ArticleNature protocols2021
Dual detection of chromatin accessibility and DNA methylation using ATAC-Me.
Article in Nature protocols, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
11 citing papers in PubMed, 43 citations in OpenAlex.
- Fundamentals of DNA methylation in development.Pediatric research · 2025Review
- Temporally discordant chromatin accessibility and DNA demethylation define short- and long-term enhancer regulation during cell fate specification.Cell reports · 2025Article
- Translation of Epigenetics in Cell-Free DNA Liquid Biopsy Technology and Precision Oncology.Current issues in molecular biology · 2024Review
- ROCCO: a robust method for detection of open chromatin via convex optimization.Bioinformatics (Oxford, England) · 2023Article
- Cross-tissue patterns of DNA hypomethylation reveal genetically distinct histories of cell development.BMC genomics · 2023Article
- Associations between DNA methylation and gene regulation depend on chromatin accessibility during transgenerational plasticity.BMC biology · 2023Article
- Computational Methods for Single-cell DNA Methylome Analysis.Genomics, proteomics & bioinformatics · 2023Review
- Epigenetic modulation of cell fate during pancreas development.Trends in developmental biology · 2023Article
- Genomic landscapes of bacterial transposons and their applications in strain improvement.Applied microbiology and biotechnology · 2022Review
- Investigating chromatin accessibility during development and differentiation by ATAC-sequencing to guide the identification of cis-regulatory elements.Biochemical Society transactions · 2022Article
- Dual detection of chromatin accessibility and DNA methylation using ATAC-Me.Nature protocols · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
The epigenome is multidimensional, with individual molecular components operating on different levels to control transcriptional output. Techniques that combine measurements of these features can reveal their precise correspondence in genomic space, or temporal connectivity, to better understand how they jointly regulate genes. ATAC-Me is an integrated method to probe DNA methylation and chromatin accessibility from a single DNA fragment library. Intact nuclei undergo Tn5 transposition to isolate DNA fragments within nucleosome-free regions. Isolated fragments are exposed to sodium bisulfite before library amplification and sequencing. A typical ATAC-Me experiment detects ~60,000-75,000 peak regions (P < 0.05), covering ~3-4 million CpG sites with at least 5× coverage. These sites display a range of methylation values depending on the cellular and genomic context. The approach is well suited for time course studies that aim to capture chromatin and DNA methylation dynamics in tandem during cellular differentiation. The protocol is completed in 2 d with standard molecular biology equipment and expertise. Analysis of resulting data uses publicly available software requiring basic bioinformatics skills to interpret results.
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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.