ArticleF1000Research
Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR.
Article in F1000Research. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
What it found
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The trial behind it
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Who cites it
68 citing papers in PubMed, 89 citations in OpenAlex.
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- Antagonistic histone H2A variants and autonomous heterochromatin formation shape epigenomic patterns in Arabidopsis.Nature communications · 2026Article
- Dynamics of intronic polyadenylation in the hematopoietic lineage and its regulation by DNA methylation.Genome research · 2026Article
- Multi-omic identification of key transcriptional regulatory programs during endurance exercise training in rats.Nature communications · 2026Article
- Integrative Multi-omics Analysis of the Human Skeletal Muscle Response to Endurance or Resistance Exercise: Findings from the Molecular Transducers of Physical Activity Consortium (MoTrPAC).bioRxiv : the preprint server for biology · 2026Article
- Multi-Omic, Multi-Tissue Responses to Acute Exercise in Sedentary Adults: Findings from the Molecular Transducers of Physical Activity Consortium.bioRxiv : the preprint server for biology · 2026Article
- BenchmarkingInternational journal of molecular sciences · 2026Article
- CEI: A Clonal Expansion Identifier for T-cell receptor clones following SARS-CoV-2 vaccination.ArXiv · 2026Article
- Intra-tumoral epigenetic heterogeneity and aberrant molecular clocks in hepatocellular carcinoma.medRxiv : the preprint server for health sciences · 2025Article
- The Transcriptional and Translational Landscape of Plant Adaptation to Low Temperatures.International journal of molecular sciences · 2025Article
- Hyperbaric Oxygen Regulates Tumor pH to Boost Copper-Doped Hydroxyethyl Starch Conjugate Nanoparticles Against Cancer Stem Cells.Exploration (Beijing, China) · 2025Article
- Chronic Morphine Treatment Leads to a Global DNA Hypomethylation via Active and Passive Demethylation Mechanisms in mESCs.International journal of molecular sciences · 2025Article
- Complementary genetic and epigenetic changes facilitate rapid adaptation to multiple global change stressors.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- From genes to therapy: a lipid Metabolism-Related genetic risk model predicts HCC outcomes and enhances immunotherapy.BMC cancer · 2025Article
- edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets.Nucleic acids research · 2025Article
- DNA methylation modulates nucleosome retention in sperm and H3K4 methylation deposition in early mouse embryos.Nature communications · 2025Article
- Insights intoBiomolecules · 2025Article
- Molecular responses of chicken embryos to maternal heat stress through DNA methylation and gene expression: a pilot study.Environmental epigenetics · 2025Article
- Genetic variation drives cancer cell adaptation to ECM stiffness.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- The mitochondrial multi-omic response to exercise training across rat tissues.Cell metabolism · 2024Article
8 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cytosine methylation is an important DNA epigenetic modification. In vertebrates, methylation occurs at CpG sites, which are dinucleotides where a cytosine is immediately followed by a guanine in the DNA sequence from 5' to 3'. When located in the promoter region of a gene, DNA methylation is often associated with transcriptional silencing of the gene. Aberrant DNA methylation is associated with the development of various diseases such as cancer. Bisulfite sequencing (BS-seq) is the current "gold-standard" technology for high-resolution profiling of DNA methylation. Reduced representation bisulfite sequencing (RRBS) is an efficient form of BS-seq that targets CpG-rich DNA regions in order to save sequencing costs. A typical bioinformatics aim is to identify CpGs that are differentially methylated (DM) between experimental conditions. This workflow demonstrates that differential methylation analysis of RRBS data can be conducted using software and methodology originally developed for RNA-seq data. The RNA-seq pipeline is adapted to methylation by adding extra columns to the design matrix to account for read coverage at each CpG, after which the RRBS and RNA-seq pipelines are almost identical. This approach is statistically natural and gives analysts access to a rich collection of analysis tools including generalized linear models, gene set testing and pathway analysis. The article presents a complete start to finish case study analysis of RRBS profiles of different cell populations from the mouse mammary gland using the Bioconductor package edgeR. We show that lineage-committed cells are typically hyper-methylated compared to progenitor cells and this is true on all the autosomes but not the sex chromosomes. We demonstrate a strong negative correlation between methylation of promoter regions and gene expression as measured by RNA-seq for the same cell types, showing that methylation is a regulatory mechanism involved in epithelial linear commitment.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.