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Tag: DMR
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…
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)…
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…
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…
Is bisulfite-seq data from different studies comparable with each other?
Is bisulfite-seq data from different studies comparable with each other? 1 Hi all, I am conducting a study which involves the comparison between more than 3 experimental conditions. In particular, I would like to study the methylation status of samples and to find differentially methylated regions between these conditions. Let’s…
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…
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…
Characterization of H3K9me3 and DNA methylation co-marked CpG-rich regions during mouse development | BMC Genomics
CHMs are stable during mouse development To explore the co-localization between H3K9me3 and DNA methylation, we collected public H3K9me3 chromatin immunoprecipitation sequencing (ChIP-seq) and whole-genome bisulfite sequencing (WGBS) data during mouse pre-implantation embryogenesis [11], PGC development [12], spermatogenesis [13, 14], retina development [15], heart and liver development after gastrulation [16,17,18]…
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…
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…
Genome-wide epigenetic dynamics during postnatal skeletal muscle growth in Hu sheep
Global changes of the transcriptome during postnatal muscle growth The number of myofibers is thought to remain fixed following birth, muscle fiber hypertrophy growth is the primaryway of muscle growth. The average CSA is generally used to measure the hypertrophy of skeletal muscle fibers. To systematically identify the growth of postnatal…
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 …
Interpreting the CpG pearson correlation plot
Interpreting the CpG pearson correlation plot 0 I have performed DMR analysis using Methylkit and have generated the correlation plot but i am not able to interpret it completely. Apart from the correlation % what do the bar plots, color and x and y axis signify? Differential-methylation • 33 views…
GOSt Plot
I have been using GOSt in R to run GO analysis and create a plot with various terms highlighted. All went well, data exported etc but as someone relatively unfamiliar with R I have two questions. How do I change the point size on the plot? I know how to…
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…
Genome-Wide Association Study of Alopecia Areata in Taiwan
Introduction Alopecia areata (AA) is one of Taiwan’s most common autoimmune hair diseases and incidence rate of AA is 0.22%.1–3 The main symptoms of AA are rapid, non-scarring hair loss that affects body hair, facial hair, eyelashes, and brows.1,2 In the United States, the prevalence of AA is estimated to…
Aedes aegypti Argonaute 2 controls arbovirus infection and host mortality
Generation and characterization of Ago2 knockout mutants To demonstrate the essential function of Ago2 in the Ae. aegypti siRNA pathway, we used CRISPR/Cas9 to knock out Ago2 and then investigated its role in defending against arbovirus infection (Fig. 1a). Ae. aegypti Ago2 (AeAgo2) has four exons and four predicated functional domains,…
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…
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…
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…
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…
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…
RepeatMasker error when trying to generate repeat sequence distribution pie chart (all code and errors provided)
RepeatMasker error when trying to generate repeat sequence distribution pie chart (all code and errors provided) 0 Hi, Any answers would be highly appreciated as I’ve been stuck on this for a while. I analyze epigenetic data and process DMR lists and I’m currently having issues producing a pie chart…
what annotation file to I use?
DMR Analysis for RRBS: what annotation file to I use? 0 Hi, I’m interested in running a DMR analysis on RRBS data. I was wondering what type of annotation file I need for the program (i.e methylkit or others) to identify promoters vs introns etc. Would a gtf file be…
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,…
CGmaptools DMR output issue
CGmaptools DMR output issue 0 I have a question regarding the use of CGmaptools for dmr analysis. I have a dataset of 6 CGmap files which I have intersected using the cgmaptools intersect function in preparation for DMR analysis. However, when I run cgmaptools dmr, my script returns an empty…
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…
Filtering of mCs before downstream DMR analysis
Filtering of mCs before downstream DMR analysis 0 Hi, I am working with a WGBS dataset and have done alignment and methylation calling with Bismark and DMR analysis with metilene. So far I have only filtered on read depth before DMR calling, but I was wondering if it is necessary…
Bioconductor – REMP
DOI: 10.18129/B9.bioc.REMP This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see REMP. Repetitive Element Methylation Prediction Bioconductor version: 3.13 Machine learning-based tools to predict DNA methylation of locus-specific repetitive elements (RE) by learning surrounding genetic and epigenetic information. These tools provide genomewide…
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…
DNA Methylation Plays Key Role in Tomato Domestication & Metabolic Diversity
This study is led by Dr. Shouchuang Wang (Sanya Nanfan Research Institute of Hainan University), revealing the role of epigenetic variation in tomato domestication and metabolic diversity from the perspective of population DNA methylation. The breeding history of tomato which is a world recognized model plant with high nutritional value…
One-Time Procedure May Potentially End Insulin Dependency in Type 2 Diabetes Patients
As of 2019, the latest year for which data are available, more than 37 million people in the United States—or 11.3 percent of the country’s population—are living with diabetes, according to the U.S. Centers for Disease Control and Prevention. Among them, 8.5 million are adults who are undiagnosed or unaware…
Can an Endoscopic Procedure Treat Type 2 Diabetes?
An investigational outpatient endoscopic procedure may help eliminate the need for insulin in people with type 2 diabetes, early research suggests. Called re-cellularization via electroporation therapy (ReCET), the technology, manufactured by Endogenex, uses a specialized catheter to deliver alternating electric pulses to the duodenum to induce cellular regeneration. This process…
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,…
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…
Drug-induced loss of imprinting revealed using bioluminescent reporters of Cdkn1c
Allis, C. D. & Jenuwein, T. The molecular hallmarks of epigenetic control. Nat. Rev. Genet. 17, 487–500 (2016). Article CAS PubMed Google Scholar Zhao, Z. & Shilatifard, A. Epigenetic modifications of histones in cancer. Genome Biol. 20, 1–16 (2019). Article Google Scholar Greenberg, M. V. C. & Bourc’his, D. The…
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)…
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…
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;…
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…
Subset count data in DGEList using edgeR/DESeq2
Subset count data in DGEList using edgeR/DESeq2 1 @0f752196 Last seen 1 day ago United Kingdom Hello, I have an enormous methylation dataset (12.6Gb) that is proving too much for my computer to handle. This data is loaded in to R as a DGEList (with counts, samples, genes and a…
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…
Introduction to DNA Methylation Analysis: From Wet Lab Experiments to Bioinformatics Analysis
Methylation is one of the most classical epigenetic modifications in eukaryotes. DNA methylation regulates gene expression and has important implications in both growth and disease-related research. DNA methylation affects the maturation of germ cells or embryonic cells subject to specific gene expression. It has also been widely studied and applied…
Long-range phasing of dynamic, tissue-specific and allele-specific regulatory elements
Baylin, S. B. & Jones, P. A. A decade of exploring the cancer epigenome – biological and translational implications. Nat. Rev. Cancer 11, 726–734 (2011). CAS PubMed PubMed Central Article Google Scholar Greenberg, M. V. C. & Bourc’his, D. The diverse roles of DNA methylation in mammalian development and disease….
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…
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…
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…
The ENmix DNA methylation analysis pipeline for Illumina BeadChip and comparisons with seven other preprocessing pipelines | Clinical Epigenetics
Methylation analysis pipelines The ENmix pipeline performs data preprocessing in a stepwise way, including ENmix background correction [1], RELIC dye bias correction [3], optional inter-array normalization, RCP probe-type bias correction [2], quality control, filtering of low-quality data points, and imputation. ENmix background correction employs a mixture of exponential and truncated…
How to analyze Infinium Mouse Methylation BeadChip array data?
Hi! I played around with the Illumina mouse demo data and ENmix. The following code worked for me and you should end up with normalized beta values for subsequent limma analysis (or DMR analysis folowing the ENmix vignette). #setwd() #download the Infinium_Mouse_Methylation_v1.0_A1_GS_Manifest_File.csv file from Illumina HP to working directory (=…
Bioconductor – ramr
DOI: 10.18129/B9.bioc.ramr Detection of Rare Aberrantly Methylated Regions in Array and NGS Data Bioconductor version: Release (3.13) ramr is an R package for detection of low-frequency aberrant methylation events in large data sets obtained by methylation profiling using array or high-throughput bisulfite sequencing. In addition, package provides functions…
Using MethylKit with gemBS output files
Using MethylKit with gemBS output files 0 Hi, I was just wondering if anyone is familiar with using gemBS output files for MethylKit such as the ones below *_3_lane_gembs_cpg.bed.gz *_3_lane_gembs_cpg.txt.gz With the following columns Contig Pos0 Pos1 Ref Call Flags Meth non_conv conv support_call total I tried running methylKit but…
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.,…
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…
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…