83,295 results match your criteria dna methylation


Absence of CG methylation alters the long non-coding transcriptome landscape in multiple species.

FEBS Lett 2021 May 5. Epub 2021 May 5.

Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.

The non-coding regions throughout the genome are in large part comprised of transposable elements (TEs), some of which are functionalized with long intergenic non-coding RNAs (lincRNAs). DNA methylation is predominantly associated with TEs, but little is known about its contribution to the transcription of lincRNAs. Here, we examine the lincRNA profiles of DNA methylation-related mutants of five species, Arabidopsis, rice, tomato, maize, and mouse, to elucidate patterns in lincRNA regulation under altered DNA methylation status. Read More

View Article and Full-Text PDF

Whole Genomic DNA Methylation Profiling of CpG Sites in Promoter Regions of Dorsal Root Ganglion in Diabetic Neuropathic Pain Mice.

J Mol Neurosci 2021 May 5. Epub 2021 May 5.

Department of Neurobiology, School of Basic Medical Sciences, Advanced Innovation Center for Human Brain Protection, Capital Medical University, 100069, Beijing, China.

DNA methylation and demethylation play an important role in neuropathic pain. In general, DNA methylation of CpG sites in the promoter region impedes gene expression, whereas DNA demethylation contributes to gene expression. Here, we evaluated the methylation status of CpG sites in genomic DNA promoter regions in dorsal root ganglions (DRGs) of diabetic neuropathic pain (DNP) mice. Read More

View Article and Full-Text PDF

Activation-induced deaminase is critical for the establishment of DNA methylation patterns prior to the germinal center reaction.

Nucleic Acids Res 2021 May 5. Epub 2021 May 5.

Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain.

Activation-induced deaminase (AID) initiates antibody diversification in germinal center B cells by deaminating cytosines, leading to somatic hypermutation and class-switch recombination. Loss-of-function mutations in AID lead to hyper-IgM syndrome type 2 (HIGM2), a rare human primary antibody deficiency. AID-mediated deamination has been proposed as leading to active demethylation of 5-methycytosines in the DNA, although evidence both supports and casts doubt on such a role. Read More

View Article and Full-Text PDF

-MagnetoMethyl IP: a magnetic nanoparticle-mediated immunoprecipitation and electrochemical detection method for global DNA methylation.

Analyst 2021 May 5. Epub 2021 May 5.

Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, QLD 4111, Australia. and School of Environment and Science (ESC), Griffith University, Nathan Campus, QLD 4111, Australia.

The quantification of global 5-methylcytosine (5mC) content has emerged as a promising approach for the diagnosis and prognosis of cancers. However, conventional methods for the global 5mC analysis require large quantities of DNA and may not be useful for liquid biopsy applications, where the amount of DNA available is limited. Herein, we report magnetic nanoparticles-assisted methylated DNA immunoprecipitation (e-MagnetoMethyl IP) coupled with electrochemical quantification of global DNA methylation. Read More

View Article and Full-Text PDF

DNA methylation-based profiling of bone and soft tissue tumours: a validation study of the 'DKFZ Sarcoma Classifier'.

J Pathol Clin Res 2021 May 5. Epub 2021 May 5.

Research Department of Pathology, University College London, UCL Cancer Institute, London, UK.

Diagnosing bone and soft tissue neoplasms remains challenging because of the large number of subtypes, many of which lack diagnostic biomarkers. DNA methylation profiles have proven to be a reliable basis for the classification of brain tumours and, following this success, a DNA methylation-based sarcoma classification tool from the Deutsches Krebsforschungszentrum (DKFZ) in Heidelberg has been developed. In this study, we assessed the performance of their classifier on DNA methylation profiles of an independent data set of 986 bone and soft tissue tumours and controls. Read More

View Article and Full-Text PDF

The shifting landscape of genetic alterations separating endometriosis and ovarian endometrioid carcinoma.

Am J Cancer Res 2021 15;11(4):1754-1769. Epub 2021 Apr 15.

Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy Cluj-Napoca, Cluj 400337, Romania.

Ovarian cancer is one of the most common cancers worldwide, and is associated with a prior diagnosis of endometriosis in several cases. Our aim was to correlate genetic and methylation profile of ovarian endometrioid ovarian cancer and endometriosis patients. We evaluated the genetic profile of 50 ovarian endometriosis and 20 ovarian endometrioid carcinoma samples using next generation sequencing technology. Read More

View Article and Full-Text PDF

Optimal tissue sampling during ERCP and emerging molecular techniques for the differentiation of benign and malignant biliary strictures.

Therap Adv Gastroenterol 2021 15;14:17562848211002023. Epub 2021 Apr 15.

Department of Gastroenterology & Hepatology, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, Room Na-609, Rotterdam, 3015 GD, The Netherlands.

Patients with cholangiocarcinoma have poor survival since the majority of patients are diagnosed at a stage precluding surgical resection, due to locally irresectable tumors and/or metastases. Optimization of diagnostic strategies, with a principal role for tissue diagnosis, is essential to detect cancers at an earlier stage amenable to curative treatment. Current barriers for a tissue diagnosis include both insufficient tissue sampling and a difficult cyto- or histopathological assessment. Read More

View Article and Full-Text PDF

The genomic landscape of carcinomas with mucinous differentiation.

Sci Rep 2021 May 4;11(1):9478. Epub 2021 May 4.

Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, Box 20, New York, NY, 10065, USA.

Mucinous carcinomas can arise in any organ with epithelial cells that produce mucus. While mucinous tumors from different organs are histologically similar, it remains to be elucidated whether they share molecular alterations. Here we analyzed a total of 902 patients across six cancer types by comparing mucinous and non-mucinous samples, integrating text mining of pathology reports, gene expression, methylation, mutational and copy-number profiling. Read More

View Article and Full-Text PDF

Moderate DNA hypomethylation suppresses intestinal tumorigenesis by promoting caspase-3 expression and apoptosis.

Oncogenesis 2021 May 4;10(5):38. Epub 2021 May 4.

Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.

Global DNA hypomethylation is a most common epigenetic alteration in human neoplasia. However, accumulative evidence shows that global DNA hypomethylation impacts tumorigenesis in a tissue-specific manner, promoting tumorigenesis in some but suppressing tumorigenesis in others including colorectal cancer. The underlying mechanisms, especially how DNA hypomethylation suppresses tumorigenesis, remain largely unknown. Read More

View Article and Full-Text PDF

Detection of Molecular Signatures of Homologous Recombination Deficiency in Bladder Cancer.

Clin Cancer Res 2021 May 4. Epub 2021 May 4.

Children's Hospital Informatics Program at the Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School

Purpose: PARP inhibitors are approved for use in breast, ovarian, prostate and pancreatic cancer, which are the solid tumor types that most frequently have alterations in key homologous recombination (HR) genes, such as However, the frequency of HR deficiency in other solid tumor types, including bladder cancer, is less well characterized.

Experimental Design: Specific DNA aberration profiles (mutational signatures) are induced by homologous recombination deficiency (HRD) and the presence of these "genomic scars" can be used to assess the presence or absence of HR deficiency in a given tumor biopsy even in the absence of an observed alteration of an HR gene. Using whole exome and whole genome data, we measured various HR deficiency-associated mutational signatures in bladder cancer. Read More

View Article and Full-Text PDF

Development of a prognostic risk model for clear cell renal cell carcinoma by systematic evaluation of DNA methylation markers.

Clin Epigenetics 2021 May 4;13(1):103. Epub 2021 May 4.

Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands.

Background: Current risk models for renal cell carcinoma (RCC) based on clinicopathological factors are sub-optimal in accurately identifying high-risk patients. Here, we perform a head-to-head comparison of previously published DNA methylation markers and propose a potential prognostic model for clear cell RCC (ccRCC).

Patients And Methods: Promoter methylation of PCDH8, BNC1, SCUBE3, GREM1, LAD1, NEFH, RASSF1A, GATA5, SFRP1, CDO1, and NEURL was determined by nested methylation-specific PCR. Read More

View Article and Full-Text PDF

Statin therapy is associated with epigenetic modifications in individuals with type 2 diabetes.

Epigenomics 2021 May 5. Epub 2021 May 5.

Department of Clinical Sciences, Epigenetics & Diabetes Unit, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö 205 02, Sweden.

Statins lower cholesterol and reduce the risk of cardiovascular disease. However, the exact mechanisms of statins remain unknown. We investigated whether statin therapy associates with epigenetics in type 2 diabetes (T2D) patients. Read More

View Article and Full-Text PDF

Saliva Gene Promoter Hypermethylation as a Biomarker in Oral Cancer.

J Clin Med 2021 Apr 29;10(9). Epub 2021 Apr 29.

Department of Surgery and Medical-Surgical Specialties, Medicine and Dentistry School, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.

Oral carcinogenesis is a multistep process characterized by a summation of multiple genetic and epigenetic alterations in key regulatory genes. The silencing of genes by aberrant promoter hypermethylation is thought to be an important epigenetic event in cancer development and progression which has great potential as a biomarker for early diagnosis, tumor molecular subtyping, prognosis, monitoring, and therapy. Aberrant DNA methylation has been detected in different liquid biopsies, which may represent a potential alternative to solid biopsies. Read More

View Article and Full-Text PDF

High-Throughput Detection of Multiple miRNAs and Methylated DNA by Droplet Digital PCR.

J Pers Med 2021 Apr 29;11(5). Epub 2021 Apr 29.

Department of Pathology, University of Maryland School of Medicine, 10 S. Pine St., Baltimore, MD 21201, USA.

Altered miRNA expression and DNA methylation have highly active and diverse roles in carcinogenesis. Simultaneous detection of the molecular aberrations may have a synergistic effect on the diagnosis of malignancies. Herein, we develop a high-throughput assay for detecting multiple miRNAs and DNA methylation using droplet digital PCR (ddPCR) coupled with a 96-microwell plate. Read More

View Article and Full-Text PDF

CpG Methylation Profiles of HIV-1 Pro-Viral DNA in Individuals on ART.

Viruses 2021 04 29;13(5). Epub 2021 Apr 29.

Department of Molecular Biology and Microbiology, Tufts University, Boston, MA 02129, USA.

The latent HIV-1 reservoir is comprised of stably integrated and intact proviruses with limited to no viral transcription. It has been proposed that latent infection may be maintained by methylation of pro-viral DNA. Here, for the first time, we investigate the cytosine methylation of a replication competent provirus (AMBI-1) found in a T cell clone in a donor on antiretroviral therapy (ART). Read More

View Article and Full-Text PDF

DNA Methylation Change Profiling of Colorectal Disease: Screening towards Clinical Use.

Authors:
Joo Mi Yi

Life (Basel) 2021 Apr 30;11(5). Epub 2021 Apr 30.

Department of Microbiology and Immunology, College of Medicine, Inje University, Busan 47392, Korea.

Colon cancer remains one of the leading causes of cancer-related deaths worldwide. Transformation of colon epithelial cells into invasive adenocarcinomas has been well known to be due to the accumulation of multiple genetic and epigenetic changes. In the past decade, the etiology of inflammatory bowel disease (IBD) which is characterized by chronic inflammation of the intestinal mucosa, was only partially explained by genetic studies providing susceptibility loci, but recently epigenetic studies have provided critical evidences affecting IBD pathogenesis. Read More

View Article and Full-Text PDF

Novel dopamine receptor 3 antagonists inhibit the growth of primary and temozolomide resistant glioblastoma cells.

PLoS One 2021 4;16(5):e0250649. Epub 2021 May 4.

Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States of America.

Treatment for the lethal primary adult brain tumor glioblastoma (GBM) includes the chemotherapy temozolomide (TMZ), but TMZ resistance is common and correlates with promoter methylation of the DNA repair enzyme O-6-methylguanine-DNA methyltransferase (MGMT). To improve treatment of GBMs, including those resistant to TMZ, we explored the potential of targeting dopamine receptor signaling. We found that dopamine receptor 3 (DRD3) is expressed in GBM and is also a previously unexplored target for therapy. Read More

View Article and Full-Text PDF

Evaluation of the Genetic Association and Methylation of Immune Response Pathway Genes with the Risk of Chronic Periodontitis in the Uighur Population.

Genet Test Mol Biomarkers 2021 May 4. Epub 2021 May 4.

Department of Endodontics, First Affiliated Hospital of Xinjiang Medical University, and College of Stomatology of Xinjiang Medical University, Urumqi, China.

The aim of this study was to explore the possible associations between single nucleotide polymorphisms (SNPs) and DNA methylation levels of seven genes in the inflammatory response pathway with susceptibility to chronic periodontitis (CP) among the Uighur population of the Xinjiang Autonomous Region of China. A total of 444 eligible subjects (279 CP patients and 165 healthy controls) were enrolled in the study. Genomic DNA was obtained from gingival tissue for genotyping eight SNPs and performing methylation measurements of seven genes. Read More

View Article and Full-Text PDF

Novel and emerging biotechnological crop protection approaches.

Plant Biotechnol J 2021 May 4. Epub 2021 May 4.

Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics, CREA-VE), Via XXVIII Aprile 26, 31015, Conegliano, TV, Italy.

Traditional breeding or Genetically Modified Organisms (GMOs) have for a long time been the sole approaches to effectively cope with biotic and abiotic stresses and implement the quality traits of crops. However, emerging diseases as well as unpredictable climate changes affecting agriculture over the entire globe forces scientists to find alternative solutions required to quickly overcome seasonal crises. In this review, we first focus on cisgenesis and genome editing as challenging biotechnological approaches for breeding crops more tolerant to biotic and abiotic stresses. Read More

View Article and Full-Text PDF

Genome-wide DNA methylation analysis and biochemical responses provide insights into the initial domestication of halophyte Puccinellia tenuiflora.

Plant Cell Rep 2021 May 4. Epub 2021 May 4.

Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.

Key Message: Puccinellia tenuiflora was domesticated for two years by growing it under non-saline conditions, providing epigenetic and biochemical insights into the initial domestication of extreme halophytes. Some halophytes have economic value as crop species. The domestication of halophytes may offer hope in solving the problem of soil salinization. Read More

View Article and Full-Text PDF

Molecular and morphological findings in a sample of oral surgery patients: What can we learn for multivariate concepts for age estimation?

J Forensic Sci 2021 May 4. Epub 2021 May 4.

Institute of Legal Medicine, University Hospital Duesseldorf, Duesseldorf, Germany.

It has already been proposed that a combined use of different molecular and morphological markers of aging in multivariate models may result in a greater accuracy of age estimation. However, such an approach can be complex and expensive, and not every combination may be useful. The significance and usefulness of combined analyses of D-aspartic acid in dentine, pentosidine in dentine, DNA methylation in buccal swabs at five genomic regions (PDE4C, RPA2, ELOVL2, DDO, and EDARADD), and third molar mineralization were tested by investigating a sample of 90 oral surgery patients. Read More

View Article and Full-Text PDF

The relationship of childhood trauma and DNA methylation of NMDA receptor genes in first-episode schizophrenia.

Epigenomics 2021 May 4. Epub 2021 May 4.

Department of Internal Medicine, Division of Clinical Immunology, Ribeirão Preto Medical School, University of São Paulo, 14049 9002, Brazil.

We investigated and DNA methylation in first-episode schizophrenia patients, their nonaffected siblings and age- and sex-matched controls testing for associations between DNA methylation and exposition to childhood trauma. The Childhood Trauma Questionnaire evaluated the history of childhood trauma. Genomic DNA was bisulfite converted and pyrosequencing was employed to quantify DNA methylation. Read More

View Article and Full-Text PDF

DNA repair in neurons and its possible link to the epigenetic machinery at enhancers.

Authors:
Gerd P Pfeifer

Epigenomics 2021 May 4. Epub 2021 May 4.

Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA.

View Article and Full-Text PDF

Early life trauma, DNA methylation and mental illness.

Authors:
Gavin P Reynolds

Epigenomics 2021 May 4. Epub 2021 May 4.

Biomolecular Sciences Research Centre, Sheffield Hallam University, Howard Street, Sheffield S1 1WB, UK.

View Article and Full-Text PDF

methylation is associated with bipolar disorder and the isoform expression and methylation of myelin genes.

Epigenomics 2021 May 4. Epub 2021 May 4.

Hospital Universitari Institut Pere Mata, Ctra. de l'Institut Pere Mata, s/n. 43206, Reus, Catalonia, Spain.

To investigate  methylation in the brains of bipolar disorder (BD) patients and its association with mRNA levels and comethylation with myelin genes. Genome-wide profiling of DNA methylation (Infinium MethylationEPIC BeadChip) corrected for glial composition and gene expression analysis in the occipital cortices of individuals with BD (n = 15) and healthy controls (n = 15) were conducted. 5-methylcytosine levels were increased and directly associated with b mRNA expression in the brains of BD patients. Read More

View Article and Full-Text PDF

Associations between Maternal Psychosocial Stress, DNA Methylation, and Newborn Birth Weight Identified by Investigating Methylation at Individual, Regional, and Genome Levels.

Hum Biol 2019 Apr;91(2):117-131

Department of Anthropology, University of Florida, Gainesville, Florida, USA.

Stress is known to affect health throughout life and into future generations, but the underlying molecular mechanisms are unknown. We tested the hypothesis that maternal psychosocial stress influences DNA methylation (DNAm), which in turn impacts newborn health outcomes. Specifically, we analyzed DNAm at individual, regional, and genome-wide levels to test for associations with maternal stress and newborn birth weight. Read More

View Article and Full-Text PDF

Detection and relevance of epigenetic markers on ctDNA: recent advances and future outlook.

Authors:
Evi Lianidou

Mol Oncol 2021 May 3. Epub 2021 May 3.

Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, University of Athens, 15771, Athens, Greece.

Liquid biopsy, a minimally invasive approach, is a highly powerful clinical tool for the real-time follow up of cancer and overcomes many limitations of tissue biopsies. Epigenetic alterations have a high potential to provide a valuable source of innovative biomarkers for cancer, owing to their stability, frequency and non-invasive accessibility in bodily fluids. Numerous DNA methylation markers are now tested in circulating tumor DNA (ctDNA) as potential biomarkers, in various types of cancer. Read More

View Article and Full-Text PDF

Site-specific identification and validation of hepatic histone nitration in vivo: Implications for alcohol-induced liver injury.

J Mass Spectrom 2021 Jun;56(6):e4713

Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 E. Fowler Ave, Tampa, FL, 33620, USA.

Oxidative and nitrative stress have been implicated in the molecular mechanisms underlying a variety of biological processes and disease states including cancer, aging, cardiovascular disease, neurological disorders, diabetes, and alcohol-induced liver injury. One marker of nitrative stress is the formation of 3-nitrotyrosine, or protein tyrosine nitration (PTN), which has been observed during inflammation and tissue injury; however, the role of PTN in the progression or possibly the pathogenesis of disease is still unclear. We show in a model of alcohol-induced liver injury that an increase in PTN occurs in hepatocyte nuclei within the liver of wild-type male C57BL/6J mice following chronic ethanol exposure (28 days). Read More

View Article and Full-Text PDF

FVE promotes RNA-directed DNA methylation by facilitating the association of RNA polymerase V with chromatin.

Plant J 2021 May 3. Epub 2021 May 3.

National Institute of Biological Sciences, Beijing, 102206, China.

Association of RNA polymerase V (Pol V) with chromatin is a critical step for RNA- directed DNA methylation (RdDM) in plants. Although the methylated-DNA-binding proteins SUVH2 and SUVH9 and the chromatin-remodeler-containing complex DDR are known to be required for the association of Pol V with chromatin, the molecular mechanisms underlying the association of Pol V with different chromatin environments remain largely unknown. Here we found that SUVH9 interacts with FVE, a homologue of the mammalian retinoblastoma-associated protein, which has been previously identified as a shared subunit of the histone deacetylase complex and the polycomb-type histone H3K27 trimethyltransferase complex. Read More

View Article and Full-Text PDF

Inflammatory bowel disease and psoriasis: modernizing the multidisciplinary approach.

J Intern Med 2021 May 4. Epub 2021 May 4.

From the, Department of Medicine, Karolinska Institutet, Solna, Stockholm, Sweden.

Psoriasis and inflammatory bowel disease (IBD) are immune-mediated diseases occurring in barrier organs whose main task is to protect the organism from attack. These disorders are highly prevalent especially in northern Europe where psoriasis has a prevalence of around 3-4% and IBD around 0.3%. Read More

View Article and Full-Text PDF