ArticleNucleic acids research2004
Quantitative sequential chromatin immunoprecipitation, a method for analyzing co-occupancy of proteins at genomic regions in vivo.
Article in Nucleic acids research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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Who cites it
62 citing papers in PubMed.
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- Emerging role of epigenetic regulations in periodontitis: a literature review.American journal of translational research · 2022Review
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- The New Model of Snail Expression Regulation: The Role of MRTFs in Fast and Slow Endothelial-Mesenchymal Transition.International journal of molecular sciences · 2020Article
- Endodermal Maternal Transcription Factors Establish Super-Enhancers during Zygotic Genome Activation.Cell reports · 2019Article
- Heterodimeric capping protein is required for stereocilia length and width regulation.The Journal of cell biology · 2017Article
- Mediator Undergoes a Compositional Change during Transcriptional Activation.Molecular cell · 2016Article
- reChIP-seq reveals widespread bivalency of H3K4me3 and H3K27me3 in CD4(+) memory T cells.Nature communications · 2016Article
- Continual removal of H3K9 promoter methylation by Jmjd2 demethylases is vital for ESC self-renewal and early development.The EMBO journal · 2016Article
- Affinity and competition for TBP are molecular determinants of gene expression noise.Nature communications · 2016Article
- Mechanism of Wnt signaling induced down regulation of mrhl long non-coding RNA in mouse spermatogonial cells.Nucleic acids research · 2016Article
- Uncoupling histone turnover from transcription-associated histone H3 modifications.Nucleic acids research · 2015Article
- Genome-wide view of TGFβ/Foxh1 regulation of the early mesendoderm program.Development (Cambridge, England) · 2014Article
- Review
- Coregulator control of androgen receptor action by a novel nuclear receptor-binding motif.The Journal of biological chemistry · 2014Article
- Toward single-molecule optical mapping of the epigenome.ACS nano · 2014Article
2 more citing papers are in PubMed but not listed here.
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Abstract
Sequential chromatin immunoprecipitation (SeqChIP) is a procedure in which formaldehyde-crosslinked, protein-DNA complexes from living cells are subjected to two sequential immunoprecipitations with antibodies of different specificity. SeqChIP has been used to address, in a qualitative manner, whether two proteins can simultaneously co-occupy a stretch of DNA in vivo. Here, we expand on our earlier work and describe theoretical and practical considerations for performing and interpreting SeqChIP experiments in a quantitative manner. We provide a detailed experimental procedure for designing and performing SeqChIP experiments as well as experimental examples of the three possible outcomes: full co-occupancy, no co-occupancy and partial co-occupancy. In some cases of partial co-occupancy, the order of immunoprecipitations in SeqChIP can strongly influence the outcome. We experimentally confirm a quantitative parameter that provides a measure of co-occupancy of two proteins on a given region of DNA and provide information on how to interpret the results of SeqChIP experiments. Our quantitative treatment of SeqChIP data substantially expands the usefulness of the technique for elucidating molecular mechanisms in vivo.
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