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https://www.readbyqxmd.com/read/28527333/transcriptome-wide-analysis-of-jasmonate-treated-by-2-cells-reveals-new-transcriptional-regulators-associated-with-alkaloid-formation-in-tobacco
#1
Yuping Yang, Pengcheng Yan, Che Yi, Wenzheng Li, Yuhui Chai, Lingling Fei, Ping Gao, Heping Zhao, Yingdian Wang, Michael P Timko, Bingwu Wang, Shengcheng Han
Jasmonates (JAs) are well-known regulators of stress, defence, and secondary metabolism in plants, with JA perception triggering extensive transcriptional reprogramming, including both activation and/or repression of entire metabolic pathways. We performed RNA sequencing based transcriptomic profiling of tobacco BY-2 cells before and after treatment with methyl jasmonate (MeJA) to identify novel transcriptional regulators associated with alkaloid formation. A total of 107,140 unigenes were obtained through de novo assembly, and at least 33,213 transcripts (31%) encode proteins, in which 3419 transcription factors (TFs) were identified, representing 72 gene families, as well as 840 transcriptional regulators (TRs) distributed among 19 gene families...
May 4, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28526543/thyroid-hormone-biosynthesis-machinery-is-altered-in-the-ischemic-myocardium-an-epigenomic-study
#2
Carolina Gil-Cayuela, Esther Roselló-LLetí, Estefanía Tarazón, Ana Ortega, Juan Sandoval, Luis Martínez-Dolz, Juan Cinca, Esther Jorge, José Ramón González-Juanatey, Francisca Lago, Miguel Rivera, Manuel Portolés
BACKGROUND: Abnormal thyroid hormone (TH) metabolism is significantly associated with impaired left ventricular (LV) function and death. Although TH was traditionally thought to be produced exclusively by the thyroid gland, an increasing number of studies report TH production in other tissues. Based on these findings, we evaluated whether the genes required for TH biosynthesis are expressed in the human heart, and whether their expression is altered in patients with ischemic cardiomyopathy (ICM) and is related to epigenetic variations...
May 11, 2017: International Journal of Cardiology
https://www.readbyqxmd.com/read/28526340/unfolding-the-pathogenesis-of-scleroderma-through-genomics-and-epigenomics
#3
REVIEW
Pei-Suen Tsou, Amr H Sawalha
With unknown etiology, scleroderma (SSc) is a multifaceted disease characterized by immune activation, vascular complications, and excessive fibrosis in internal organs. Genetic studies, including candidate gene association studies, genome-wide association studies, and whole-exome sequencing have supported the notion that while genetic susceptibility to SSc appears to be modest, SSc patients are genetically predisposed to this disease. The strongest genetic association for SSc lies within the MHC region, with loci in HLA-DRB1, HLA-DQB1, HLA-DPB1, and HLA-DOA1 being the most replicated...
May 16, 2017: Journal of Autoimmunity
https://www.readbyqxmd.com/read/28525753/the-u6-snrna-m-6-a-methyltransferase-mettl16-regulates-sam-synthetase-intron-retention
#4
Kathryn E Pendleton, Beibei Chen, Kuanqing Liu, Olga V Hunter, Yang Xie, Benjamin P Tu, Nicholas K Conrad
Maintenance of proper levels of the methyl donor S-adenosylmethionine (SAM) is critical for a wide variety of biological processes. We demonstrate that the N(6)-adenosine methyltransferase METTL16 regulates expression of human MAT2A, which encodes the SAM synthetase expressed in most cells. Upon SAM depletion by methionine starvation, cells induce MAT2A expression by enhanced splicing of a retained intron. Induction requires METTL16 and its methylation substrate, a vertebrate conserved hairpin (hp1) in the MAT2A 3' UTR...
May 18, 2017: Cell
https://www.readbyqxmd.com/read/28523964/epigenetics-in-endometrial-carcinogenesis-part-2-histone-modifications-chromatin-remodeling-and-noncoding-rnas
#5
Carla Bartosch, José Manuel Lopes, Carmen Jerónimo
Carcinogenesis is a multistep multifactorial process that involves the accumulation of genetic and epigenetic alterations. In the past two decades, there has been an exponential growth of knowledge establishing the importance of epigenetic changes in cancer. Our work focused on reviewing the main role of epigenetics in the pathogenesis of endometrial carcinoma, highlighting the reported results concerning each epigenetic mechanistic layer. In a previous review, we assessed DNA methylation alterations. The present review examines the contribution of histone modifications, chromatin remodeling and noncoding RNA alterations for endometrial carcinogenesis...
May 19, 2017: Epigenomics
https://www.readbyqxmd.com/read/28523539/the-role-of-noncoding-rnas-in-neurodevelopmental-disorders-the-case-of-rett-syndrome
#6
Aida Obiols-Guardia, Sònia Guil
Current technologies have demonstrated that only a small fraction of our genes encode for protein products. The vast majority of the human transcriptome corresponds to noncoding RNA (ncRNA) of different size, localization, and expression profile. Despite the fact that a biological function remains yet to be determined for most ncRNAs, growing evidence points to their crucial regulatory roles at all stages in gene expression regulation, including transcriptional and posttranscriptional control, so that proper cell homeostasis seems to depend largely on a variety of ncRNA-mediated regulatory networks...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28523538/mecp2-a-modulator-of-neuronal-chromatin-organization-involved-in-rett-syndrome
#7
Alexia Martínez de Paz, Juan Ausió
From an epigenetic perspective, the genomic chromatin organization of neurons exhibits unique features when compared to somatic cells. Methyl CpG binding protein 2 (MeCP2), through its ability to bind to methylated DNA, seems to be a major player in regulating such unusual organization. An important contribution to this uniqueness stems from the intrinsically disordered nature of this highly abundant chromosomal protein in neurons. Upon its binding to methylated/hydroxymethylated DNA, MeCP2 is able to recruit a plethora of interacting protein and RNA partners...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28522286/increased-proportions-of-functionally-impaired-regulatory-t-cell-subsets-in-systemic-sclerosis
#8
Emese Ugor, Diána Simon, Giovanni Almanzar, Ramóna Pap, József Najbauer, Péter Németh, Péter Balogh, Martina Prelog, László Czirják, Tímea Berki
Treg abnormalities have been implicated in the pathogenesis of systemic sclerosis (SSc). Treg subpopulations and their cytokines, IL-10 and TGF-β in the peripheral blood of early stage SSc patients were investigated. We hypothesized that epigenetically regulated methylation of the FOXP3 promoter and enhancer regions are altered in Tregs of SSc patients, which might be involved in the T cell imbalance. CD4+CD25+Foxp3+CD127- Treg cells were significantly elevated in patients with diffuse cutaneous SSc and in patients with anti-Scl-70/RNA-Pol-III autoantibody positivity and with lung fibrosis...
May 15, 2017: Clinical Immunology: the Official Journal of the Clinical Immunology Society
https://www.readbyqxmd.com/read/28521734/higher-order-organisation-of-extremely-amplified-potentially-functional-and-massively-methylated-5s-rdna-in-european-pikes-esox-sp
#9
Radka Symonová, Konrad Ocalewicz, Lech Kirtiklis, Giovanni Battista Delmastro, Šárka Pelikánová, Sonia Garcia, Aleš Kovařík
BACKGROUND: Pikes represent an important genus (Esox) harbouring a pre-duplication karyotype (2n = 2x = 50) of economically important salmonid pseudopolyploids. Here, we have characterized the 5S ribosomal RNA genes (rDNA) in Esox lucius and its closely related E. cisalpinus using cytogenetic, molecular and genomic approaches. Intragenomic homogeneity and copy number estimation was carried out using Illumina reads. The higher-order structure of rDNA arrays was investigated by the analysis of long PacBio reads...
May 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28521327/epigenomics-pharmacoepigenomics-and-personalized-medicine-in-cervical-cancer
#10
Shama Prasada Kabekkodu, Sanjiban Chakrabarty, Supriti Ghosh, Angela Brand, Kapaettu Satyamoorthy
Epigenomics encompasses the study of genome-wide changes in DNA methylation, histone modifications and noncoding RNAs leading to altered transcription, chromatin structure, and posttranscription RNA processing, respectively, resulting in an altered rate of gene expression. The role of epigenetic modifications facilitating human diseases is well established. Previous studies have identified histone and cytosine code during normal and pathological conditions with special emphasis on how these modifications regulate transcriptional events...
May 19, 2017: Public Health Genomics
https://www.readbyqxmd.com/read/28515681/the-activity-induced-long-non-coding-rna-meg3-modulates-ampa-receptor-surface-expression-in-primary-cortical-neurons
#11
Men C Tan, Jocelyn Widagdo, Yu Q Chau, Tianyi Zhu, Justin J-L Wong, Allen Cheung, Victor Anggono
Transcription of new RNA is crucial for maintaining synaptic plasticity, learning and memory. Although the importance of synaptic plasticity-related messenger RNAs (mRNAs) is well established, the role of a large group of long non-coding RNAs (lncRNAs) in long-term potentiation (LTP) is not known. In this study, we demonstrated the expression of a lncRNA cluster, namely maternally expressed gene 3 (Meg3), retrotransposon-like gene 1-anti-sense (Rtl1-AS), Meg8 and Meg9, which is located in the maternally imprinted Dlk1-Dio3 region on mouse chromosome 12qF1, in primary cortical neurons following glycine stimulation in an N-Methyl-D-aspartate receptor (NMDAR)-dependent manner...
2017: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/28510691/nf-%C3%AE%C2%BAb-upregulation-through-epigenetic-silencing-of-ldoc1-drives-tumor-biology-and-specific-immunophenotype-in-group-a-ependymoma
#12
Andrea M Griesinger, Davis A Witt, Sydney T Grob, Sabrina R Georgio Westover, Andrew M Donson, Bridget Sanford, Jean M Mulcahy Levy, Randall Wong, Daniel C Moreira, John A DeSisto, Ilango Balakrishnan, Lindsey M Hoffman, Michael H Handler, Kenneth L Jones, Rajeev Vibhakar, Sujatha Venkataraman, Nicholas K Foreman
Background.: Inflammation has been identified as a hallmark of high-risk Group A (GpA) ependymoma (EPN). Chronic interleukin (IL)-6 secretion from GpA tumors drives an immune suppressive phenotype by polarizing infiltrating monocytes. This study determines the mechanism by which IL-6 is dysregulated in GpA EPN. Methods.: Twenty pediatric GpA and 21 pediatric Group B (GpB) EPN had gene set enrichment analysis for MSigDB Hallmark gene sets performed. Protein and RNA from patients and cell lines were used to validate transcriptomic findings...
May 16, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/28507114/antiviral-activity-of-nordihydroguaiaretic-acid-and-its-derivative-tetra-o-methyl-nordihydroguaiaretic-acid-against-west-nile-virus-and-zika-virus
#13
Teresa Merino-Ramos, Nereida Jiménez de Oya, Juan-Carlos Saiz, Miguel A Martín-Acebes
Flaviviruses are positive strand RNA viruses distributed all over the world that infect millions of people every year, and for which no specific antiviral agents have been approved. These viruses include the mosquito-borne West Nile virus (WNV) responsible for outbreaks of meningitis and encephalitis. Considering that nordihydroguaiaretic acid (NDGA) has been previously shown to inhibit the multiplication of the related dengue virus and hepatitis C virus, we have evaluated the effect of NDGA, and its methylated derivative tetra-O-methyl nordihydroguaiaretic (M4N), on the infection of WNV...
May 15, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28506242/an-imprinted-non-coding-genomic-cluster-at-14q32-defines-clinically-relevant-molecular-subtypes-in-osteosarcoma-across-multiple-independent-datasets
#14
Katherine E Hill, Andrew D Kelly, Marieke L Kuijjer, William Barry, Ahmed Rattani, Cassandra C Garbutt, Haydn Kissick, Katherine Janeway, Antonio Perez-Atayde, Jeffrey Goldsmith, Mark C Gebhardt, Mohamed S Arredouani, Greg Cote, Francis Hornicek, Edwin Choy, Zhenfeng Duan, John Quackenbush, Benjamin Haibe-Kains, Dimitrios Spentzos
BACKGROUND: A microRNA (miRNA) collection on the imprinted 14q32 MEG3 region has been associated with outcome in osteosarcoma. We assessed the clinical utility of this miRNA set and their association with methylation status. METHODS: We integrated coding and non-coding RNA data from three independent annotated clinical osteosarcoma cohorts (n = 65, n = 27, and n = 25) and miRNA and methylation data from one in vitro (19 cell lines) and one clinical (NCI Therapeutically Applicable Research to Generate Effective Treatments (TARGET) osteosarcoma dataset, n = 80) dataset...
May 15, 2017: Journal of Hematology & Oncology
https://www.readbyqxmd.com/read/28504695/epigenetic-pathway-inhibitors-represent-potential-drugs-for-treating-pancreatic-and-bronchial-neuroendocrine-tumors
#15
K E Lines, M Stevenson, P Filippakopoulos, S Müller, H E Lockstone, B Wright, S Grozinsky-Glasberg, A B Grossman, S Knapp, D Buck, C Bountra, R V Thakker
Cancer is associated with alterations in epigenetic mechanisms such as histone modifications and methylation of DNA, and inhibitors targeting epigenetic mechanisms represent a novel class of anti-cancer drugs. Neuroendocrine tumors (NETs) of the pancreas (PNETs) and bronchus (BNETs), which may have 5-year survivals of <50% and as low as 5%, respectively, represent targets for such drugs, as >40% of PNETs and ~35% of BNETs have mutations of the multiple endocrine neoplasia type 1 (MEN1) gene, which encodes menin that modifies histones by interacting with histone methyltransferases...
May 15, 2017: Oncogenesis
https://www.readbyqxmd.com/read/28504680/nm-seq-maps-2-o-methylation-sites-in-human-mrna-with-base-precision
#16
Qing Dai, Sharon Moshitch-Moshkovitz, Dali Han, Nitzan Kol, Ninette Amariglio, Gideon Rechavi, Dan Dominissini, Chuan He
The ribose of RNA nucleotides can be 2'-O-methylated (Nm). Despite advances in high-throughput detection, the inert chemical nature of Nm still limits sensitivity and precludes mapping in mRNA. We leveraged the differential reactivity of 2'-O-methylated and 2'-hydroxylated nucleosides to periodate oxidation to develop Nm-seq, a sensitive method for transcriptome-wide mapping of Nm with base precision. Nm-seq uncovered thousands of Nm sites in human mRNA with features suggesting functional roles.
May 15, 2017: Nature Methods
https://www.readbyqxmd.com/read/28503769/identification-of-factors-required-for-m-6-a-mrna-methylation-in-arabidopsis-reveals-a-role-for-the-conserved-e3-ubiquitin-ligase-hakai
#17
Kamil Růžička, Mi Zhang, Ana Campilho, Zsuzsanna Bodi, Muhammad Kashif, Mária Saleh, Dominique Eeckhout, Sedeer El-Showk, Hongying Li, Silin Zhong, Geert De Jaeger, Nigel P Mongan, Jan Hejátko, Ykä Helariutta, Rupert G Fray
N6-adenosine methylation (m(6) A) of mRNA is an essential process in most eukaryotes, but its role and the status of factors accompanying this modification are still poorly understood. Using combined methods of genetics, proteomics and RNA biochemistry, we identified a core set of mRNA m(6) A writer proteins in Arabidopsis thaliana. The components required for m(6) A in Arabidopsis included MTA, MTB, FIP37, VIRILIZER and the E3 ubiquitin ligase HAKAI. Downregulation of these proteins led to reduced relative m(6) A levels and shared pleiotropic phenotypes, which included aberrant vascular formation in the root, indicating that correct m(6) A methylation plays a role in developmental decisions during pattern formation...
May 15, 2017: New Phytologist
https://www.readbyqxmd.com/read/28502757/the-placental-imprinted-dlk1-dio3-domain-a-new-link-to-pre-and-postnatal-growth-in-humans
#18
Anna Prats-Puig, Gemma Carreras-Badosa, Judit Bassols, Patricia Cavelier, Agnés Magret, Cristina Sabench, Francis de Zegher, Lourdes Ibáñez, Robert Feil, Abel López-Bermejo
BACKGROUND: The developmentally important DLK1-DIO3 imprinted domain on human chromosome 14 is regulated by two differentially methylated regions(DMRs), the IG-DMR and the MEG3 DMR. OBJECTIVES: The aim was to determine the natural variation in DNA methylation at these DMRs in human placentas, and to determine its link to gene expression levels at the domain. Second, to explore whether the domain's methylation and gene expression correlate with pre- and early-postnatal growth of the conceptus...
May 11, 2017: American Journal of Obstetrics and Gynecology
https://www.readbyqxmd.com/read/28501774/tuning-of-major-signaling-networks-tgf-%C3%AE-wnt-notch-and-hedgehog-by-mirnas-in-human-stem-cells-commitment-to-different-lineages-possible-clinical-application
#19
REVIEW
Sedigheh Fekri Aval, Hajie Lotfi, Roghayeh Sheervalilou, Nosratollah Zarghami
Two distinguishing characteristics of stem cells, their continuous division in the undifferentiated state and growth into any cell types, are orchestrated by a number of cell signaling pathways. These pathways act as a niche factor in controlling variety of stem cells. The core stem cell signaling pathways include Wingless-type (Wnt), Hedgehog (HH), and Notch. Additionally, they critically regulate the self-renewal and survival of cancer stem cells. Conversely, stem cells' main properties, lineage commitment and stemness, are tightly controlled by epigenetic mechanisms such as DNA methylation, histone modifications and non-coding RNA-mediated regulatory events...
May 11, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28501566/dna-methylation-regulated-gene-expression-in-organ-fibrosis
#20
REVIEW
Xiangyu Zhang, Min Hu, Xing Lyu, Chun Li, Victor J Thannickal, Yan Y Sanders
DNA methylation is a major epigenetic mechanism to regulate gene expression. Epigenetic regulation, including DNA methylation, histone modifications and RNA interference, results in heritable changes in gene expression independent of alterations in DNA sequence. Epigenetic regulation often occurs in response to aging and environment stimuli, including exposures and diet. Studies have shown that DNA methylation is critical in the pathogenesis of fibrosis involving multiple organs sytems, contributing to significant morbidity and mortality...
May 10, 2017: Biochimica et Biophysica Acta
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