Tag: DMRs

Transcription factor-mediated direct cellular reprogramming yields cell-type specific DNA methylation signature

iISC-BOs exhibit a CpG methylation signature that closely resembles ISC-BOs Genomic DNA was extracted from MEFs, iISC-BOs, and ISC-BOs, and high-resolution methylome analysis was performed using the PBAT method (Fig. 1A). The genome-wide methylation states of cytosine-containing sequences such as CpG, CHH, and CHG were compared among the samples. The data…

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Conserved and divergent gene regulatory programs of the mammalian neocortex

Nucleus preparation from frozen brain tissue for Chromium single-cell multiome ATAC and gene expression analysis M1 tissue was obtained from three human donors (male, aged 42, 29 and 58 years), three macaque donors (male, aged 6 (Macaca mulatta), 6 (M. mulatta) and 14 (Macaca fascicularis) years), three marmoset (Callithrix jacchus)…

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Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain

Mouse brain tissues All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee under protocol number 18-00006. Adult (P56) C57BL/6J male mice were purchased from the Jackson Laboratory at 7 weeks of age and maintained in the Salk animal barrier facility on 12-h dark–light…

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Methylation Analysis Tutorial in R_part1

The code and approaches that I share here are those I am using to analyze TCGA methylation data. At the bottom of the page, you can find references used to make this tutorial. If you are coming from a computer background, please bear with a geneticist who tried to code…

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Transgenerational epigenetic effects imposed by neonicotinoid thiacloprid exposure

This study is aimed at revealing the transgenerational effects of thia. We chose the developmental window from embryonic days 6.5 to E15.5 because of its importance in germ cell program establishment. The mice breeding was described in the Materials and Methods section “Mouse treatment and dissection.” The design of the…

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Measuring DNA in dead nerve cells may help diagnose Alzheimer’s

A novel technique that detects DNA from dead nerve cells in the blood may help diagnose Alzheimer’s disease and predict its development with a five-year window among people with mild cognitive impairment, a new study showed. The work was led by scientists at Resonant, a subsidiary of Renew Biotechnologies, which…

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New Biomarker Promises Earlier Diagnosis of Alzheimer’s Disease

Credit: Naeblys / Getty Images Renew Biotechnologies’ subsidiary Resonant recently published research in the journal Frontiers in Neurology of a new blood biomarker that promises earlier diagnosis of Alzheimer’s disease (AD). The approach, which centers on the use of cell-free DNA (cfDNA) analyzes differential methylation regions (DMRs) to identify biomarkers…

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epialleleR: an R/Bioconductor package for sensitive allele-specific methylation analysis in NGS data | GigaScience

Abstract Low-level mosaic epimutations within the BRCA1 gene promoter occur in 5–8% of healthy individuals and are associated with a significantly elevated risk of breast and ovarian cancer. Similar events may also affect other tumor suppressor genes, potentially being a significant contributor to cancer burden. While this opens a new…

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TET2 modulates spatial relocalization of heterochromatin in aged hematopoietic stem and progenitor cells

Animal models Animal studies were approved by the Institutional Animal Care Use Committee of the Institute of Biosciences and Technology, Texas A&M University (AUP 2020-0195). Most mouse strains bear a C57BL/6 genetic background unless otherwise noted. All the animals were housed in a certified animal facility with a standard dark/light…

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Cell-Free Liquid Biopsy Test for Ovarian Cancer Proves 91% Accurate

ovarian cancer | Image credit: Crystal light – stock.adobe.com A recent analysis investigating the use of an experimental cell-free DNA (cfDNA) liquid biopsy found that the test was 91% accurate at identifying early-stage epithelial ovarian cancer (EOC), a higher rate than that of other tests currently available. The study, published…

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Cell-Free DNA Methylation Liquid Biopsy Discriminates Ovarian Cancer – Consumer Health News

THURSDAY, Oct. 19, 2023 (HealthDay News) — A classifier based on cell-free DNA (cfDNA) methylation liquid biopsy can discriminate high-grade serous ovarian carcinoma (HGSOC) from benign masses, according to a study published online Oct. 9 in Clinical Cancer Research. David N. Buckley, from the University of Southern California in Los…

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Cell-Free DNA Methylation Liquid Biopsy Discriminates Ovarian Cancer | Health

THURSDAY, Oct. 19, 2023 (HealthDay News) — A classifier based on cell-free DNA (cfDNA) methylation liquid biopsy can discriminate high-grade serous ovarian carcinoma (HGSOC) from benign masses, according to a study published online Oct. 9 in Clinical Cancer Research. David N. Buckley, from the University of Southern California in Los…

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Detection of Neuron-Derived cfDNA in Blood Plasma: A New Diagnostic Approach for Neurodegenerative Conditions

1Brigham Young University, United States 2The University of Utah, United States The final, formatted version of the article will be published soon. Notify me Receive an email when it is updated You just subscribed to receive the final version of the article …

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Diagnosing and monitoring pancreatic cancer through cell-free DNA methylation: progress and prospects | Biomarker Research

The exploration of methylated biomarkers in plasma for pancreatic cancer is still in its early stages, and the number of studies conducted to date for this purpose is limited. Analysis of cfDNA methylation patterns in pancreatic cancer has been approached both at the whole genome level and by identifying and…

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Program for Overlapping DMRs (Differentially Methylated Regions) Between Groups

Program for Overlapping DMRs (Differentially Methylated Regions) Between Groups 0 I have the methylation results from 3 different groups (young, adult, old) that I’ve processed and have used mcomp to merge ratio files from the same group together and did group comparisons (i.e. young_Vs_adult, adult_Vs_old, young_Vs_old). I’m looking for a…

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Altered cfDNA fragmentation profile in hypomethylated regions as diagnostic markers in breast cancer

Background: Breast cancer, the most common malignancy in women worldwide, has been proven to have both altered plasma cell-free DNA (cfDNA) methylation and fragmentation profiles. Nevertheless, simultaneously detecting both of them for breast cancer diagnosis has never been reported. Moreover, although fragmentation pattern of cfDNA is determined by nuclease digestion…

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Additional file 1 of Altered cfDNA fragmentation profile in hypomethylated regions as diagnostic markers in breast cancer

dataset posted on 2023-09-23, 03:17 authored by Jun Wang, Yanqin Niu, Ming Yang, Lirong Shu, Hongxian Wang, Xiaoqian Wu, Yaqin He, Peng Chen, Guocheng Zhong, Zhixiong Tang, Shasha Zhang, Qianwen Guo, Yun Wang, Li Yu, Deming Gou Additional file 1: Table S1. Summary of patients and samples analyzed in this…

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Systemic epigenome-wide association study of elk treponeme-associated hoof disease

Study samples were obtained from Rocky Mountain elk collected in Washington, Idaho, and South Dakota and from Roosevelt elk from Washington, Oregon, and California. Only cases with required metadata (location of collection and sex) and confirmed diagnosis of TAHD present or not detected were included in the analysis. Treponeme-associated hoof…

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BiocMAP: a Bioconductor-friendly, GPU-accelerated pipeline for bisulfite-sequencing data | BMC Bioinformatics

Overview In the first alignment module, FASTQ files are checked with FastQC 0.11.8 [15], and by default samples that fail the “Adapter Content” metric are trimmed using Trim Galore! 0.6.6 [16] (see Methods: Configuration for alternative trimming options). The resulting FASTQ files are aligned to a reference genome using the…

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Molecular control of endurance training adaptation in male mouse skeletal muscle

A surprisingly low number of genes define the trained muscle To study differences between untrained and endurance-trained muscles (in the present study, muscle always refers to quadriceps), mice were exercised by treadmill running on 5 d per week for 1 h. After 4 weeks, a significant improvement in running performance was observed (Extended…

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Top 25 Bioconductor Interview Questions and Answers

Bioconductor is an open-source software project that provides tools for the analysis and comprehension of high-throughput genomic data. It’s a powerful tool, widely used in bioinformatics and computational biology to process and analyze intricate biological data. Bioconductor’s strength lies in its vast array of packages specifically tailored for genomics research,…

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Evaluation of the pooled sample method in Infinium MethylationEPIC BeadChip array by comparison with individual samples

Background: The pooled sample method is used in epigenomic research and expression analysis and is a cost-effective screening approach for small amounts of DNA. Evaluation of the pooled sample method in epigenomic studies is performed using the Illumina Infinium Methylation 450K BeadChip array; however, subsequent reports on the updated 850K…

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Analysis of Methylation in Esophageal Tumors, Nonmalignant Tissue

Cell type-specific partially methylated domains and differentially methylated domains found in normal cells persist in malignant cells, researchers from Cedars-Sinai Medical Center in Los Angeles and elsewhere report in Genome Biology. They analyzed the whole-genome bisulfite sequencing profiles of 45 esophageal tumors, representing both the squamous cell carcinoma and adenocarcinoma…

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A tool for rapid, automated characterization of population epigenomics in plants

Creation and sequencing of epigenetically diverse plant populations To induce epigenetic variation, A. thaliana seeds were treated with three different concentrations of zebularine. We will describe these three different zebularine concentration groups, and our water and DMSO controls as “populations” throughout the remainder of this paper. Plants displayed stunted vegetative…

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Transient naive reprogramming corrects hiPS cells functionally and epigenetically

Cell culture All cell lines used and derived by different approaches in this study are listed in Supplementary Table 1. Detailed information about the experimental design, materials and reagents is presented in the Reporting Summary. Primary human adult dermal fibroblasts (HDFa) from three different female donors were obtained from Gibco…

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Differentially expressed genes in breast cancer

Introduction Breast cancer represents the most frequently diagnosed and fatal malignant neoplasm among women worldwide. In 2020, breast cancer accounted for the fifth-highest rate of cancer death.1 Current data indicates that cancer is both a hereditary and epigenetic disease. Many major aspects of tumor biology are controlled by epigenetic modifications,…

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Bioconductor – RRBSdata

DOI: 10.18129/B9.bioc.RRBSdata     This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see RRBSdata. An RRBS data set with 12 samples and 10,000 simulated DMRs Bioconductor version: 3.14 RRBS data set comprising 12 samples with simulated differentially methylated regions (DMRs). Author: Katja Hebestreit, Hans-Ulrich…

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Study investigates genetic and DNA methylation variation in four Chinese ethnic groups

(A) The genetic structure of the population based on population SNPs. (B) The epigenetic structure of the population based on ethnic-specific DNA methylation sites. (C) The distribution curve of correlation values estimated between overall genetic distances and CpG methylation Manhattan distances of CpGs sorted with the values of Pst, the…

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SOMNiBUS and WGBS Offer Insights into SSc Pathogenesis

A new study has re-analyzed data obtained by whole genome bisulfate sequencing (WGBS) using the newly developed regional analysis approach known as SOMNiBUS and achieved additional insights into the cytosine DNA methylation patterns and pathogenesis of systemic sclerosis (SSc). The study, published in Clinical Epigenetics, also found their approach generated…

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Assessing Methylation-Based Sequencing as a Risk-Stratifying Tool in MDS

Methylation-based sequencing appears to be a viable risk-assessment tool for myelodysplastic syndromes (MDS), according to a study presented at the 2023 American Society of Clinical Oncology Annual Meeting. “MDS risk stratification is key for [making] optimal treatment decisions. DNA methylation is associated with MDS biology due to frequent somatic mutations…

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Epigenomics Data Analysis Service – CD Genomics

Epigenomics, a rapidly advancing field within genomics, delves into the intricate mechanisms that regulate gene expression through chemical modifications to DNA and associated proteins. These epigenetic changes have profound implications for various biological processes and can influence the development of diseases. As the understanding of epigenomics expands, so does the…

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Novel insights into systemic sclerosis using a sensitive computational method to analyze whole-genome bisulfite sequencing data

Background: Abnormal DNA methylation is thought to contribute to the onset and progression of systemic sclerosis. Currently, the most comprehensive assay for profiling DNA methylation is whole-genome bisulfite sequencing (WGBS), but its precision depends on read depth and it may be subject to sequencing errors. SOMNiBUS, a method for regional…

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Oncogenic Transformation Drives DNA Methylation Loss and Transcriptional Activation of Transposable Element Loci | Cancer Research

Transposable elements (TEs) are typically silenced by DNA methylation and repressive histone modifications in differentiated healthy human tissues. However, TE expression increases in a wide range of cancers and is correlated with global hypomethylation of cancer genomes. We assessed expression and DNA methylation of TEs in fibroblast cells that were…

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Epigenetic profiling identifies potential COPD treatment targets

Genome-wide DNA methylation changes occur early in human lung fibroblasts during COPD and progress with disease development. A. Lung function data of COPD (II-IV) and no COPD (ex-smoker controls) donors used in this study. The lung function between the two groups is significantly different. B. Schematic diagram illustrating the experimental…

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multiple testing in 450K array data

multiple testing in 450K array data 0 I am going slightly mad trying to find how people, if at all, deal with such a large number of probes in 450K array data (don’t even want to think about EPIC/850K arrays!). Surely when identifying DMRs or DMPs, using (close to) all…

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Uropathogenic Escherichia coli infection-induced epithelial trained immunity impacts urinary tract disease outcome

Ethics statement All animal experimentation was conducted according to the National Institutes of Health guidelines for the housing and care of laboratory animals. All experiments were performed in accordance with institutional regulations after review and approval by the Animal Studies Committee at Washington University School of Medicine in St Louis,…

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High-resolution Nanopore methylome-maps reveal random hyper-methylation at CpG-poor regions as driver of chemoresistance in leukemias

Nanopore reads coupled to a novel computational method extends analyses of differential methylation to sparse CpGs (outside CpG islands) We analyzed tumor samples at diagnosis (T) and relapse (R) from three AML patients (UD5, UD10 and AML2) who received standard chemotherapy and relapsed with chemoresistant disease (supplementary Table 1). DNA from…

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Comprehensive DNA methylation analysis indicates that pancreatic intraepithelial neoplasia lesions are acinar-derived and epigenetically primed for carcinogenesis | Cancer Research

Pancreatic ductal adenocarcinoma (PDAC) is believed to arise from the accumulation of a series of somatic mutations and is also frequently associated with pancreatic intraepithelial neoplasia (PanIN) lesions. However, there is still debate as to whether the cell-type-of-origin of PanINs and PDACs in humans is acinar or ductal. As cell…

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Something wrong with my code concerning bsseq visualization

Here is my code: #### library(bsseq) library(bsseqData) ## —-showData—————————————————————– data(BS.cancer.ex) BS.cancer.ex <- updateObject(BS.cancer.ex) BS.cancer.ex pData(BS.cancer.ex) ## —-smooth,eval=FALSE——————————————————– # BS.cancer.ex.fit <- BSmooth( # BSseq = BS.cancer.ex, # BPPARAM = MulticoreParam(workers = 1), # verbose = TRUE) ## —-showDataFit————————————————————– data(BS.cancer.ex.fit) BS.cancer.ex.fit <- updateObject(BS.cancer.ex.fit) BS.cancer.ex.fit ## —-cpgNumbers————————————————————— ## The average coverage of CpGs…

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How to add gene information below the BSmooth result ?

Here is the tutorial (Analyzing WGBS data with bsseq) I want to use this method to visualize differential dmr regions on the same gene. Here is my code: if (!require(“BiocManager”, quietly = TRUE)) install.packages(“BiocManager”) BiocManager::install(“bsseq”) BiocManager::install(“bsseqData”) library(bsseq) library(bsseqData) data(BS.cancer.ex.fit) BS.cancer.ex.fit <- updateObject(BS.cancer.ex.fit) BS.cancer.ex.fit class(BS.cancer.ex.fit) ## data(BS.cancer.ex.fit) # BS.cancer.ex.fit <- updateObject(BS.cancer.ex.fit)…

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Homer annotatePeaks for enrichment analysis

Homer annotatePeaks for enrichment analysis 0 I want to test differentially methylated regions (DMRs; identified in whole genome bisulfite sequencing data) for enrichment of certain genomic features. For example, do I see more DMRs in promoters than I would expect by chance? It was suggested to me that a simple…

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Bumhunter function in minfi

I am working with 450K methylation data and have a genomic ratio set object (GRset) I have a design matrix as such using design <- model.matrix(~0+Mutation+cov1+cov2+cov3, data = pData(GRset)) head(design) Absent Present cov1 cov2.1 cov2.2 cov2.3 cov3 sample1 1 0 0 0 1 0 0.5276 sample2 1 0 0 0…

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Assessing the risk of excess folic acid intake

Both high FA and low FA intake increases de novo mutation rate and disrupt genome DNA methylation in the offspring. a Violin Plot of DNSNV/DNM (de novo mutation) counts among the three different FA dietary groups (sample size for each group was as follows; combined panel: 0.3 ppm group n = 26;…

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DMRcaller Min. Reads per Cytosine

DMRcaller Min. Reads per Cytosine 0 Hello! I’m a tech who’s starting a Ph.D. in August, so I am very new to bioinformatics. I’m wondering if anyone has some guidance on choosing min. reads per cytosine when calling DMRs. I am using DMRcaller on WGBS data. I have 3 biological…

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Bioconductor – DMRcaller

DOI: 10.18129/B9.bioc.DMRcaller     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see DMRcaller. Differentially Methylated Regions caller Bioconductor version: 3.12 Uses Bisulfite sequencing data in two conditions and identifies differentially methylated regions between the conditions in CG and non-CG context. The input is…

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Transcriptional reprogramming of skeletal muscle stem cells by the niche environment

Isolation of pure populations of MuSCs and niche cells by fluorescence-activated cell sorting (FACS) Hindlimb muscles were dissected from young (4–6 weeks old) or aged (22–26 months old) C57BL/6J (Jackson Laboratory, 000664) mice and minced until no visible tissue chunks were visible. Muscle was then digested in a 15 ml Falcon…

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Download “Epigenetic Memory” Phenomenon in Induced Pluripotent Stem Cells. PDF

reVIeWS “Epigenetic Memory” Phenomenon in Induced Pluripotent Stem Cells E.A. Vaskova1,2,3, A.E. Stekleneva1,2,3, S.P. Medvedev1,2,3, S.M. Zakian1,2,3,* 1Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, prosp. Akad. Lavrentyeva, 10, Novosibirsk, Russia, 630090 2Meshalkin State Research Institute of Circulation Pathology, Rechkunovskaya Str., 15, Novosibirsk, Russia, 630055 3Institute of…

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NODULIN HOMEOBOX is required for heterochromatin homeostasis in Arabidopsis

NDX is a heterochromatin-associated factor To understand the genome-wide regulatory roles of NDX, we first analyzed its genomic distribution. For this, we performed chromatin immunoprecipitation sequencing (ChIP-seq) in 10-day old Arabidopsis seedlings expressing N-terminally and C-terminally tagged NDX fusion proteins (flag-NDX/ndx1-1(FRI)/flc-2 and NDX-GFP/ndx1-1(FRI)/flc-2, respectively) expressed from their endogenous promoter21,32. The…

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Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer

Mapping molecular changes across malignant transformation We generated single-cell data for 81 samples collected from eight FAP and seven non-FAP donors (Fig. 1a and Supplementary Tables 1 and 2). For each tissue, we performed matched scATAC-seq and snRNA-seq (10x Genomics). We obtained high-quality single-cell chromatin accessibility profiles for 447,829 cells…

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DMRs, how common are they and how long?

DMRs, how common are they and how long? 1 Hi! Does anyone know how common differentially methylated regions (DMRs) (or just methylated regions) are? Say, in a 10,000bp region how many DMRs can one expect? Also, does anyone know about the distribution of the size/length of DMRs, i.e. how many…

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Placenta has clues for an early diagnosis of ASD

The researchers of the‘UC Davis MIND during their research they used the genomic sequencing to find a DNA methylation signature in the placenta of infants diagnosed with autism. This hallmark has been linked to early fetal neurodevelopment. Thanks to this study, a new human gene linked to fetal brain development…

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Frontiers | DNA Methylation and RNA-Sequencing Analysis Show Epigenetic Function During Grain Filling in Foxtail Millet (Setaria italica L.)

Introduction Gene expression is not only controlled by DNA sequences but also by epigenetic marks in eukaryotes. DNA methylation as one of the important epigenetic modifications has been demonstrated as closely related to gene expression in biological processes, such as transcriptional activity, developmental regulation, and environmental responses (Maunakea et al.,…

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An epigenetic basis of inbreeding depression in maize

INTRODUCTION Charles R. Darwin documented inbreeding depression as growth disadvantages from self-fertilization compared to outcrossing in many plants (1). Prevailing hypotheses suggest that inbreeding depression results from the exposure of deleterious recessive alleles and/or loss of overdominant alleles due to increased homozygosity (2, 3) or reduced recombination frequency in some…

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Integrated bioinformatics analysis to identify abnormal CC

Introduction In recent years, the morbidity and mortality of colon cancer have increased rapidly, both being ranked fourth worldwide. Although surgery-based comprehensive treatments improve the prognosis of colon cancer, because of the lack of available means for early diagnosis, the mortality level remains high for patients with advanced-stage cancer. The…

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