ArticleNucleic acids research2021
To mock or not: a comprehensive comparison of mock IP and DNA input for ChIP-seq.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Chromatin Immunoprecipitation (ChIP) to Investigate Histone-Modifications in Smut Fungi.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Binding profiles for 961Genome research · 2024Article
- aChIP is an efficient and sensitive ChIP-seq technique for economically important plant organs.Nature plants · 2024Article
- Representing core gene expression activity relationships using the latent structure implicit in Bayesian networks.Bioinformatics (Oxford, England) · 2024Article
- Improving rigor and reproducibility in chromatin immunoprecipitation assay data analysis workflows with Rocketchip.bioRxiv : the preprint server for biology · 2024Article
- Less-is-more: selecting transcription factor binding regions informative for motif inference.Nucleic acids research · 2024Article
- Differential Analysis of Protein-DNA Binding Using ChIP-Seq Data.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Elegant Nematodes Improve Our Understanding of Human Neuronal Diseases, the Role of Pollutants and Strategies of Resilience.Environmental science & technology · 2023Review
- Post-transcriptional control of a stemness signature by RNA-binding protein MEX3A regulates murine adult neurogenesis.Nature communications · 2023Article
- Greenscreen: A simple method to remove artifactual signals and enrich for true peaks in genomic datasets including ChIP-seq data.The Plant cell · 2022Article
- Building integrative functional maps of gene regulation.Human molecular genetics · 2022Article
- Chromatin structure can introduce systematic biases in genome-wide analyses ofOpen research Europe · 2022Article
- Nuclear translocation of vitellogenin in the honey bee (Apidologie · 2022Article
- Genetic Variants in Transcription Factor Binding Sites in Humans: Triggered by Natural Selection and Triggers of Diseases.International journal of molecular sciences · 2021Review
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
Chromatin immunoprecipitation (IP) followed by sequencing (ChIP-seq) is the gold standard to detect transcription-factor (TF) binding sites in the genome. Its success depends on appropriate controls removing systematic biases. The predominantly used controls, i.e. DNA input, correct for uneven sonication, but not for nonspecific interactions of the IP antibody. Another type of controls, 'mock' IP, corrects for both of the issues, but is not widely used because it is considered susceptible to technical noise. The tradeoff between the two control types has not been investigated systematically. Therefore, we generated comparable DNA input and mock IP experiments. Because mock IPs contain only nonspecific interactions, the sites predicted from them using DNA input indicate the spurious-site abundance. This abundance is highly correlated with the 'genomic activity' (e.g. chromatin openness). In particular, compared to cell lines, complex samples such as whole organisms have more spurious sites-probably because they contain multiple cell types, resulting in more expressed genes and more open chromatin. Consequently, DNA input and mock IP controls performed similarly for cell lines, whereas for complex samples, mock IP substantially reduced the number of spurious sites. However, DNA input is still informative; thus, we developed a simple framework integrating both controls, improving binding site detection.
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Registered trials
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