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Journal articles on the topic 'R-methylation'

Author: Grafiati

Published: 9 March 2023

Last updated: 31 July 2025

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1

Lin, Kaixin, Xiaolin Wang, Yanxin Luo, and Huichuan Yu. "Abstract 3485: Global DNA methylation level is associated with the sensitivity of cytotoxic and senotherapeutic drugs in gastrointestinal tumors." Cancer Research 84, no. 6_Supplement (2024): 3485. http://dx.doi.org/10.1158/1538-7445.am2024-3485.

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Abstract Background: Gastrointestinal cancer has become a severe burden around the world. Marker-guided treatment and clinical trials with sensitive anti-tumor drugs are critical for improving cancer survival. The decreasing DNA methylation levels of repetitive elements, such as LINE-1 and ALU, have been identified as the common biomarkers in cancer and aging. However, it remains unclear whether the methylation levels of repetitive elements can imply the drug sensitivity in gastrointestinal cancer. We investigated the association of LINE-1 and ALU methylations with the sensitivity of cytotoxic

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Saadatmand, Forough, Muneer Abbas, Victor Apprey, Krishma Tailor, and Bernard Kwabi-Addo. "Sex differences in saliva-based DNA methylation changes and environmental stressor in young African American adults." PLOS ONE 17, no. 9 (2022): e0273717. http://dx.doi.org/10.1371/journal.pone.0273717.

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Background Low socioeconomic status neighborhood exposure to stress and violence may be sources of negative stimuli that poses significant health risks for children, adolescents and throughout the life course of an individual. The study aims to investigate if aberrant epigenetic DNA methylation changes may be a potential mechanism for regulating neighborhood exposures and health outcomes. Methods Exposure to environmental stressors identified in 98 young African American (AA) adults aged 18–25 years old from the Washington D.C., area were used in the study. We correlated the association betwee

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Abula, Abudureyimu, Xiaona Li, Xing Quan, et al. "Molecular mechanism of RNase R substrate sensitivity for RNA ribose methylation." Nucleic Acids Research 49, no. 8 (2021): 4738–49. http://dx.doi.org/10.1093/nar/gkab202.

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Abstract RNA 2′-O-methylation is widely distributed and plays important roles in various cellular processes. Mycoplasma genitalium RNase R (MgR), a prokaryotic member of the RNase II/RNB family, is a 3′-5′ exoribonuclease and is particularly sensitive to RNA 2′-O-methylation. However, how RNase R interacts with various RNA species and exhibits remarkable sensitivity to substrate 2′-O-methyl modifications remains elusive. Here we report high-resolution crystal structures of MgR in apo form and in complex with various RNA substrates. The structural data together with extensive biochemical analys

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Walker, Elsbeth L. "Paramutation of the r1 Locus of Maize Is Associated With Increased Cytosine Methylation." Genetics 148, no. 4 (1998): 1973–81. http://dx.doi.org/10.1093/genetics/148.4.1973.

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Abstract In paramutation two alleles of a gene interact so that one of the alleles is epigenetically silenced. The silenced state is then genetically transmissible for many generations. The large (220 kbp) multigenic complex R-r is paramutable: its level of expression is changed during paramutation. R-r was found to exhibit increases in its level of cytosine methylation (C-methylation) following paramutation. These C-methylation changes are localized to the 5′ portions of the two genes in the complex that are most sensitive to paramutation. These methylation changes flank a small region called

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Barré-Villeneuve, Clément, and Jacinthe Azevedo-Favory. "R-Methylation in Plants: A Key Regulator of Plant Development and Response to the Environment." International Journal of Molecular Sciences 25, no. 18 (2024): 9937. http://dx.doi.org/10.3390/ijms25189937.

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Although arginine methylation (R-methylation) is one of the most important post-translational modifications (PTMs) conserved in eukaryotes, it has not been studied to the same extent as phosphorylation and ubiquitylation. Technical constraints, which are in the process of being resolved, may partly explain this lack of success. Our knowledge of R-methylation has recently evolved considerably, particularly in metazoans, where misregulation of the enzymes that deposit this PTM is implicated in several diseases and cancers. Indeed, the roles of R-methylation have been highlighted through the anal

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Li, Xiao-Hong, Mei-Yin Lu, Jia-Li Niu, Dong-Yan Zhu, and Bin Liu. "cfDNA Methylation Profiles and T-Cell Differentiation in Women with Endometrial Polyps." Cells 11, no. 24 (2022): 3989. http://dx.doi.org/10.3390/cells11243989.

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DNA methylation is a part of the regulatory mechanisms of gene expression, including chromatin remodeling and the activity of microRNAs, which are involved in the regulation of T-cell differentiation and function. However, the role of cfDNA methylation in T-cell differentiation is entirely unknown. In patients with endometrial polyps (EPs), we have found an imbalance of T-cell differentiation and an aberrant cfDNA methylation profile, respectively. In this study, we investigated the relationship between cfDNA methylation profiles and T-cell differentiation in 14 people with EPs and 27 healthy

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Vertino, Paula M., and Paul A. Wade. "R Loops: Lassoing DNA Methylation at CpGi." Molecular Cell 45, no. 6 (2012): 708–9. http://dx.doi.org/10.1016/j.molcel.2012.03.014.

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Karataş, Esra, Mehmet Gürbilek, and Gamze Demirel. "Relationship between Klotho gene methylation level and diet habit." Cukurova Medical Journal 49, no. 4 (2024): 965–73. https://doi.org/10.17826/cumj.1551174.

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Purpose: This study aimed to determine the relationship between the methylation level of the Klotho gene and nutritional habits. Materials and Methods: From our healthy sample group consisting of 20 people, two groups were created: 10 people fed with carbohydrates and 10 people had protein. Initially, a food consumption frequency determination form was administered as a survey to individuals. Based on the results of this survey, the amounts of food consumed by the participants (g/cc) were determined. According to the findings of the survey, two groups were formed: those classified as carbohydr

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Jiang, Xinyin, Chauntelle Jack-Roberts, Kaydine Edwards, Ella Gilboa, Ikhtiyor Djuraev, and Mudar Dalloul. "Association of Methylation-Related Nutrient Intake and Status with Offspring DNA Methylation in Pregnant Women with and Without Gestational Diabetes Mellitus." Current Developments in Nutrition 4, Supplement_2 (2020): 1016. http://dx.doi.org/10.1093/cdn/nzaa054_088.

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Abstract Objectives Gestational diabetes mellitus (GDM) is associated with alterations in DNA methylation in the placenta and offspring tissues. Nutrients participating in the methionine cycle (e.g., choline, betaine, folate, vitamin B12, methionine) influence the supply of methyl groups. The objective of this research was to determine whether maternal intake and status of these nutrients during pregnancy may interact with the GDM status to shape the offspring epigenome. Methods We conducted 3-day dietary recalls and collected blood samples from pregnant women with and without GDM (n = 22/grou

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Su, Shian, Quentin Gouil, Marnie E. Blewitt, Dianne Cook, Peter F. Hickey, and Matthew E. Ritchie. "NanoMethViz: An R/Bioconductor package for visualizing long-read methylation data." PLOS Computational Biology 17, no. 10 (2021): e1009524. http://dx.doi.org/10.1371/journal.pcbi.1009524.

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A key benefit of long-read nanopore sequencing technology is the ability to detect modified DNA bases, such as 5-methylcytosine. The lack of R/Bioconductor tools for the effective visualization of nanopore methylation profiles between samples from different experimental groups led us to develop the NanoMethViz R package. Our software can handle methylation output generated from a range of different methylation callers and manages large datasets using a compressed data format. To fully explore the methylation patterns in a dataset, NanoMethViz allows plotting of data at various resolutions. At

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Jintaridth, Pornrutsami, and Apiwat Mutirangura. "Distinctive patterns of age-dependent hypomethylation in interspersed repetitive sequences." Physiological Genomics 41, no. 2 (2010): 194–200. http://dx.doi.org/10.1152/physiolgenomics.00146.2009.

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Interspersed repetitive sequences (IRSs) are a major contributor to genome size and may contribute to cellular functions. IRSs are subdivided according to size and functionally related structures into short interspersed elements, long interspersed elements (LINEs), DNA transposons, and LTR-retrotransposons. Many IRSs may produce RNA and regulate genes by a variety of mechanisms. The majority of DNA methylation occurs in IRSs and is believed to suppress IRS activities. Global hypomethylation, or the loss of genome-wide methylation, is a common epigenetic event not only in senescent cells but al

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He, Y., R. Zhang, J. Chen, J. Tan, M. Wang, and X. Wu. "The ability of arsenic metabolism affected the expression of lncRNA PANDAR, DNA damage, or DNA methylation in peripheral blood lymphocytes of laborers." Human & Experimental Toxicology 39, no. 5 (2019): 605–13. http://dx.doi.org/10.1177/0960327119897101.

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Arsenic has been associated with significant effects on human health. Exposure to inorganic arsenic has been associated with the changes in gene expression. Promoter of CDKN1A antisense DNA damage activated RNA (PANDAR) expression is induced by p53 protein and DNA damage response. Here, we investigated whether the ability of arsenic metabolism in individuals affected the expression of PANDAR, DNA damage, and DNA methylation. Levels of gene expression and DNA damage were examined by the quantitative polymerase chain reaction and DNA methylation was measured by the methylation-sensitive high-res

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He, Shiwei, Yuan Wu, Shuidi Yan, et al. "Methylation of CYP1A1 and VKORC1 promoter associated with stable dosage of warfarin in Chinese patients." PeerJ 9 (June 22, 2021): e11549. http://dx.doi.org/10.7717/peerj.11549.

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Objective To investigate the association between DNA methylation and the stable warfarin dose through genome-wide DNA methylation analysis and pyrosequencing assay. Method This study included 161 patients and genome-wide DNA methylation analysis was used to screen potential warfarin dose-associated CpGs through Illumina Infinium HumanMethylation 450 K BeadChip; then, the pyrosequencing assay was used to further validate the association between the stable warfarin dose and alterations in the methylation of the screened CpGs. GenomeStudio Software and R were used to analyze the differentially me

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Zhang, Lei, Rui Ma, Qingxiang Yu, and Lihua Sun. "Cyclin-dependent kinase 6 body methylation and association with prognosis of patients with acute myeloid leukemia." Journal of Clinical Oncology 40, no. 16_suppl (2022): e19000-e19000. http://dx.doi.org/10.1200/jco.2022.40.16_suppl.e19000.

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e19000 Background: Cyclin-dependent kinase 6 (CDK6) plays critical roles in leukemogenesis and leukemia stem cells activation, and its inhibition has emerged as a novel therapeutic strategy in acute myeloid leukemia (AML) management. However, association between CDK6 methylation and prognosis in patients with AML remains unclear. Methods: Methylation profile, somatic alterations, and CDK6 gene expression data of 200 clinically annotated patients with de novo AML were retrieved from the TCGA Pan-Cancer Atlas project deposited in the UCSC Xena database. Specifically, methylation levels of all 64

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Shao, Zonghong, Yue Ren, and Rong Fu. "Preliminary Study on the Abnormal DNA Methylation in T Cells from the Patients with Immune Related Pancytopenia." Blood 124, no. 21 (2014): 5156. http://dx.doi.org/10.1182/blood.v124.21.5156.5156.

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Abstract Objective To explore the global DNA methylation and the expression of regulatory genes for methylation in CD4 + T cells of the patients with immune related pancytopenia (IRP) and explore the role of methylation in pathogenesis of IRP. Methods Thirty IRP patients (untreated, n=15; remission, n=15) and 15 healthy donors as controls were enrolled from December 2012 to December 2013. CD4+ T cells were sorted by immunomagnetic separation. The global DNA methylation was tested with enzyme-linked immunosorbent assay (ELISA). The mRNA levels of DNA methylation-related regulating genes, DNA me

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Fujiyoshi, Sunao, Shohei Honda, Eiso Hiyama, and Akinobu Taketomi. "Investigation of aberrant DNA methylation in association with cisplatin-resistant hepatoblastoma." Journal of Clinical Oncology 37, no. 4_suppl (2019): 258. http://dx.doi.org/10.1200/jco.2019.37.4_suppl.258.

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258 Background: Cisplatin (CDDP) is a key-drug of mainstream treatment for hepatoblastoma (HB), but 22.3% of HB patients have resistance to CDDP, and their prognoses are poor. We investigated methylation status of HB patients and identified CDDP resistant candidate genes in HB. Methods: First, we performed a genome-wide methylation array analysis of 11 resected HB tumors. These cases included six cases of RECIST (Response Evaluation Criteria In Solid Tumors) CR or PR (S group) and five cases of SD or PD (R group). We analyzed methylation status of these patients, comparing with clinical course

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Schafer, Eric S., Rumen Kostadinov, Peter Murakami, et al. "Lineage, Fusion Partner and Age Differences in the Methylome of MLL-r Leukemias." Blood 120, no. 21 (2012): 3506. http://dx.doi.org/10.1182/blood.v120.21.3506.3506.

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Abstract Abstract 3506 Background: MLL gene rearrangements (MLL-r) are seen in all ages in both acute lymphocytic leukemia (ALL) and acute myeloid leukemia (AML). The most common fusion partners are AF4, AF9 and ENL/ELL. Murine models suggest that the expression of MLL fusion proteins is necessary but not sufficient for leukemogenesis, but true cooperating lesions have been difficult to identify. Our lab and others have previously shown that MLL-r infant ALL can be defined by a unique signature characterized by genome-wide hypermethylated CpG islands leading to tumor suppressor gene silencing.

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Vidovič, Eva, Sebastian Pelikan, Marija Atanasova, et al. "DNA Methylation Patterns in Relation to Acute Severity and Duration of Anxiety and Depression." Current Issues in Molecular Biology 45, no. 9 (2023): 7286–303. http://dx.doi.org/10.3390/cimb45090461.

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Depression and anxiety are common mental disorders that often occur together. Stress is an important risk factor for both disorders, affecting pathophysiological processes through epigenetic changes that mediate gene–environment interactions. In this study, we explored two proposed models about the dynamic nature of DNA methylation in anxiety and depression: a stable change, in which DNA methylation accumulates over time as a function of the duration of clinical symptoms of anxiety and depression, or a flexible change, in which DNA methylation correlates with the acute severity of clinical sym

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Walker, Ms Lauryn, Dr Masar Radhi, Dr Helen Knight, and Dr Stuart Smith. "DYSREGULATION OF M6A RNA METHYLATION, R-LOOPS AND THE DNA DAMAGE RESPONSE IN PAEDIATRIC HIGH-GRADE GLIOMAS." Neuro-Oncology 26, Supplement_7 (2024): vii14—vii15. http://dx.doi.org/10.1093/neuonc/noae158.057.

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Abstract AIMS Paediatric high-grade gliomas (pHGG) are virtually incurable malignant brain tumours. The regulation of R- loops is necessary for ensuring genomic stability. The formation of R-loops at DNA damage sites promotes DNA repair via m6A methylation of the RNA strand. We aimed to investigate whether m6A methylation, R-loop homeostasis and the DNA damage response is dysregulated in pHGG and whether inhibitors, such as ATM inhibitors, could be potential therapeutics for pHGG. METHOD To assess the global levels of m6A, R-loops, yH2AX, total ATM and phosphorylated ATM in paediatric HGG cell

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Maugeri, Andrea, Martina Barchitta, Matteo Fallico, Niccolò Castellino, Michele Reibaldi, and Antonella Agodi. "Characterization of SIRT1/DNMTs Functions and LINE-1 Methylation in Patients with Age-Related Macular Degeneration." Journal of Clinical Medicine 8, no. 2 (2019): 159. http://dx.doi.org/10.3390/jcm8020159.

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Previous studies proposed the application of DNA methylation signatures as clinical biomarkers of age-related macular degeneration (AMD). However, the characterization of Long Interspersed Nuclear Element-1 (LINE-1) methylation levels—a surrogate marker of global DNA methylation—in AMD patients has not been investigated so far. In the present study, we first characterized DNA methyltransferases (DNMTs) and Sirtuin 1 (SIRT1) functions in blood samples of 40 AMD patients and 10 age- and sex-matched controls. Then, we evaluated whether changes in DNMTs functions were associated with different LIN

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Shi, Alvin, Abdullah Ali, Gordon Cann, et al. "Methylation-based prediction of myelodysplastic syndrome survival outcomes." Journal of Clinical Oncology 41, no. 16_suppl (2023): 7058. http://dx.doi.org/10.1200/jco.2023.41.16_suppl.7058.

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7058 Background: Myelodysplastic syndromes (MDS) are a heterogeneous group of myeloid malignancies associated with a myriad of deleterious outcomes and a 5-year relative survival of 37%. MDS risk stratification is key for optimal treatment decisions. DNA methylation is associated with MDS biology due to frequent somatic mutations in genes (i.e. TET2, DNMT3A, IDH1, IDH2, and WT1) that affect DNA methylation. We hypothesized that methylation-based markers may help stratify risk and improve IPSS-R (the Revised International Prognostic Scoring System). Here, we evaluated the potential of both Bone

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Franzago, Marica, Paola Borrelli, Marta Di Nicola, et al. "From Mother to Child: Epigenetic Signatures of Hyperglycemia and Obesity during Pregnancy." Nutrients 16, no. 20 (2024): 3502. http://dx.doi.org/10.3390/nu16203502.

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Background: In utero exposure to maternal hyperglycemia and obesity can trigger detrimental effects in the newborn through epigenetic programming. We aimed to assess the DNA methylation levels in the promoters of MC4R and LPL genes from maternal blood, placenta, and buccal swab samples collected in children born to mothers with and without obesity and Gestational Diabetes Mellitus (GDM). Methods: A total of 101 Caucasian mother–infant pairs were included in this study. Sociodemographic characteristics, clinical parameters, physical activity, and adherence to the Mediterranean diet were evaluat

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Houde, A. A., J. St-Pierre, M. F. Hivert, et al. "Placental lipoprotein lipase DNA methylation levels are associated with gestational diabetes mellitus and maternal and cord blood lipid profiles." Journal of Developmental Origins of Health and Disease 5, no. 2 (2014): 132–41. http://dx.doi.org/10.1017/s2040174414000038.

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Placental lipoprotein lipase (LPL) is crucial for placental lipid transfer. ImpairedLPLgene expression and activity were reported in pregnancies complicated by gestational diabetes mellitus (GDM) and intra-uterine growth restriction. We hypothesized that placentalLPLDNA methylation is altered by maternal metabolic status and could contribute to fetal programming. The objective of this study was thus to assess whether placentalLPLDNA methylation is associated with GDM and both maternal and newborn lipid profiles. Placenta biopsies were sampled at delivery from 126 women including 27 women with

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Schafer, Eric, Rafael Irizarry, Sandeep Negi, et al. "Promoter hypermethylation in MLL-r infant acute lymphoblastic leukemia: biology and therapeutic targeting." Blood 115, no. 23 (2010): 4798–809. http://dx.doi.org/10.1182/blood-2009-09-243634.

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Abstract Cooperating leukemogenic events in MLL-rearranged (MLL-r) infant acute lymphoblastic leukemia (ALL) are largely unknown. We explored the role of promoter CpG island hypermethylation in the biology and therapeutic targeting of MLL-r infant ALL. The HELP (HpaII tiny fragment enrichment by ligation-mediated polymerase chain reaction [PCR]) assay was used to examine genome-wide methylation of a cohort of MLL-r infant leukemia samples (n = 5), other common childhood ALLs (n = 5), and normals (n = 5). Unsupervised analysis showed tight clustering of samples into their known biologic groups,

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Saied, Marwa, Sabah Khaled, Thomas Down, et al. "Genome Wide Study of DNA Methylation In AML." Blood 116, no. 21 (2010): 3618. http://dx.doi.org/10.1182/blood.v116.21.3618.3618.

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Abstract Abstract 3618 DNA methylation is the most stable epigenetic modification and has a major role in cancer initiation and progression. The two main aims for this research were, firstly, to use the genome wide analysis of DNA methylation to better understand the development of acute myeloid leukemia (AML). The second aim was to detect differentially methylated genes/regions between certain subtypes of AML and normal bone marrow (NBM). We used the methylated DNA immunoprecipitation technique followed by high-throughput sequencing by Illumina Genome Analyser II (MeDIP -seq) for 9 AML sample

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Mah, Clarence K., Jill P. Mesirov, and Lukas Chavez. "An accessible GenePattern notebook for the copy number variation analysis of Illumina Infinium DNA methylation arrays." F1000Research 7 (December 5, 2018): 1897. http://dx.doi.org/10.12688/f1000research.16338.1.

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Illumina Infinium DNA methylation arrays are a cost-effective technology to measure DNA methylation at CpG sites genome-wide and across cohorts of normal and cancer samples. While copy number alterations are commonly inferred from array-CGH, SNP arrays, or whole-genome DNA sequencing, Illumina Infinium DNA methylation arrays have been shown to detect copy number alterations at comparable sensitivity. Here we present an accessible, interactive GenePattern notebook for the analysis of copy number variation using Illumina Infinium DNA methylation arrays. The notebook provides a graphical user int

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Barve, Vega, Shah, et al. "Perturbation of Methionine/S-adenosylmethionine Metabolism as a Novel Vulnerability in MLL Rearranged Leukemia." Cells 8, no. 11 (2019): 1322. http://dx.doi.org/10.3390/cells8111322.

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Leukemias bearing mixed lineage leukemia (MLL) rearrangement (MLL-R) resulting in expression of oncogenic MLL fusion proteins (MLL-FPs) represent an especially aggressive disease subtype with the worst overall prognoses and chemotherapeutic response. MLL-R leukemias are uniquely dependent on the epigenetic function of the H3K79 methyltransferase DOT1L, which is misdirected by MLL-FPs activating gene expression, driving transformation and leukemogenesis. Given the functional necessity of these leukemias to maintain adequate methylation potential allowing aberrant activating histone methylation

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Chang, Xiaojing, Jinguo Ma, Xiaoying Xue, et al. "DNMT family induces down-regulation of NDRG1 via DNA methylation and clinicopathological significance in gastric cancer." PeerJ 9 (September 16, 2021): e12146. http://dx.doi.org/10.7717/peerj.12146.

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Background Aberrant DNA methylation of tumor suppressor genes is a common event in the development and progression of gastric cancer (GC). Our previous study showed NDRG1, which could suppress cell invasion and migration, was frequently down-regulated by DNA methylation of its promoter in GC. Purpose and Methods To analyze the relationship between the expression and DNA methylation of NDRG1 and DNA methyltransferase (DNMT) family. We performed a comprehensive comparison analysis using 407 patients including sequencing analysis data of GC from TCGA. Results NDRG1 was down-regulated in GC, and w

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Isubakova, Daria S., Olga S. Tsymbal, Nikolai V. Litviakov, Ivan V. Milto, and Ravil M. Takhauov. "Relationship between methylation of promoters of apoptosis genes in blood lymphocytes with the frequency of chromosomal aberrations and the dose of radiation." Ecological genetics 20, no. 4 (2022): 315–23. http://dx.doi.org/10.17816/ecogen109119.

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BACKGROUND: Impaired apoptosis can have serious consequences: the accumulation of mutant cells, the development of teratogenic effects and malignant neoplasms. In this regard, the study of the mechanisms of changes in the activity of apoptosis due to methylation under the influence of long-term irradiation is urgent. AIM: The study of the degree of methylation of gene promoters involved in the induction of apoptosis in the personnel of the Siberian Chemical Plant, exposed to long-term technogenic irradiation of ionizing radiation in the course of their professional activities. MATE

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Donoghue, M. J., B. L. Patton, J. R. Sanes, and J. P. Merlie. "An axial gradient of transgene methylation in murine skeletal muscle: genomic imprint of rostrocaudal position." Development 116, no. 4 (1992): 1101–12. http://dx.doi.org/10.1242/dev.116.4.1101.

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We previously used mice bearing a myosin light chain-chloramphenicol acetyltransferase (MLC1-CAT) transgene to show that adult muscle cells bear a heritable, cell autonomous memory of their rostrocaudal position. CAT mRNA and protein are expressed in a &gt; 100-fold rostrocaudal gradient in skeletal muscles of developing and adult MLC1-CAT mice (Donoghue, M. J., Merlie, J. P., Rosenthal, N. and Sanes, J. R. (1991). Proc. Natl. Acad. Sci. USA 88, 5847–5851; Donoghue, M. J., Alvarez, J. D., Merlie, J. P. and Sanes, J. R. (1991). J. Cell Biol. 115, 423–434). Moreover, both in primary cultures

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Shi, Qi, Nana Feng, Qingyun Ma, et al. "ZNF354C Mediated by DNMT1 Ameliorates Lung Ischemia-Reperfusion Oxidative Stress Injury by Reducing TFPI Promoter Methylation to Upregulate TFPI." Oxidative Medicine and Cellular Longevity 2022 (July 19, 2022): 1–18. http://dx.doi.org/10.1155/2022/7288729.

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Background. Pulmonary ischemia reperfusion- (I/R-) induced dysfunction is a significant clinical problem after lung transplantation. In this study, we aim to explore the molecular mechanism of lung I/R injury (LIRI). Methods. Bioinformatic analysis of gene involved in oxidative stress. A HUVEC oxygen glucose deprivation/reoxygenation (OGD/R) model and I/R mouse model were first established via I/R. The cellular proliferation, migration, reactive oxygen species (ROS), and parameters of lung injury were assessed via CCK-8, EdU staining, Transwell, cellular ROS kit, and H&E staining. We also

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Stoccoro, Andrea, Martina Lari, Lucia Migliore, and Fabio Coppedè. "Associations between Circulating Biomarkers of One-Carbon Metabolism and Mitochondrial D-Loop Region Methylation Levels." Epigenomes 8, no. 4 (2024): 38. http://dx.doi.org/10.3390/epigenomes8040038.

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Background/Objectives: One-carbon metabolism is a critical pathway for epigenetic mechanisms. Circulating biomarkers of one-carbon metabolism have been associated with changes in nuclear DNA methylation levels in individuals affected by age-related diseases. More and more studies are showing that even mitochondrial DNA (mtDNA) could be methylated. In particular, methylation of the mitochondrial displacement (D-loop) region modulates the gene expression and replication of mtDNA and, when altered, can contribute to the development of human illnesses. However, no study until now has demonstrated

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Caspers, Maarten, Sara Blocquiaux, Ruben Charlier, et al. "Intensity-Specific Differential Leukocyte DNA Methylation in Physical (In)Activity: An Exploratory Approach." Twin Research and Human Genetics 21, no. 2 (2018): 101–11. http://dx.doi.org/10.1017/thg.2018.10.

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The aim of this exploratory study was to investigate how sedentary behavior (SB) and physical activity (PA) influence DNA methylation at a global, gene-specific, and health-related pathway level. SB, light PA (LPA), and moderate-to-vigorous PA (MVPA) were assessed objectively for 41 Flemish men using the SenseWear Pro 3 Armband. CpG site-specific methylation in leukocytes was determined using the Illumina HumanMethylation 450 BeadChip. Correlations were calculated between time spent on the three PA intensity levels and global DNA methylation, using a z-score-based method to determine global DN

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Knödlseder, Nastassia, Guillermo Nevot, Maria-José Fábrega, et al. "Engineering selectivity of Cutibacterium acnes phages by epigenetic imprinting." PLOS Pathogens 18, no. 3 (2022): e1010420. http://dx.doi.org/10.1371/journal.ppat.1010420.

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Cutibacterium acnes (C. acnes) is a gram-positive bacterium and a member of the human skin microbiome. Despite being the most abundant skin commensal, certain members have been associated with common inflammatory disorders such as acne vulgaris. The availability of the complete genome sequences from various C. acnes clades have enabled the identification of putative methyltransferases, some of them potentially belonging to restriction-modification (R-M) systems which protect the host of invading DNA. However, little is known on whether these systems are functional in the different C. acnes str

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Patel, Manishkumar S., Ellen K. Kendall, Sarah Ondrejka, et al. "Gene Expression and Epigenetic Analysis in Relapsed/Refractory Diffuse Large B Cell Lymphoma Provides Insights into Evolution of Treatment Resistance to R-CHOP." Blood 136, Supplement 1 (2020): 26. http://dx.doi.org/10.1182/blood-2020-138645.

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Background Diffuse large B cell lymphoma (DLBCL) is curable in ~60-70% of patients using standard chemoimmunotherapy, but the prognosis is poor for relapsed/refractory (R/R) DLBCL. Therefore, understanding the underlying molecular mechanisms will facilitate early prediction and effective management of resistance to therapy. Recent studies of paired diagnostic-relapse biopsies from patients have relied on a single "omics" approach, examining either gene expression or epigenetic evolution. Here we present a combined analysis of gene expression and DNA methylation profiles of paired diagnostic-re

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Phipson, Belinda, Jovana Maksimovic, and Alicia Oshlack. "missMethyl: an R package for analyzing data from Illumina’s HumanMethylation450 platform." Bioinformatics 32, no. 2 (2015): 286–88. http://dx.doi.org/10.1093/bioinformatics/btv560.

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Abstract Summary: DNA methylation is one of the most commonly studied epigenetic modifications due to its role in both disease and development. The Illumina HumanMethylation450 BeadChip is a cost-effective way to profile &gt;450 000 CpGs across the human genome, making it a popular platform for profiling DNA methylation. Here we introduce missMethyl, an R package with a suite of tools for performing normalization, removal of unwanted variation in differential methylation analysis, differential variability testing and gene set analysis for the 450K array. Availability and implementation: mi

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Vasilyev, S. A., E. N. Tolmacheva, E. A. Sazhenova, et al. "LINE-1 methylation index correlates with sister chromatid exchanges and chromatid but not chromosome aberrations in personnel from a nuclear chemical facility with incorporated plutonium-239." Генетика 60, no. 4 (2024): 114–22. http://dx.doi.org/10.31857/s0016675824040106.

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The level of chromosomal abnormalities in the somatic cells of adult individuals is characterized by significant interindividual variability, which may be partly affected by the genetic and epigenetic background. The epigenetic landscape in cells is largely determined by genome methylation. This study aimed to analyse the relationships between global genome methylation and the frequencies of chromosome abnormalities in lymphocytes of plutonium workers. The frequencies of chromosome aberrations, micronuclei, aneuploidy of chromosomes 2, 7, 8, 12, X and Y and sister chromatid exchanges were anal

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Ribeiro, Andre M., Hiruni Wijesena, Daniel C. Ciobanu, Steve Horvath, and Matthew L. Spangler. "PSIII-7 Relationship of Age and Genetics with the Methylation Profile of Beef Cattle." Journal of Animal Science 99, Supplement_1 (2021): 159. http://dx.doi.org/10.1093/jas/skab054.272.

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Abstract This study aimed to compare models for the prediction of cow age from DNA methylation profiles and estimate the heritability of the proportion of methylated sites (PM) and methylation status at each site (MS). Methylation data from blood samples of cows (n=136) were generated from the HorvathMammalMethylChip40 array that consists of 34,324 CpG sites that mapped to the bovine genome. Methylation status was determined by the distribution of the methylation values, with values above, within and below 2 standard deviations classified as methylated (2), intermediately methylated (1) and un

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Tawbi, H. A., S. Buch, P. Pancoska, et al. "Prediction of response to alkylator-based chemotherapy in metastatic melanoma (MM) using gene expression and promoter methylation signatures." Journal of Clinical Oncology 27, no. 15_suppl (2009): 9009. http://dx.doi.org/10.1200/jco.2009.27.15_suppl.9009.

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9009 Background: Temozolomide and dacarbazine (TMZ and DTIC) remain the mainstay of alkylator-based chemotherapy for MM, despite response rates of 10–15% and the absence of any impact on survival. Classification of patients according to responsiveness can guide the individualization of therapy and inform approaches to abrogate mechanisms of chemotherapy resistance. Epigenetic mechanisms play an important role in regulation of genes associated with resistance and were evaluated in tandem with gene expression profiling in biological samples from MM patients (pts) to refine our understanding of t

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Toussirot, E., S. Pasquereau, C. Vauchy, et al. "POS0329 ABERRANT GLOBAL DNA METHYLATION IN PERIPHERAL BLOOD CELL SUBPOPULATIONS OF PATIENTS WITH AXIAL SPONDYLOARTHRITIS." Annals of the Rheumatic Diseases 81, Suppl 1 (2022): 416–17. http://dx.doi.org/10.1136/annrheumdis-2022-eular.1876.

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BackgroundAxial spondyloarthritis (axSpA) corresponds to a group of chronic inflammatory diseases mainly affecting the axial skeleton. TNFα and IL-17A have been identified as key inflammatory mediators driving the inflammatory process of axSpA. Epigenetics refers to different mechanisms that alter gene expression without involving changes in DNA sequence. DNA methylation is an important epigenetic mechanism, playing a role in gene expression regulation. It is recognized that aberrant DNA methylation can result in immune cell autoreactivity.Objectivesepigenetic features have been rarely evaluat

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Hulme, Bethany, Altug Didikoglu, Steven Bradburn, et al. "Epigenetic Regulation of BMAL1 with Sleep Disturbances and Alzheimer’s Disease." Journal of Alzheimer's Disease 77, no. 4 (2020): 1783–92. http://dx.doi.org/10.3233/jad-200634.

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Background: An early symptom of Alzheimer’s disease (AD) is a disturbance of the circadian rhythm that is associated with disrupted sleep/wake cycles. Objective: To investigate if BMAL1, a key gene that drives the circadian cycle, is epigenetically regulated in brains in relation to longitudinal changes in cognition, sleep quality, and AD neuropathology. Methods: Frontal cortex tissues were acquired from the Manchester Brain Bank (N = 96). DNA methylation at six CpG sites at the promoter of BMAL1, determined using bisulfite pyrosequencing, was tested for associations with Braak stage, CERAD sc

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Steinicke, Til L., Salvatore Benfatto, Maria de los Reyes Capilla Guerra, et al. "Rapid Epigenomic Classification of Acute Leukemia." Blood 144, Supplement 1 (2024): 273. https://doi.org/10.1182/blood-2024-200868.

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Introduction Accurate molecular subtyping of acute leukemia (AL) is imperative for optimal risk stratification and treatment selection. Currently, diagnostic categories in AL are based on morphologic, immunophenotypic, and genetic features. However, these methods do not capture the full biological heterogeneity observed in AL, limiting further refinement of diagnostic and predictive categories. Additionally, current diagnostic approaches require a multitude of tests to be run in parallel, which can be costly, require special expertise, and lead to delays in care. To address these challenges, w

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Walker, Lauryn, Masar Radhi, Helen Knight, and Stuart Smith. "THE LINK BETWEEN M6A RNA METHYLATION AND R LOOPS IN PAEDIATRIC HIGH-GRADE GLIOMAS AND EPENDYMOMAS." Neuro-Oncology 25, Supplement_3 (2023): iii15. http://dx.doi.org/10.1093/neuonc/noad147.060.

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Abstract AIMS Paediatric high-grade glioma (HGG) and ependymoma (EPN) are two devastating malignant tumours of the central nervous system that unfortunately carry a poor prognosis. As R loops are a known source of genomic instability in eukaryotic cells and have previously been revealed to undergo m6A RNA methylation, we sought to investigate the potential link between m6A methylation and R loops in relation to the pathogenesis of paediatric gliomas. METHOD Paediatric HGG cell lines including KNS42, GCE62 and SF188, and paediatric EPN cell lines including BXD- 1425EPN and EPN9, were utilised f

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Spadotto, Valeria, Roberto Giambruno, Enrico Massignani, et al. "PRMT1-mediated methylation of the microprocessor-associated proteins regulates microRNA biogenesis." Nucleic Acids Research 48, no. 1 (2019): 96–115. http://dx.doi.org/10.1093/nar/gkz1051.

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Abstract MicroRNA (miRNA) biogenesis is a tightly controlled multi-step process operated in the nucleus by the activity of the Microprocessor and its associated proteins. Through high resolution mass spectrometry (MS)- proteomics we discovered that this complex is extensively methylated, with 84 methylated sites associated to 19 out of its 24 subunits. The majority of the modifications occurs on arginine (R) residues (61), leading to 81 methylation events, while 30 lysine (K)-methylation events occurs on 23 sites of the complex. Interestingly, both depletion and pharmacological inhibition of t

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Andreopoulos, Bill, and Dimitris Anastassiou. "Integrated Analysis Reveals hsa-miR-142 as a Representative of a Lymphocyte-Specific Gene Expression and Methylation Signature." Cancer Informatics 11 (January 2012): CIN.S9037. http://dx.doi.org/10.4137/cin.s9037.

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Gene expression profiling has provided insights into different cancer types and revealed tissue-specific expression signatures. Alterations in microRNA expression contribute to the pathogenesis of many types of human diseases. Few studies have integrated all levels of gene expression, miRNA and methylation to uncover correlations between these data types. We performed an integrated profiling to discover instances of miRNAs associated with a gene expression and DNA methylation signature across multiple cancer types. Using data from The Cancer Genome Atlas (TCGA), we revealed a concordant gene e

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Lu, Xiaolan, Xiangwen Gu, Yong Li, et al. "Biochemical characterization of RNase R 2′-O-methylation sensitivity." Biochimie 212 (September 2023): 106–13. http://dx.doi.org/10.1016/j.biochi.2023.04.016.

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Zhong, Xingming, Fenpin Jin, Chuican Huang, Mengxuan Du, Mengge Gao, and Xiangcai Wei. "DNA methylation of AMHRII and INSR gene is associated with the pathogenesis of Polycystic Ovary Syndrome (PCOS)." Technology and Health Care 29 (March 25, 2021): 11–25. http://dx.doi.org/10.3233/thc-218002.

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BACKGROUND: Polycystic ovary syndrome (PCOS) is a common gynecologic endocrinopathy, characterized by menstrual disorders, ovulation disorders, polycystic ovary, hyperandrogen syndrome and insulin resistance. At present, the etiology and exact pathogenesis of PCOS are still unclear. Anti-Müllerian hormone is a local regulator secreted by ovarian granulosa cells, and participates in regulating the occurrence and development of PCOS. Insulin resistance is another important pathophysiological feature of PCOS. Although the expression of anti-müllerian hormone receptor (AMHR) and insulin receptor (

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Iwagami, Shiro, Yoshifumi Baba, Masayuki Watanabe, et al. "The association between smoking and LINE-1 hypomethylation (global DNA hypomethylation) in normal esophageal epithelium of patients with esophageal squamous cell carcinoma." Journal of Clinical Oncology 30, no. 4_suppl (2012): 41. http://dx.doi.org/10.1200/jco.2012.30.4_suppl.41.

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41 Background: DNA methylation is a major epigenetic mechanism in X-chromosome inactivation, imprinting and repression of transposable elements and endogenous retroviral sequences. Global DNA hypomethylation appears to play an important role in genomic instability, leading to cancer development. DNA methylation in the long interspersed nucleotide element-1, L1 (LINE-1) repetitive element is a good indicator of global DNA methylation level. Smoking and alcohol is extremely important as the etiology of esophageal squamous cell carcinoma. Nonetheless, whether or not smoking and alcohol affect LIN

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Shi, Yiming, Yingying Qin, Yunshen Li, et al. "Comparative Analysis of CXCR5 Circulating DNA Methylation Levels in Autoimmune Rheumatic Diseases." Immunity, Inflammation and Disease 13, no. 1 (2025). https://doi.org/10.1002/iid3.70128.

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ABSTRACTObjectiveTo assess CXC chemokine receptor 5 (CXCR5) circulating DNA methylation differences in autoimmune rheumatic diseases and their relation with clinical features.MethodsTargeted methylation sequencing was performed using peripheral blood from 164 rheumatoid arthritis (RA), 30 systemic lupus erythematosus (SLE), 30 ankylosing spondylitis (AS), 30 psoriatic arthritis (PsA), 24 Sjögren's syndrome (SS) patients, and 30 healthy controls (HC).ResultsSignificant differences in CXCR5 cg19599951 methylation were found between RA and HC, as well as AS and SLE. RA patients exhibited higher m

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Li, Yuan, Zhiming Wang, Xiuwen Wu, et al. "Intestinal mucosa-derived DNA methylation signatures in the penetrating intestinal mucosal lesions of Crohn’s disease." Scientific Reports 11, no. 1 (2021). http://dx.doi.org/10.1038/s41598-021-89087-6.

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AbstractThe purpose of this study was to evaluate genome-wide DNA methylation changes in intestinal mucosa tissue of adult patients with Crohn's disease comprehensively. DNA methylation chip was used to analyze abnormal methylation sites among penetrating and non-penetrating intestinal mucosa tissue of Crohn's disease and normal intestinal mucosa tissue of healthy controls. Methylation abnormalities of different locus were verified by pyrosequencing and quantitative polymerase chain reaction. Differential DNA methylation sites were participated in the positive regulation of apoptosis and the p

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