Abstract
Chromatin immunoprecipitation followed by next-generation DNA sequencing (ChIP-seq) has been used to identify transcription factor (TF) binding proteins throughout the genome. Unfortunately, this approach traditionally requires commercially available, ChIP-seq grade antibodies that frequently fail to generate acceptable datasets. To obtain data for the many TFs for which there is no appropriate antibody, we recently developed a new method for performing ChIP-seq by epitope tagging endogenous TFs using CRISPR/Cas9 genome editing technology (CETCh-seq). Here, we describe our general protocol of CETCh-seq for both adherent and nonadherent cell lines using a commercially available FLAG antibody.
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References
Landt SG, Marinov GK, Kundaje A et al (2012) ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res 22(9):1813–1831
Savic D, Partridge EC, Newberry KM et al (2015) CETCh-seq: CRISPR epitope tagging ChIP-seq of DNA-binding proteins. Genome Res 25(10):1581–1589
Acknowledgments
Research reported in this publication was supported by the National Human Genome Research Institute of the National Institutes of Health under Award Number U54HG006998 to R.M.M. and E.M.M. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. This work was also supported by funds from The HudsonAlpha Institute for Biotechnology.
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Meadows, S.K. et al. (2020). Epitope Tagging ChIP-Seq of DNA Binding Proteins Using CETCh-Seq. In: Kidder, B. (eds) Stem Cell Transcriptional Networks. Methods in Molecular Biology, vol 2117. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0301-7_1
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DOI: https://doi.org/10.1007/978-1-0716-0301-7_1
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Publisher Name: Humana, New York, NY
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Online ISBN: 978-1-0716-0301-7
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