scholarly journals Cell type‐specific DNA methylation analysis of the prefrontal cortex of patients with schizophrenia

2021 ◽  
Author(s):  
Junko Ueda ◽  
Miki Bundo ◽  
Yutaka Nakachi ◽  
Kiyoto Kasai ◽  
Tadafumi Kato ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Prefrontal Cortex ◽  
Cell Type ◽  
Methylation Analysis ◽  
Cell Type Specific ◽  
Dna Methylation Analysis

scholarly journals eFORGE v2.0: updated analysis of cell type-specific signal in epigenomic data

2019 ◽  
Vol 35 (22) ◽  
pp. 4767-4769 ◽  
Author(s):  
Charles E Breeze ◽  
Alex P Reynolds ◽  
Jenny van Dongen ◽  
Ian Dunham ◽  
John Lazar ◽  
...  
Keyword(s):  
Supplementary Information ◽  
Supplementary Data ◽  
Cell Type ◽  
Web Tool ◽  
Methylation Analysis ◽  
450K Array ◽  
Composition Effects ◽  
Epigenome Editing ◽  
Cell Type Specific ◽  
Dna Methylation Analysis

Abstract Summary The Illumina Infinium EPIC BeadChip is a new high-throughput array for DNA methylation analysis, extending the earlier 450k array by over 400 000 new sites. Previously, a method named eFORGE was developed to provide insights into cell type-specific and cell-composition effects for 450k data. Here, we present a significantly updated and improved version of eFORGE that can analyze both EPIC and 450k array data. New features include analysis of chromatin states, transcription factor motifs and DNase I footprints, providing tools for epigenome-wide association study interpretation and epigenome editing. Availability and implementation eFORGE v2.0 is implemented as a web tool available from https://eforge.altiusinstitute.org and https://eforge-tf.altiusinstitute.org/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Cell-type-specific DNA methylation analysis of the frontal cortices of mutant Polg1 transgenic mice with neuronal accumulation of deleted mitochondrial DNA

2022 ◽  
Vol 15 (1) ◽  
Author(s):  
Hiroko Sugawara ◽  
Miki Bundo ◽  
Takaoki Kasahara ◽  
Yutaka Nakachi ◽  
Junko Ueda ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Mitochondrial Dna ◽  
Transgenic Mice ◽  
Molecular Motor ◽  
Methylation Analysis ◽  
Behavioral Abnormalities ◽  
Gene Environment ◽  
Postmortem Brains ◽  
Cell Type Specific ◽  
Dna Methylation Analysis

AbstractBipolar disorder (BD) is a severe psychiatric disorder characterized by repeated conflicting manic and depressive states. In addition to genetic factors, complex gene–environment interactions, which alter the epigenetic status in the brain, contribute to the etiology and pathophysiology of BD. Here, we performed a promoter-wide DNA methylation analysis of neurons and nonneurons derived from the frontal cortices of mutant Polg1 transgenic (n = 6) and wild-type mice (n = 6). The mutant mice expressed a proofreading-deficient mitochondrial DNA (mtDNA) polymerase under the neuron-specific CamK2a promoter and showed BD-like behavioral abnormalities, such as activity changes and altered circadian rhythms. We identified a total of 469 differentially methylated regions (DMRs), consisting of 267 neuronal and 202 nonneuronal DMRs. Gene ontology analysis of DMR-associated genes showed that cell cycle-, cell division-, and inhibition of peptide activity-related genes were enriched in neurons, whereas synapse- and GABA-related genes were enriched in nonneurons. Among the DMR-associated genes, Trim2 and Lrpprc showed an inverse relationship between DNA methylation and gene expression status. In addition, we observed that mutant Polg1 transgenic mice shared several features of DNA methylation changes in postmortem brains of patients with BD, such as dominant hypomethylation changes in neurons, which include hypomethylation of the molecular motor gene and altered DNA methylation of synapse-related genes in nonneurons. Taken together, the DMRs identified in this study will contribute to understanding the pathophysiology of BD from an epigenetic perspective.

scholarly journals P46.03 DNA Methylation Analysis in Smokers and Non-Smokers (Passive and ex-Smokers)

2021 ◽  
Vol 16 (3) ◽  
pp. S490
Author(s):  
D.M. Aguilar-Beltrán ◽  
A.G. Alcázar-Ramos ◽  
A.L. Vega-Rodríguez ◽  
D.G. García-Gutiérrez ◽  
A.D. Bertadillo-Jilote ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Methylation Analysis ◽  
Dna Methylation Analysis

scholarly journals DNA Methylation in Solid Tumors: Functions and Methods of Detection

2021 ◽  
Vol 22 (8) ◽  
pp. 4247
Author(s):  
Andrea Martisova ◽  
Jitka Holcakova ◽  
Nasim Izadi ◽  
Ravery Sebuyoya ◽  
Roman Hrstka ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Solid Tumors ◽  
Epigenetic Modification ◽  
Single Gene ◽  
Restriction Enzymes ◽  
Methylation Analysis ◽  
Cpg Dinucleotides ◽  
Sequencing Technologies ◽  
Genome Level ◽  
Dna Methylation Analysis

DNA methylation, i.e., addition of methyl group to 5′-carbon of cytosine residues in CpG dinucleotides, is an important epigenetic modification regulating gene expression, and thus implied in many cellular processes. Deregulation of DNA methylation is strongly associated with onset of various diseases, including cancer. Here, we review how DNA methylation affects carcinogenesis process and give examples of solid tumors where aberrant DNA methylation is often present. We explain principles of methods developed for DNA methylation analysis at both single gene and whole genome level, based on (i) sodium bisulfite conversion, (ii) methylation-sensitive restriction enzymes, and (iii) interactions of 5-methylcytosine (5mC) with methyl-binding proteins or antibodies against 5mC. In addition to standard methods, we describe recent advances in next generation sequencing technologies applied to DNA methylation analysis, as well as in development of biosensors that represent their cheaper and faster alternatives. Most importantly, we highlight not only advantages, but also disadvantages and challenges of each method.

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