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https://www.readbyqxmd.com/read/30121964/insights-from-multidimensional-analyses-of-the-pan-cancer-dna-methylome-heterogeneity-and-the-uncanonical-cpg-gene-associations
#1
Yang Liu, Rongyao Huang, Yu Liu, Wanlu Song, Yuting Wang, Yang Yang, Shengcheng Dong, Xuerui Yang
Although the DNA methylome profiles have been available in large cancer cohorts such as The Cancer Genome Atlas (TCGA), integrative analysis of the DNA methylome architectures in a pan-cancer manner is still limited. In the present study, we aimed to systematically dissect the insightful features related to the inter-tumoral DNA methylome heterogeneity in a pan-cancer context of 21 cancers in TCGA. First, pan-cancer clustering of the DNA methylomes revealed convergence of cancers and, meanwhile, new classifications of cancer subtypes, which are often associated to prognostic differences...
August 19, 2018: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/30121862/search-of-somatic-mutations-of-nkx2-5-and-gata4-genes-in-chinese-patients-with-sporadic-congenital-heart-disease
#2
Jie Yin, Jianhua Qian, Genyin Dai, Chunli Wang, Yuming Qin, Ting Xu, Zewei Li, Han Zhang, Shiwei Yang
Congenital heart disease (CHD) usually occurs sporadically, with only a minority of cases associated with a known genetic mechanism. Cardiac-specific transcription factors NKX2-5 and GATA4 play key roles in the mammalian heart development, and the affected cardiac tissues of CHD patients are prone to somatic mutations which thus participate in the pathogenesis of CHD. We collected 98 patients with sporadic CHD, extracted genomic DNA from cardiac tissues and blood, and then screened NKX2-5 and GATA4 genes using PCR-direct sequence analysis...
August 18, 2018: Pediatric Cardiology
https://www.readbyqxmd.com/read/30121809/penaeid-shrimp-brachyury-sequence-analysis-and-expression-during-gastrulation
#3
Philip L Hertzler, Jiankai Wei, Andrew P Droste, Jianbo Yuan, Jianhai Xiang
Gastrulation occurs by a variety of morphogenetic movements, often correlated with diverse expression of the T-box transcription factor Brachyury (Bra). Bra may be expressed in ectoderm, mesoderm, or endoderm, but its role in cell fate specification or regulation of gastrulation movements has not been studied in the development of crustaceans. Penaeid shrimp (Decapoda: Dendrobranchiata: Penaeidae) develop by complete cleavage and gastrulation by invagination to a free-swimming nauplius larva. Penaeid gastrulation diverges from other decapods and from insects, occurring early at a low cell number with the formation of a radial invagination...
August 18, 2018: Development Genes and Evolution
https://www.readbyqxmd.com/read/30121749/milr2-a-novel-tetr-family-regulator-involved-in-5-oxomilbemycin-a3-a4-biosynthesis-in-streptomyces-hygroscopicus
#4
Keke Wei, Yuanjie Wu, Lei Li, Weihong Jiang, Jinfeng Hu, Yinhua Lu, Shaoxin Chen
Milbemycins produced by several Streptomyces species are a group of 16-membered macrolides with potent insecticidal and anthelminthic activity. Milbemycin A3/A4, the main components of the milbemycins biosynthetic pathway, and 5-oxomilbemycin A3/A4, the analogs of milbemycin A3/A4 without the reduction of the C-5 keto group, have been developed as acaricides, insecticides, and anthelmintics. However, so far, little is known about the regulation of milbemycins biosynthesis, which has greatly hampered the generation of high producing strains by metabolic engineering...
August 18, 2018: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/30121655/zbtb16-overexpression-enhances-white-adipogenesis-and-induces-brown-like-adipocyte-formation-of-bovine-white-intramuscular-preadipocytes
#5
Shengjuan Wei, Mengmeng Zhang, Yueying Zheng, Peishi Yan
BACKGROUND/AIMS: Our study aims to characterize functions of ZBTB16 gene in the process of intramuscular fat (IMF) deposition and metabolism of bovine, thereby providing insights into mechanisms for the use of ZBTB16 in fat management. METHODS: Primary preadipocytes derived from bovine IMF tissue were isolated and used as the in vitro cell model. An adenovirus Ad-ZBTB16 was transfected into bovine preadipocytes to overexpress the ZBTB16 gene. By using real-time quantitative PCR (RT-qPCR), western blotting, Oil Red-O staining, glycerol-3-phosphate dehydrogenase (GPDH) activity assay, and cell counting kit-8 (CCK-8) test, adipogenic and proliferative signals in adipocytes were monitored to investigate effects of ZBTB16 on adipogenesis of bovine preadipocytes...
August 17, 2018: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/30121393/an-integrative-analysis-of-transcriptome-and-epigenome-features-of-ascl1-positive-lung-adenocarcinomas
#6
Naoya Miyashita, Masafumi Horie, Hiroshi I Suzuki, Masahito Yoshihara, Dijana Djureinovic, Johan Persson, Hans Brunnström, Cecilia Lindskog, Hedvig Elfving, Patrick Micke, Akira Saito, Takahide Nagase
A subgroup of lung adenocarcinoma shows neuroendocrine differentiation and expression of achaete-scute complex homolog 1 (ASCL1), common to high-grade neuroendocrine tumors, small cell lung cancer and large cell neuroendocrine carcinoma. The aim of this study was to characterize clinical and molecular features of ASCL1-positive lung adenocarcinoma by utilizing recent transcriptome profiling in multiple patient cohorts and genome-wide epigenetic profiling including data from The Cancer Genome Atlas (TCGA). The ASCL1-positive subtype of lung adenocarcinoma developed preferentially in current or former smokers and usually did not harbor epidermal growth factor receptor (EGFR) mutations...
August 16, 2018: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/30121333/the-ezh2-h3k27me3-dnmt1-complex-orchestrates-epigenetic-silencing-of-the-wwc1-gene-a-hippo-yap-pathway-upstream-effector-in-breast-cancer-epithelial-cells
#7
Xiong Liu, Chun Li, Rengdong Zhang, Wenjun Xiao, Xia Niu, Xiajun Ye, Zijia Li, Yuxian Guo, Junyu Tan, Yaochen Li
It is well known that epithelial-mesenchymal transition (EMT) can confer cancer cells with invasive and migratory capabilities associated with distant metastasis. As a key upstream factor in the Hippo pathway, Kibra (wwc1 gene) has been shown to suppress EMT in breast cancer cells, and we have found that its expression is reduced or lost completely in both human breast cancer cell lines and clinical tissue samples, particularly in triple negative breast cancer (TNBC). Unfortunately, the molecular mechanisms underlying this progression-associated event remain to be elucidated...
August 16, 2018: Cellular Signalling
https://www.readbyqxmd.com/read/30121325/sequential-deletion-of-acmnpv-homologous-regions-leads-to-reductions-in-budded-virus-production-and-late-protein-expression
#8
Maike Bossert, Eric B Carstens
Homologous regions (hrs) have been predicted to act as origins of baculovirus DNA replication. Hrs have also been shown to function as enhancers of virus transcription. Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) carries eight hrs. In order to assess the role of hrs in virus replication in vivo, we applied a two-step RED recombination system for site-specific mutagenesis to sequentially delete each hr from a bacmid copy of AcMNPV. We then characterized the ability of the bacmids carrying different numbers of hrs or no hr to produce polyhedra and budded virus in transfected cells...
August 16, 2018: Virus Research
https://www.readbyqxmd.com/read/30121256/dna-methylation-and-the-yap-wwtr1-pathway-prevent-pathological-remodeling-during-bladder-obstruction-by-limiting-expression-of-bdnf
#9
Martin Sidler, Karen J Aitken, Jia-Xin Jiang, Chris Sotiropoulos, Prateek Aggarwal, Arsalan Anees, Cynthia Chong, Aliza Siebenaller, Thenuka Thanabalasingam, J Maxwell White, Sanaa Choufani, Rosanna Weksberg, Bruno Sangiorgi, Jeff Wrana, Paul Delgado-Olguin, Darius J Bägli
Chronic bladder obstruction and bladder smooth muscle cell (BSMC) stretch provide fibrotic and mechanical environments that can induce epigenetic change. Therefore, we examined the role of DNA methylation in bladder pathology and transcriptional control. Sprague-Dawley female rats underwent partial bladder obstruction by ligation of a silk suture around the proximal urethra next to a 0.9 mm steel rod. Sham operation comprised passing the suture around the urethra. After two weeks, rats were randomized to normal saline or DNA methyltransferase inhibitor, 5-aza-2-deoxycytidine (DAC) at 1 mg/kg, 3 times/week intraperitoneally...
August 16, 2018: American Journal of Pathology
https://www.readbyqxmd.com/read/30120951/feature-selection-using-logistic-regression-in-case-control-dna-methylation-data-of-parkinson-s-disease-a-comparative-study
#10
Aishwarya Kakade, Baby Kumari, Pankaj Singh Dholaniya
Parkinson's Disease (PD) is described as a progressive neurological disorder caused by the degeneration of dopaminergic neurons in substantia nigra pars compacta. The pathogenesis of the disease is not fully understood but it has been linked with complex genetic, epigenetic and environmental interactions. A substantial number of studies have shown the role of epigenetic modifications in support of the progression of PD. In the present study, we have analyzed the data containing methylation patterns of 1726 transcripts captured over from 66 samples of 450k, which includes 43 controls and 23 diseased samples...
August 15, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30120929/modulation-of-xenobiotic-nuclear-receptors-in-high-fat-diet-induced-non-alcoholic-fatty-liver-disease
#11
Xilin Li, Zemin Wang, James E Klaunig
Non-alcoholic fatty liver disease (NAFLD) is the most common chronic liver disease in the western countries. The histological spectrum of NAFLD includes simple steatosis, steatohepatitis, fibrosis, cirrhosis and even hepatocellular carcinoma. Nuclear receptors are a large group of ligand-dependent transcription factors that sense the environmental and endogenous changes and regulate numerous physiological and pathological processes. Accumulating evidence has suggested that a dysregulation of nuclear receptors in NAFLD may effect on the metabolism of endogenous and exogenous chemicals in the liver...
August 15, 2018: Toxicology
https://www.readbyqxmd.com/read/30120848/crispr-cas9-mediated-disruption-of-the-ie-0-and-ie-2-as-a-therapeutic-approach-to-bmnpv-in-transgenic-silkworm
#12
Zhanqi Dong, Zhigang Hu, Qi Qin, Feifan Dong, Liang Huang, Jiangqiong Long, Peng Chen, Cheng Lu, Minhui Pan
CRISPR/Cas9 system is a powerful tool for the treatment of infectious diseases. In our previous study, we knocked out the Bombyx mori nucleopolyhedrovirus (BmNPV) key genes and BmNPV-dependent host factor to generate transgenic antiviral strains. To further expand the range of target genes for BmNPV and more effectively prevent and control pathogenic infections, we performed gene editing and antiviral analysis by constructing a target-directed baculovirus early transcriptional activator immediate early-0 (ie-0) and ie-2 transgenic silkworm line...
August 18, 2018: Insect Molecular Biology
https://www.readbyqxmd.com/read/30120376/mir-22-suppresses-dna-ligase-iii-addiction-in-multiple-myeloma
#13
Daniele Caracciolo, Maria Teresa Di Martino, Nicola Amodio, Eugenio Morelli, Martina Montesano, Cirino Botta, Francesca Scionti, Daniela Talarico, Emanuela Altomare, Maria Eugenia Gallo Cantafio, Valeria Zuccalà, Lorenza Maltese, Katia Todoerti, Marco Rossi, Mariamena Arbitrio, Antonino Neri, Pierosandro Tagliaferri, Pierfrancesco Tassone
Multiple myeloma (MM) is a hematologic malignancy characterized by high genomic instability. Here we provide evidence that hyper-activation of DNA ligase III (LIG3) is crucial for genomic instability and survival of MM cells. LIG3 mRNA expression in MM patients correlates with shorter survival and even increases with more advanced stage of disease. Knockdown of LIG3 impairs MM cells viability in vitro and in vivo, suggesting that neoplastic plasmacells are dependent on LIG3-driven repair. To investigate the mechanisms involved in LIG3 expression, we investigated the post-transcriptional regulation...
August 17, 2018: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/30120223/epigenetic-dysregulation-of-naive-cd4-t-cell-activation-genes-in-childhood-food-allergy
#14
David Martino, Melanie Neeland, Thanh Dang, Joanna Cobb, Justine Ellis, Alice Barnett, Mimi Tang, Peter Vuillermin, Katrina Allen, Richard Saffery
Food allergy poses a significant clinical and public health burden affecting 2-10% of infants. Using integrated DNA methylation and transcriptomic profiling, we found that polyclonal activation of naive CD4+ T cells through the T cell receptor results in poorer lymphoproliferative responses in children with immunoglobulin E (IgE)-mediated food allergy. Reduced expression of cell cycle-related targets of the E2F and MYC transcription factor networks, and remodeling of DNA methylation at metabolic (RPTOR, PIK3D, MAPK1, FOXO1) and inflammatory genes (IL1R, IL18RAP, CD82) underpins this suboptimal response...
August 17, 2018: Nature Communications
https://www.readbyqxmd.com/read/30120107/ifn-%C3%AE-response-mediator-gbp-1-represses-human-cell-proliferation-by-inhibiting-the-hippo-signaling-transcription-factor-tead
#15
Bea Unterer, Veit Wiesmann, Mekala Gunasekaran, Heinrich Sticht, Clara Tenkerian, Jürgen Behrens, Maria Leone, Felix B Engel, Nathalie Britzen-Laurent, Elisabeth Naschberger, Thomas Wittenberg, Michael Stürzl
Interferon-gamma (IFN‑γ) is a pleiotropic cytokine that exerts important functions in inflammation, infectious diseases and cancer. The large GTPase human guanylate-binding protein 1 (GBP‑1) is among the most strongly IFN‑γ-induced cellular proteins. Previously it has been shown that GBP-1 mediates manifold cellular responses to IFN‑γ including the inhibition of proliferation, spreading, migration, and invasion and through this exerts anti-tumorigenic activity. However, the mechanisms of GBP-1 anti-tumorigenic activities remain poorly understood...
August 17, 2018: Biochemical Journal
https://www.readbyqxmd.com/read/30119690/functional-crispr-screen-identifies-ap1-associated-enhancer-regulating-foxf1-to-modulate-oncogene-induced-senescence
#16
Ruiqi Han, Li Li, Alejandro Piñeiro Ugalde, Arieh Tal, Zohar Manber, Eric Pinto Barbera, Veronica Della Chiara, Ran Elkon, Reuven Agami
BACKGROUND: Functional characterization of non-coding elements in the human genome is a major genomic challenge and the maturation of genome-editing technologies is revolutionizing our ability to achieve this task. Oncogene-induced senescence, a cellular state of irreversible proliferation arrest that is enforced following excessive oncogenic activity, is a major barrier against cancer transformation; therefore, bypassing oncogene-induced senescence is a critical step in tumorigenesis...
August 17, 2018: Genome Biology
https://www.readbyqxmd.com/read/30119050/inhibitor-of-dna-binding-2-inhibits-epithelial-mesenchymal-transition-via-up-regulation-of-notch3-in-breast-cancer
#17
Xiao-Fen Wen, Min Chen, Yang Wu, Min-Na Chen, Aleksandra Glogowska, Thomas Klonisch, Guo-Jun Zhang
Breast cancer is the second leading cause of cancer death in women worldwide. Incurable metastatic breast disease presents a major clinical challenge and is the main cause of breast cancer-related death. The epithelial-mesenchymal transition (EMT) is a critical early promoter of metastasis. In the present study, we identified a novel role for the inhibitor of DNA binding 2 (Id2), a member of the basic helix-loop-helix protein family, during the EMT of breast cancer. Expression of Id2 was positively correlated with Notch3 in breast cancer cells...
August 14, 2018: Translational Oncology
https://www.readbyqxmd.com/read/30118947/identification-and-expression-of-transcription-factor-sox2-in-large-yellow-croaker-larimichthys-crocea
#18
Yong-Hua Jiang, Kun-Huang Han, Shu-Hong Wang, Yun Chen, Yi-Lei Wang, Zi-Ping Zhang
As an important transcription and pluripotency factor, Sox2 plays its functions essentially in the regulation of self-renewal and pluripotency of embryonic and neural stem cells, as well as embryogenesis, organogenesis, neurogenesis and regeneration. The data is lacking on Sox2 in large yellow croaker (Larimichthys crocea) (Lc-Sox2) which is a limitation on the generation of induced pluripotent stem cells (iPSCs). In this study, Lc-sox2 was cloned by RACE (rapid amplification of cDNA ends) and analyzed by Bioinformatics...
July 26, 2018: Theriogenology
https://www.readbyqxmd.com/read/30118861/expression-purification-and-molecular-characterization-of-a-novel-transcription-factor-kccbf3-from-kandelia-candel
#19
Zhaokui Du, Junmin Li
Kandelia candel, a major species of mangrove in the tropical and subtropical area, is susceptible to low temperature in winter. K. candel was introduced into Zhejiang Province (the northern margin of South China) several decades ago, and suffered from low temperature causing growth retardation, in server cases, even death. To explore the molecular mechanisms of cold acclimation in K. candel, a novel C-repeat binding factor gene KcCBF3 (Genbank accession no. KF111715) of 729 bp open reading frame (ORF) encoding a protein of 242 amino acid residues was isolated, expressed, purified and characterized...
August 14, 2018: Protein Expression and Purification
https://www.readbyqxmd.com/read/30118678/dismissal-of-rna-polymerase-ii-underlies-a-large-ligand-induced-enhancer-decommissioning-program
#20
Yuliang Tan, Chunyu Jin, Wubin Ma, Yiren Hu, Bogdan Tanasa, Soohwan Oh, Amir Gamliel, Qi Ma, Lu Yao, Jie Zhang, Kenny Ohgi, Wen Liu, Aneel K Aggarwal, Michael G Rosenfeld
Nuclear receptors induce both transcriptional activation and repression programs responsible for development, homeostasis, and disease. Here, we report a previously overlooked enhancer decommissioning strategy underlying a large estrogen receptor alpha (ERα)-dependent transcriptional repression program. The unexpected signature for this E2 -induced program resides in indirect recruitment of ERα to a large cohort of pioneer factor basally active FOXA1-bound enhancers that lack cognate ERα DNA-binding elements...
August 16, 2018: Molecular Cell
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