ArticleNature methods2018
A reassessment of DNA-immunoprecipitation-based genomic profiling.
Article in Nature methods, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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Who cites it
58 citing papers in PubMed.
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- HM-DyadCap - capture and mapping of 5-hydroxymethylcytosine/5-methylcytosine CpG dyads in mammalian DNA.Nucleic acids research · 2026Article
- Adenine DNA methylation associated with transcriptionally permissive chromatin is widespread across eukaryotes.Nature genetics · 2025Article
- Chemotherapy-induced CA-repeat DNA fragments in breast cancer trigger antitumor immune responses.Nature immunology · 2025Article
- Exploring the complexity of MECP2 function in Rett syndrome.Nature reviews. Neuroscience · 2025Review
- Tissue-specific localization of the ING4 targeting subunit of the HBO1 histone acetyltransferase in the cytoplasm and nucleus of secretory cells.Histochemistry and cell biology · 2025Article
- Double and single stranded detection of 5-methylcytosine and 5-hydroxymethylcytosine with nanopore sequencing.Communications biology · 2025Article
- Interrogation of the interplay between DNA N6-methyladenosine (6mA) and hypoxia-induced chromatin accessibility by a randomized empirical model (EnrichShuf).Nucleic acids research · 2024Article
- Critical assessment of nanopore sequencing for the detection of multiple forms of DNA modifications.bioRxiv : the preprint server for biology · 2024Article
- Uncovering the roles of DNA hemi-methylation in transcriptional regulation using MspJI-assisted hemi-methylation sequencing.Nucleic acids research · 2024Article
- Sequencing of NMolecular cell · 2024Article
- An Overview of Global, Local, and Base-Resolution Methods for the Detection of 5-Hydroxymethylcytosine in Genomic DNA.Methods in molecular biology (Clifton, N.J.) · 2024Review
- Adenine methylation is very scarce in theeLife · 2023Article
- Shaping eukaryotic epigenetic systems by horizontal gene transfer.BioEssays : news and reviews in molecular, cellular and developmental biology · 2023Article
- Navigating the pitfalls of mapping DNA and RNA modifications.Nature reviews. Genetics · 2023Review
- Mammalian DNA NMolecular cell · 2023Review
- Context-dependent DNA methylation signatures in animal livestock.Environmental epigenetics · 2023Article
- High-precision mapping reveals rare NCell discovery · 2022Article
- A critique of the hypothesis that CA repeats are primary targets of neuronal MeCP2.Life science alliance · 2022Article
- Means, mechanisms and consequences of adenine methylation in DNA.Nature reviews. Genetics · 2022Review
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Authors and funding
10 authors.
Funding
Abstract
DNA immunoprecipitation followed by sequencing (DIP-seq) is a common enrichment method for profiling DNA modifications in mammalian genomes. However, the results of independent DIP-seq studies often show considerable variation between profiles of the same genome and between profiles obtained by alternative methods. Here we show that these differences are primarily due to the intrinsic affinity of IgG for short unmodified DNA repeats. This pervasive experimental error accounts for 50-99% of regions identified as 'enriched' for DNA modifications in DIP-seq data. Correction of this error profoundly altered DNA-modification profiles for numerous cell types, including mouse embryonic stem cells, and subsequently revealed novel associations among DNA modifications, chromatin modifications and biological processes. We conclude that both matched input and IgG controls are essential in order for the results of DIP-based assays to be interpreted correctly, and that complementary, non-antibody-based techniques should be used to validate DIP-based findings to avoid further misinterpretation of genome-wide profiling data.
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