaling pathways. We investigated the role of Act1 in keratinocyte responses to IL-17 using a tetracycline inducible shRNA targeting TRAF3IP2. Tet exposure for seven days effectively silenced TRAF3IP2 mRNA and Act1 protein, resulting in 761 genes with significant changes in expression (495 down, 266 up, >1.5-fold, p<0.05). Gene Ontology analysis revealed that genes affected by TRAF3IP2 silencing are involved in epidermal differentiation, with early differentiation genes (KRT1, KRT10, DSC1, DSG1) being downregulated and late differentiation genes (SPRR2, SPRR3, LCE3) being upregulated...
March 5, 2017: Journal of Investigative Dermatology
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