keyword
MENU ▼
Read by QxMD icon Read
search

De novo DNA Methylation

keyword
https://www.readbyqxmd.com/read/28065650/network-dynamics-mediate-circadian-clock-plasticity
#1
Abdelhalim Azzi, Jennifer A Evans, Tanya Leise, Jihwan Myung, Toru Takumi, Alec J Davidson, Steven A Brown
A circadian clock governs most aspects of mammalian behavior. Although its properties are in part genetically determined, altered light-dark environment can change circadian period length through a mechanism requiring de novo DNA methylation. We show here that this mechanism is mediated not via cell-autonomous clock properties, but rather through altered networking within the suprachiasmatic nuclei (SCN), the circadian "master clock," which is DNA methylated in region-specific manner. DNA methylation is necessary to temporally reorganize circadian phasing among SCN neurons, which in turn changes the period length of the network as a whole...
January 2, 2017: Neuron
https://www.readbyqxmd.com/read/28064006/versatile-rna-tetra-u-helix-linking-motif-as-a-toolkit-for-nucleic-acid-nanotechnology
#2
My N Bui, M Brittany Johnson, Mathias Viard, Emily Satterwhite, Angelica N Martins, Zhihai Li, Ian Marriott, Kirill A Afonin, Emil F Khisamutdinov
RNA nanotechnology employs synthetically modified ribonucleic acid (RNA) to engineer highly stable nanostructures in one, two, and three dimensions for medical applications. Despite the tremendous advantages in RNA nanotechnology, unmodified RNA itself is fragile and prone to enzymatic degradation. In contrast to use traditionally modified RNA strands e.g. 2'-fluorine, 2'-amine, 2'-methyl, we studied the effect of RNA/DNA hybrid approach utilizing a computer-assisted de novo RNA tetra-uracil (tetra-U) motif as a toolkit to address questions related to assembly efficiency, versatility, stability, and the production costs of hybrid RNA/DNA nanoparticles...
January 4, 2017: Nanomedicine: Nanotechnology, Biology, and Medicine
https://www.readbyqxmd.com/read/28026094/phenotypic-characteristics-of-aged-cd4-cd28-null-t-lymphocytes-are-determined-by-changes-in-the-whole-genome-dna-methylation-pattern
#3
Beatriz Suarez-Álvarez, Ramón M Rodríguez, Karin Schlangen, Aroa Baragaño Raneros, Leonardo Márquez-Kisinousky, Agustín F Fernández, Carmen Díaz-Corte, Ana M Aransay, Carlos López-Larrea
Aging is associated with a progressive loss of the CD28 costimulatory molecule in CD4(+) lymphocytes (CD28(null) T cells), which is accompanied by the acquisition of new biological and functional properties that give rise to an impaired immune response. The regulatory mechanisms that govern the appearance and function of this cell subset during aging and in several associated inflammatory disorders remain controversial. Here, we present the whole-genome DNA methylation and gene expression profiles of CD28(null) T cells and its CD28(+) counterpart...
December 27, 2016: Aging Cell
https://www.readbyqxmd.com/read/28003281/dnmt3a-in-leukemia
#4
Lorenzo Brunetti, Michael C Gundry, Margaret A Goodell
DNA methylation is an epigenetic process involved in development, aging, and cancer. Although the advent of new molecular techniques has enhanced our knowledge of how DNA methylation alters chromatin and subsequently affects gene expression, a direct link between epigenetic marks and tumorigenesis has not been established. DNMT3A is a de novo DNA methyltransferase that has recently gained relevance because of its frequent mutation in a large variety of immature and mature hematologic neoplasms. DNMT3A mutations are early events during cancer development and seem to confer poor prognosis to acute myeloid leukemia (AML) patients making this gene an attractive target for new therapies...
December 21, 2016: Cold Spring Harbor Perspectives in Medicine
https://www.readbyqxmd.com/read/28003272/cancer-specific-changes-in-dna-methylation-reveal-aberrant-silencing-and-activation-of-enhancers-in-leukemia
#5
Ying Qu, Lee Siggens, Lina Cordeddu, Verena I Gaidzik, Kasper Karlsson, Lars Bullinger, Konstanze Döhner, Karl Ekwall, Sören Lehmann, Andreas Lennartsson
Acute myeloid leukemia (AML) is characterized by an impaired differentiation process leading to an accumulation of immature blasts in the blood. One feature of cytogenetically normal AML is alterations to the DNA methylome. Here we have analyzed 57 AML patients with normal karyotype using Illuminas 450 k array and show that aberrant DNA methylation is significantly altered at enhancer regions and that the methylation levels at specific enhancers predict overall survival of AML patients. The majority of sites that become differentially methylated in AML occur in regulatory elements of the human genome...
December 21, 2016: Blood
https://www.readbyqxmd.com/read/27991732/acute-myeloid-leukemia-associated-dnmt3a-p-arg882his-mutation-in-a-patient-with-tatton-brown-rahman-overgrowth-syndrome-as-a-constitutional-mutation
#6
Rika Kosaki, Hiroshi Terashima, Masaya Kubota, Kenjiro Kosaki
DNA methylation plays a critical role in both embryonic development and tumorigenesis and is mediated through various DNA methyltransferases. Constitutional mutations in the de novo DNA methyltransferase DNMT3A cause a recently identified Tatton-Brown-Rahman overgrowth syndrome (TBRS). Somatically acquired mutations in DNMT3A are causally associated with acute myeloid leukemia (AML), and p.Arg882His represents the most prevalent hotspot. So far, no patients with TBRS have been reported to have subsequently developed AML...
January 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/27935870/changes-in-the-methylation-status-of-the-oct3-4-nanog-and-sox2-promoters-in-stem-cells-during-regeneration-of-rat-tracheal-epithelium-after-injury
#7
Ying Zhou, Nan Song, Xin Li, Ying Han, Zihan Ren, Jing-Xian Xu, Yu-Chen Han, Fang Li, Xinshan Jia
We investigated the relationship between promoter methylation and tracheal stem cell activation. We developed a model of rat tracheal epithelium regeneration after 5-fluorouracil (5-FU)-induced injury. Using immunohistochemistry and Western blotting, the expression levels of the stem cell pluripotency regulator Oct3/4 and differentiation marker CK14 were measured after 5-FU treatment. The methylation status of the Oct3/4, Nanog, and Sox2 promoters was investigated using methylation-specific PCR. Additionally, the effects of 5-azacytidine (5-azaC), a demethylating agent, on Oct3/4, Nanog, and Sox2 mRNA and protein expression were evaluated...
December 7, 2016: Oncotarget
https://www.readbyqxmd.com/read/27934997/lead-pb-exposure-reduces-global-dna-methylation-level-by-non-competitive-inhibition-and-alteration-of-dnmt-expression
#8
Oscar F Sanchez, Jinyoung Lee, Nathaphon Yu King Hing, Seong-Eun Kim, Jennifer L Freeman, Chongli Yuan
Low-dose exposure to lead (Pb) is connected to developmental neurological alterations by inducing molecular changes, such as aberrant gene expression patterns. The attributing molecular mechanism, however, is not well-elucidated. In this study, we revealed epigenetic features and mechanisms that can alter gene expression patterns by identifying changes in DNA methyltransferase (DNMT) activity, expression pattern and DNA methylation level using moelcular studies and a zebrafish animal model. We characterized the effects of Pb on the activities of various DNMTs in vitro and determined the molecular role of Pb in modulating DNMT activity via kinetic experiments...
December 9, 2016: Metallomics: Integrated Biometal Science
https://www.readbyqxmd.com/read/27915479/trends-in-next-generation-sequencing-and-a-new-era-for-whole-genome-sequencing
#9
REVIEW
Sang Tae Park, Jayoung Kim
This article is a mini-review that provides a general overview for next-generation sequencing (NGS) and introduces one of the most popular NGS applications, whole genome sequencing (WGS), developed from the expansion of human genomics. NGS technology has brought massively high throughput sequencing data to bear on research questions, enabling a new era of genomic research. Development of bioinformatic software for NGS has provided more opportunities for researchers to use various applications in genomic fields...
November 2016: International Neurourology Journal
https://www.readbyqxmd.com/read/27901321/copy-number-variants-in-a-population-based-investigation-of-klippel-trenaunay-syndrome
#10
Aggeliki Dimopoulos, Robert J Sicko, Denise M Kay, Shannon L Rigler, Ruzong Fan, Paul A Romitti, Marilyn L Browne, Charlotte M Druschel, Michele Caggana, Lawrence C Brody, James L Mills
Klippel-Trenaunay syndrome (KTS) is a rare congenital vascular disorder that is thought to occur sporadically; however, reports of familial occurrence suggest a genetic component. We examined KTS cases to identify novel, potentially causal copy number variants (CNVs). We identified 17 KTS cases from all live-births occurring in New York (1998-2010). Extracted DNA was genotyped using Illumina microarrays and CNVs were called using PennCNV software. CNVs selected for follow-up had ≥10 single nucleotide polymorphisms (SNPs) and minimal overlap with in-house controls or controls from the Database of Genomic Variants...
November 30, 2016: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/27899265/discovery-of-novel-dna-methyltransferase-3a-inhibitors-via-structure-based-virtual-screening-and-biological-assays
#11
Zhiyuan Shao, Pan Xu, Wen Xu, Linjuan Li, Shien Liu, Rukang Zhang, Yu-Chih Liu, Chenhua Zhang, Shijie Chen, Cheng Luo
DNA methyltransferases are involved in diverse biological processes and abnormal methylation patterns play essential roles in cancer initiation and progression. DNA methyltransferase 3A (DNMT3A) acting as a de novo DNA methyltransferase, has gained widespread attention especially in haematological diseases. To date, large numbers of DNMTs inhibitors have been discovered, however, the small molecular inhibitors targeting DNMT3A are still in its infancy. In this study, structure-based virtual screening in combination with biological assays was performed to discovery potent novel DNMT3A inhibitors...
January 15, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/27895716/widespread-recovery-of-methylation-at-gametic-imprints-in-hypomethylated-mouse-stem-cells-following-rescue-with-dnmt3a2
#12
Avinash Thakur, Sarah-Jayne Mackin, Rachelle E Irwin, Karla M O'Neill, Gareth Pollin, Colum Walsh
BACKGROUND: Imprinted loci are paradigms of epigenetic regulation and are associated with a number of genetic disorders in human. A key characteristic of imprints is the presence of a gametic differentially methylated region (gDMR). Previous studies have indicated that DNA methylation lost from gDMRs could not be restored by DNMT1, or the de novo enzymes DNMT3A or 3B in stem cells, indicating that imprinted regions must instead undergo passage through the germline for reprogramming. However, previous studies were non-quantitative, were unclear on the requirement for DNMT3A/B and showed some inconsistencies...
2016: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/27886677/differences-in-global-dna-methylation-of-testicular-seminoma-are-not-associated-with-changes-in-histone-modifications-clinical-prognosis-braf-mutations-or-gene-expression
#13
Louise Holm Pedersen, John E Nielsen, Gedske Daugaard, Thomas V O Hansen, Ewa Rajpert-De Meyts, Kristian Almstrup
Testicular germ cell tumours of young adults are comprised of a heterogeneous group of non-seminomas and a homogeneous group of seminomas. While the majority of seminomas retain a hypo-methylated genome, a small fraction displays a highly methylated genome, resembling hyper-methylated non-seminomas. It is well established from e.g. melanoma, colorectal and thyroid cancer that a methylated phenotype can be correlated to prognosis and can be related to BRAF mutations. In the present study we investigated the global methylation level in 67 seminomas and classified them as hypo-methylated, intermediate, patchy and hyper-methylated, respectively...
November 2016: Cancer Genetics
https://www.readbyqxmd.com/read/27884978/oestrogen-receptor-negativity-in-breast-cancer-a-cause-or-consequence
#14
REVIEW
Vijaya Narasihma Reddy Gajulapalli, Vijaya Lakshmi Malisetty, Suresh Kumar Chitta, Bramanandam Manavathi
Endocrine resistance, which occurs either by de novo or acquired route, is posing a major challenge in treating hormone-dependent breast cancers by endocrine therapies. The loss of oestrogen receptor α (ERα) expression is the vital cause of establishing endocrine resistance in this subtype. Understanding the mechanisms that determine the causes of this phenomenon are therefore essential to reduce the disease efficacy. But how we negate oestrogen receptor (ER) negativity and endocrine resistance in breast cancer is questionable...
December 2016: Bioscience Reports
https://www.readbyqxmd.com/read/27880916/nrl-regulated-transcriptome-dynamics-of-developing-rod-photoreceptors
#15
Jung-Woong Kim, Hyun-Jin Yang, Matthew John Brooks, Lina Zelinger, Gökhan Karakülah, Norimoto Gotoh, Alexis Boleda, Linn Gieser, Felipe Giuste, Dustin Thad Whitaker, Ashley Walton, Rafael Villasmil, Jennifer Joanna Barb, Peter Jonathan Munson, Koray Dogan Kaya, Vijender Chaitankar, Tiziana Cogliati, Anand Swaroop
Gene regulatory networks (GRNs) guiding differentiation of cell types and cell assemblies in the nervous system are poorly understood because of inherent complexities and interdependence of signaling pathways. Here, we report transcriptome dynamics of differentiating rod photoreceptors in the mammalian retina. Given that the transcription factor NRL determines rod cell fate, we performed expression profiling of developing NRL-positive (rods) and NRL-negative (S-cone-like) mouse photoreceptors. We identified a large-scale, sharp transition in the transcriptome landscape between postnatal days 6 and 10 concordant with rod morphogenesis...
November 22, 2016: Cell Reports
https://www.readbyqxmd.com/read/27856912/the-dna-methyltransferase-dnmt3c-protects-male-germ-cells-from-transposon-activity
#16
Joan Barau, Aurélie Teissandier, Natasha Zamudio, Stéphanie Roy, Valérie Nalesso, Yann Hérault, Florian Guillou, Déborah Bourc'his
DNA methylation is prevalent in mammalian genomes and plays a central role in the epigenetic control of development. The mammalian DNA methylation machinery is thought to be composed of three DNA methyltransferase enzymes (DNMT1, DNMT3A, and DNMT3B) and one cofactor (DNMT3L). Here, we describe the discovery of Dnmt3C, a de novo DNA methyltransferase gene that evolved via a duplication of Dnmt3B in rodent genomes and was previously annotated as a pseudogene. We show that DNMT3C is the enzyme responsible for methylating the promoters of evolutionarily young retrotransposons in the male germ line and that this specialized activity is required for mouse fertility...
November 18, 2016: Science
https://www.readbyqxmd.com/read/27854126/human-adipogenesis-is-associated-with-genome-wide-dna-methylation-and-gene-expression-changes
#17
Christa Broholm, Anders Henrik Olsson, Alexander Perfilyev, Linn Gillberg, Ninna Schiøler Hansen, Ashfaq Ali, Brynjulf Mortensen, Charlotte Ling, Allan Vaag
AIM: To define the genomic distribution and function of DNA methylation changes during human adipogenesis. METHODS: We isolated adipocyte-derived stem cells from 13 individuals and analyzed genome-wide DNA methylation and gene expression in cultured adipocyte-derived stem cells and mature adipocytes. RESULTS: We observed altered DNA methylation of 11,947 CpG sites and altered expression of 11,830 transcripts after differentiation. De novo methylation was observed across all genomic elements...
December 2016: Epigenomics
https://www.readbyqxmd.com/read/27846393/decoding-the-dna-methylome-of-mantle-cell-lymphoma-in-the-light-of-the-entire-b-cell-lineage
#18
Ana C Queirós, Renée Beekman, Roser Vilarrasa-Blasi, Martí Duran-Ferrer, Guillem Clot, Angelika Merkel, Emanuele Raineri, Nuria Russiñol, Giancarlo Castellano, Sílvia Beà, Alba Navarro, Marta Kulis, Núria Verdaguer-Dot, Pedro Jares, Anna Enjuanes, María José Calasanz, Anke Bergmann, Inga Vater, Itziar Salaverría, Harmen J G van de Werken, Wyndham H Wilson, Avik Datta, Paul Flicek, Romina Royo, Joost Martens, Eva Giné, Armando Lopez-Guillermo, Hendrik G Stunnenberg, Wolfram Klapper, Christiane Pott, Simon Heath, Ivo G Gut, Reiner Siebert, Elías Campo, José I Martín-Subero
We analyzed the in silico purified DNA methylation signatures of 82 mantle cell lymphomas (MCL) in comparison with cell subpopulations spanning the entire B cell lineage. We identified two MCL subgroups, respectively carrying epigenetic imprints of germinal-center-inexperienced and germinal-center-experienced B cells, and we found that DNA methylation profiles during lymphomagenesis are largely influenced by the methylation dynamics in normal B cells. An integrative epigenomic approach revealed 10,504 differentially methylated regions in regulatory elements marked by H3K27ac in MCL primary cases, including a distant enhancer showing de novo looping to the MCL oncogene SOX11...
November 14, 2016: Cancer Cell
https://www.readbyqxmd.com/read/27843576/micrornas-interfere-with-dna-methylation-in-rheumatoid-arthritis-synovial-fibroblasts
#19
Niharika Gaur, Emmanuel Karouzakis, Selene Glück, Edvardas Bagdonas, Astrid Jüngel, Beat A Michel, Renate E Gay, Steffen Gay, Mojca Frank-Bertoncelj, Michel Neidhart
BACKGROUND: The DNA of rheumatoid arthritis synovial fibroblasts (RASF) is globally hypomethylated; this contributes to an aggressive behaviour. In an attempt to remethylate these cells, we supplemented with methyl donors. We investigated the possible interference of microRNAs (miRs). MATERIAL AND METHODS: RASF were treated with L-methionine or betaine. Transcripts of de novo methyltransferases (DNMTs) and miRs were measured by real-time PCR, and a transcription PCR array was performed...
2016: RMD Open
https://www.readbyqxmd.com/read/27833659/identification-of-activated-enhancers-and-linked-transcription-factors-in-breast-prostate-and-kidney-tumors-by-tracing-enhancer-networks-using-epigenetic-traits
#20
Suhn Kyong Rhie, Yu Guo, Yu Gyoung Tak, Lijing Yao, Hui Shen, Gerhard A Coetzee, Peter W Laird, Peggy J Farnham
BACKGROUND: Although technological advances now allow increased tumor profiling, a detailed understanding of the mechanisms leading to the development of different cancers remains elusive. Our approach toward understanding the molecular events that lead to cancer is to characterize changes in transcriptional regulatory networks between normal and tumor tissue. Because enhancer activity is thought to be critical in regulating cell fate decisions, we have focused our studies on distal regulatory elements and transcription factors that bind to these elements...
2016: Epigenetics & Chromatin
keyword
keyword
99882
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"