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De novo DNA Methylation

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https://www.readbyqxmd.com/read/28431570/a-relative-quantitative-methylation-sensitive-amplified-polymorphism-msap-method-for-the-analysis-of-abiotic-stress
#1
Piotr T Bednarek, Renata Orłowska, Agnieszka Niedziela
BACKGROUND: We present a new methylation-sensitive amplified polymorphism (MSAP) approach for the evaluation of relative quantitative characteristics such as demethylation, de novo methylation, and preservation of methylation status of CCGG sequences, which are recognized by the isoschizomers HpaII and MspI. We applied the technique to analyze aluminum (Al)-tolerant and non-tolerant control and Al-stressed inbred triticale lines. The approach is based on detailed analysis of events affecting HpaII and MspI restriction sites in control and stressed samples, and takes advantage of molecular marker profiles generated by EcoRI/HpaII and EcoRI/MspI MSAP platforms...
April 21, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28427232/embryonic-signature-distinguishes-pediatric-and-adult-rhabdoid-tumors-from-other-smarcb1-deficient-cancers
#2
Wilfrid Richer, Julien Masliah-Planchon, Nathalie Clement, Irene Jimenez, Laetitia Maillot, David Gentien, Benoît Albaud, Walid Chemlali, Christine Galant, Frederique Larousserie, Pascaline Boudou-Rouquette, Amaury Leruste, Celine Chauvin, Zhi Yan Han, Jean-Michel Coindre, Pascale Varlet, Paul Freneaux, Dominique Ranchère-Vince, Olivier Delattre, Franck Bourdeaut
Extra-cranial rhabdoid tumors (RT) are highly aggressive malignancies of infancy, characterized by undifferentiated histological features and loss of SMARCB1 expression. The diagnosis is all the more challenging that other poorly differentiated cancers lose SMARCB1 expression, such as epithelioid sarcomas (ES), renal medullary carcinomas (RMC) or undifferentiated chordomas (UC). Moreover, late cases occurring in adults are now increasingly reported, raising the question of differential diagnoses and emphasizing nosological issues...
March 6, 2017: Oncotarget
https://www.readbyqxmd.com/read/28424740/essential-role-of-long-non-coding-rnas-in-de-novo-chromatin-modifications-the-genomic-address-code-hypothesis
#3
Ken Nishikawa, Akira R Kinjo
The epigenome, i.e., the whole of chromatin modifications, is transferred from mother to daughter cells during cell differentiation. When de novo chromatin modifications (establishment or erasure of, respectively, new or pre-existing DNA methylations and/or histone modifications) are made in a daughter cell, however, it has a different epigenome than its mother cell. Although de novo chromatin modification is an important event that comprises elementary processes of cell differentiation, its molecular mechanism remains poorly understood...
April 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/28418084/epstein-barr-virus-infection-induces-genome-wide-de-novo-dna-methylation-in-non-neoplastic-gastric-epithelial-cells
#4
Keisuke Matsusaka, Sayaka Funata, Masaki Fukuyo, Yasuyuki Seto, Hiroyuki Aburatani, Masashi Fukayama, Atsushi Kaneda
Epstein-Barr virus (EBV)-positive gastric cancer (GC) shows a higher DNA methylation epigenotype. EBV infection can causally induce genome-wide aberrant DNA methylation, as previously demonstrated by in vitro infection experiments in the low-methylation GC cell line MKN7. However, whether EBV exerts DNA methylation remodelling properties in non-neoplastic epithelial cells remains unclear. We here performed post-infection time-series DNA methylation analyses using the immortalised normal gastric epithelial cell line, GES1...
April 18, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/28392842/dna-methylation-signatures-for-2016-who-classification-subtypes-of-diffuse-gliomas
#5
Yashna Paul, Baisakhi Mondal, Vikas Patil, Kumaravel Somasundaram
BACKGROUND: Glioma is the most common of all primary brain tumors with poor prognosis and high mortality. The 2016 World Health Organization classification of the tumors of central nervous system uses molecular parameters in addition to histology to redefine many tumor entities. The new classification scheme divides diffuse gliomas into low-grade glioma (LGG) and glioblastoma (GBM) as per histology. LGGs are further divided into isocitrate dehydrogenase (IDH) wild type or mutant, which is further classified into either oligodendroglioma that harbors 1p/19q codeletion or diffuse astrocytoma that has an intact 1p/19q loci but enriched for ATRX loss and TP53 mutation...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28367907/high-resolution-profiles-of-gene-expression-and-dna-methylation-highlight-mitochondrial-modifications-during-early-embryonic-development
#6
Likun Ren, Chao Zhang, Li Tao, Jing Hao, Kun Tan, Kai Miao, Yong Yu, Linlin Sui, Zhonghong Wu, Jianhui Tian, Lei An
Well-organized mitochondrial functions and dynamics are critical for early embryonic development and are operated via a large number of mitochondria-related genes (MtGs) encoded by both the nuclear and the mitochondrial genome. However, the mechanisms underlying mitochondrial modifications during the critical window between blastocyst implantation and postimplantation organogenesis are poorly understood. Herein, we performed high-resolution dynamic profiling of MtGs to acquire a more detailed understanding of mitochondrial modifications during early development...
March 31, 2017: Journal of Reproduction and Development
https://www.readbyqxmd.com/read/28286768/epigenetic-guardian-a-review-of-the-dna-methyltransferase-dnmt3a-in-acute-myeloid-leukaemia-and-clonal-haematopoiesis
#7
REVIEW
Sabah F Chaudry, Timothy J T Chevassut
Acute myeloid leukaemia (AML) is a haematological malignancy characterized by clonal stem cell proliferation and aberrant block in differentiation. Dysfunction of epigenetic modifiers contributes significantly to the pathogenesis of AML. One frequently mutated gene involved in epigenetic modification is DNMT3A (DNA methyltransferase-3-alpha), a DNA methyltransferase that alters gene expression by de novo methylation of cytosine bases at CpG dinucleotides. Approximately 22% of AML and 36% of cytogenetically normal AML cases carry DNMT3A mutations and around 60% of these mutations affect the R882 codon...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28267064/nerve-injury-induced-epigenetic-silencing-of-opioid-receptors-controlled-by-dnmt3a-in-primary-afferent-neurons
#8
Linlin Sun, Jian-Yuan Zhao, Xiyao Gu, Lingli Liang, Shaogen Wu, Kai Mo, Jian Feng, Weixiang Guo, Jun Zhang, Alex Bekker, Xinyu Zhao, Eric J Nestler, Yuan-Xiang Tao
Opioids are the gold standard for pharmacological treatment of neuropathic pain, but their analgesic effects are unsatisfactory in part due to nerve injury-induced downregulation of opioid receptors in dorsal root ganglia (DRG) neurons. How nerve injury drives such downregulation remains elusive. DNA methyltransferase (DNMT)-triggered DNA methylation represses gene expression. We show here that blocking the nerve injury-induced increase in DRG DNMT3a (a de novo DNMT) rescued the expression of Oprm1 and Oprk1 mRNAs and their respective encoding mu-opioid receptor (MOR) and kappa-opioid receptor (KOR) proteins in the injured DRG...
March 4, 2017: Pain
https://www.readbyqxmd.com/read/28256047/maternal-mutations-of-foxf1-cause-alveolar-capillary-dysplasia-despite-not-being-imprinted
#9
Miguel Alsina Casanova, Ana Monteagudo-Sánchez, Luciana Rodiguez Guerineau, Franck Court, Isabel Gazquez Serrano, Loreto Martorell, Carlota Rovira Zurriaga, Gudrun E Moore, Miho Ishida, Montserrat Castañon, Elisenda Moliner Calderon, David Monk, Julio Moreno Hernando
Alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV) is a rare cause of pulmonary hypertension in newborns. Maternally inherited point mutations in Forkhead Box F1 gene (FOXF1), deletions of the gene, or its long-range enhancers on the maternal allele are responsible for this neonatal lethal disorder. Here, we describe monozygotic twins and one full-term newborn with ACD and gastrointestinal malformations caused by de novo mutations of FOXF1 on the maternal-inherited alleles. Since this parental transmission is consistent with genomic imprinting, the parent-of-origin specific monoallelic expression of genes, we have undertaken a detailed analysis of both allelic expression and DNA methylation...
March 3, 2017: Human Mutation
https://www.readbyqxmd.com/read/28238081/dna-methyltransferases-contribute-to-the-fungal-development-stress-tolerance-and-virulence-of-the-entomopathogenic-fungus-metarhizium-robertsii
#10
Yulong Wang, Tiantian Wang, Lintao Qiao, Jianyu Zhu, Jinrui Fan, Tingting Zhang, Zhang-Xun Wang, Wanzhen Li, Anhui Chen, Bo Huang
DNA methylation is an important epigenetic mark in mammals, plants, and fungi and depends on multiple genetic pathways involving de novo and maintenance DNA methyltransferases (DNMTases). Metarhizium robertsii, a model system for investigating insect-fungus interactions, has been used as an environmentally friendly alternative to chemical insecticides. However, little is known concerning the molecular basis for DNA methylation. Here, we report on the roles of two DNMTases (MrRID and MrDIM-2) by characterizing ΔMrRID, ΔMrDIM-2, and ΔRID/ΔDIM-2 mutants...
February 25, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28225069/testicular-dnmt3-expression-and-global-dna-methylation-are-down-regulated-by-gonadotropin-releasing-hormones-in-the-ricefield-eel-monopterus-albus
#11
Yize Zhang, Xin Sun, Lihong Zhang, Weimin Zhang
In vertebrates, DNA methyltransferase 3 (Dnmt3) homologues are responsible for de novo DNA methylation and play important roles in germ cell development. In the present study, four dnmt3 genes, dnmt3aa, dnmt3ab, dnmt3ba and dnmt3bb.1, were identified in ricefield eels. Real-time quantitative PCR analysis showed that all four dnmt3 mRNAs were detected broadly in tissues examined, with testicular expression at relatively high levels. In the testis, immunostaining for all four Dnmt3 forms was mainly localized to spermatocytes, which also contained highly methylated DNA...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28223440/idn2-interacts-with-rpa-and-facilitates-dna-double-strand-break-repair-by-homologous-recombination-in-arabidopsis
#12
Mingming Liu, Zhaoqing Ba, Pedro Costa-Nunes, Wei Wei, Lanxia Li, Fansi Kong, Yan Li, Jijie Chai, Olga Pontes, Yijun Qi
Repair of DNA double-strand breaks (DSBs) is critical for the maintenance of genome integrity. We previously showed that DSB-induced small RNAs (diRNAs) facilitate homologous recombination-mediated DSB repair in Arabidopsis thaliana Here, we show that INVOLVED IN DE NOVO2 (IDN2), a double-stranded RNA binding protein involved in small RNA-directed DNA methylation, is required for DSB repair in Arabidopsis. We find that IDN2 interacts with the heterotrimeric replication protein A (RPA) complex. Depletion of IDN2 or the diRNA binding ARGONAUTE2 leads to increased accumulation of RPA at DSB sites and mislocalization of the recombination factor RAD51...
March 2017: Plant Cell
https://www.readbyqxmd.com/read/28207953/sgs1-a-neomorphic-nac52-allele-impairing-post-transcriptional-gene-silencing-through-sgs3-downregulation
#13
Nicolas Butel, Ivan Le Masson, Nathalie Bouteiller, Hervé Vaucheret, Taline Elmayan
Post-transcriptional gene silencing (PTGS) is a defense mechanism that targets invading nucleic acids from endogenous (transposons) or exogenous (pathogens, transgenes) sources. Genetic screens based on the reactivation of silenced transgenes have long been used to identify cellular components and regulators of PTGS. Here we show that the first isolated PTGS-deficient mutant, sgs1, is impaired in the transcription factor NAC52. This mutant exhibits striking similarities to a mutant impaired in the H3K4me3 demethylase JMJ14 isolated from the same genetic screen...
May 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28198363/gut-memories-do-not-fade-epigenetic-regulation-of-lasting-gut-homing-receptor-expression-in-cd4-memory-t-cells
#14
B A Szilagyi, J Triebus, C Kressler, M de Almeida, S Tierling, P Durek, M Mardahl, A Szilagyi, S Floess, J Huehn, U Syrbe, J Walter, J K Polansky, A Hamann
The concept of a "topographical memory" in lymphocytes implies a stable expression of homing receptors mediating trafficking of lymphocytes back to the tissue of initial activation. However, a significant plasticity of the gut-homing receptor α4β7 was found in CD8(+) T cells, questioning the concept. We now demonstrate that α4β7 expression in murine CD4(+) memory T cells is, in contrast, imprinted and remains stable in the absence of the inducing factor retinoic acid (RA) or other stimuli from mucosal environments...
February 15, 2017: Mucosal Immunology
https://www.readbyqxmd.com/read/28193737/exogenous-transposable-elements-circumvent-identity-based-silencing-permitting-the-dissection-of-expression-dependent-silencing
#15
Dalen Fultz, R Keith Slotkin
The propagation of epigenetic marks has received a great deal of attention, yet the initiation of epigenetic silencing of a new transgene, virus, or transposable element (TE) remains enigmatic. The overlapping and simultaneous function of multiple silencing mechanisms has obscured this area of investigation. Here, we revealed two broad mechanisms that can initiate silencing independently: identity-based and expression-dependent silencing. We found that identity-based silencing is targeted by 21- to 22-nucleotide or 24-nucleotide small interfering RNAs (siRNAs) generated from previously silenced regions of the genome...
February 2017: Plant Cell
https://www.readbyqxmd.com/read/28182669/a-de-novo-loss-of-function-grin2a-mutation-associated-with-childhood-focal-epilepsy-and-acquired-epileptic-aphasia
#16
Kai Gao, Anel Tankovic, Yujia Zhang, Hirofumi Kusumoto, Jin Zhang, Wenjuan Chen, Wenshu XiangWei, Gil H Shaulsky, Chun Hu, Stephen F Traynelis, Hongjie Yuan, Yuwu Jiang
OBJECTIVE: N-methyl-D-aspartate receptors (NMDAR) subunit GRIN2A/GluN2A mutations have been identified in patients with various neurological diseases, such as epilepsy and intellectual disability / developmental delay (ID/DD). In this study, we investigated the phenotype and underlying molecular mechanism of a GRIN2A missense mutation identified by next generation sequencing on idiopathic focal epilepsy using in vitro electrophysiology. METHODS: Genomic DNA of patients with epilepsy and ID/DD were sequenced by targeted next-generation sequencing within 300 genes related to epilepsy and ID/DD...
2017: PloS One
https://www.readbyqxmd.com/read/28153750/rdm16-and-sta1-regulate-differential-usage-of-exon-intron-in-rna-directed-dna-methylation-pathway
#17
Ravi Datta Sharma, Bert Bogaerts, Neha Goyal
The splicing factors RDM16 and STA1 have been reported to play a role in the RNA directed DNA Methylation (RdDM) pathway. In this pathway, small interfering RNAs guide de-novo methylation of homologous DNA sequences. DNA methylation is epigenetic marks, which can suppress transposable elements, repeat sequences and genes. It also affects the chromatin structure. Upon deletion of RDM16 and STA1, previous studies based on gene level analysis were unable to find differentially spliced events implicated in RdDM pathway...
April 20, 2017: Gene
https://www.readbyqxmd.com/read/28123849/dnmt3b-modulates-the-expression-of-cancer-related-genes-and-downregulates-the-expression-of-the-gene-vav3-via-methylation
#18
Irlanda Peralta-Arrieta, Daniel Hernández-Sotelo, Yaneth Castro-Coronel, Marco Antonio Leyva-Vázquez, Berenice Illades-Aguiar
Altered promoter DNA methylation is one of the most important epigenetic abnormalities in human cancer. DNMT3B, de novo methyltransferase, is clearly related to abnormal methylation of tumour suppressor genes, DNA repair genes and its overexpression contributes to oncogenic processes and tumorigenesis in vivo. The purpose of this study was to assess the effect of the overexpression of DNMT3B in HaCaT cells on global gene expression and on the methylation of selected genes to the identification of genes that can be target of DNMT3B...
2017: American Journal of Cancer Research
https://www.readbyqxmd.com/read/28110250/detection-and-discrimination-of-maintenance-and-de-novo-cpg-methylation-events-using-methylbreak
#19
William Hsu, Augustus T Mercado, George Hsiao, Jui-Ming Yeh, Chung-Yung Chen
Understanding the principles governing the establishment and maintenance activities of DNA methyltransferases (DNMTs) can help in the development of predictive biomarkers associated with genetic disorders and diseases. A detection system was developed that distinguishes and quantifies methylation events using methylation-sensitive endonucleases and molecular beacon technology. MethylBreak (MB) is a 22-mer oligonucleotide with one hemimethylated and two unmethylated CpG sites, which are also recognition sites for Sau96I and SacII, and is attached to a fluorophore and a quencher...
May 15, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28105934/charm-discovery-of-combinatorial-chromatin-modification-patterns-in-hepatitis-b-virus-x-transformed-mouse-liver-cancer-using-association-rule-mining
#20
Sung Hee Park, Sun-Min Lee, Young-Joon Kim, Sangsoo Kim
BACKGROUND: Various chromatin modifications, identified in large-scale epigenomic analyses, are associated with distinct phenotypes of different cells and disease phases. To improve our understanding of these variations, many computational methods have been developed to discover novel sites and cell-specific chromatin modifications. Despite the availability of existing methods, there is still room for further improvement when they are applied to resolve the histone code hypothesis. Hence, we aim to investigate the development of a computational method to provide new insights into de novo combinatorial pattern discovery of chromatin modifications to characterize epigenetic variations in distinct phenotypes of different cells...
December 13, 2016: BMC Bioinformatics
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