title: A Scalable Epitope Tagging Approach for High Throughput ChIP-Seq Analysis.
abstract: Eukaryotic transcriptional factors (TFs) typically recognize short genomic sequences alone or together with other proteins to modulate gene expression. Mapping of TF-DNA interactions in the genome is crucial for understanding the gene regulatory programs in cells. While chromatin immunoprecipitation followed by sequencing (ChIP-Seq) is commonly used for this purpose, its application is severely limited by the availability of suitable antibodies for TFs. To overcome this limitation, we developed an efficient and scalable strategy named cmChIP-Seq that combines the clustered regularly interspaced short palindromic repeats (CRISPR) technology with microhomology mediated end joining (MMEJ) to genetically engineer a TF with an epitope tag. We demonstrated the utility of this tool by applying it to four TFs in a human colorectal cancer cell line. The highly scalable procedure makes this strategy ideal for ChIP-Seq analysis of TFs in diverse species and cell types.
authors.affiliation: Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.
authors.forename: Xiong
authors.initials: X
authors.lastname: Xiong
authors.affiliation: Ludwig Institute for Cancer Research , 9500 Gilman Drive, La Jolla, California 92093, United States.
authors.forename: Yanxiao
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Ludwig Institute for Cancer Research , 9500 Gilman Drive, La Jolla, California 92093, United States.|Department of Biosciences and Nutrition, Karolinska Institutet , 141 83 Huddinge, Sweden.
authors.forename: Jian
authors.initials: J
authors.lastname: Yan
authors.affiliation: Department of Biochemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.
authors.forename: Surbhi
authors.initials: S
authors.lastname: Jain
authors.affiliation: Department of Cellular and Molecular Medicine, Institute of Genome Medicine, Moores Cancer Center, University of California San Diego, School of Medicine , San Diego, California 92093, United States.
authors.forename: Sora
authors.initials: S
authors.lastname: Chee
authors.affiliation: Ludwig Institute for Cancer Research , 9500 Gilman Drive, La Jolla, California 92093, United States.|Department of Cellular and Molecular Medicine, Institute of Genome Medicine, Moores Cancer Center, University of California San Diego, School of Medicine , San Diego, California 92093, United States.
authors.forename: Bing
authors.initials: B
authors.lastname: Ren
authors.affiliation: Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.|Departments of Chemistry and Bioengineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.
authors.forename: Huimin
authors.identifier: 0000-0002-9069-6739
authors.initials: H
authors.lastname: Zhao
mesh_terms: D064113:CRISPR-Cas Systems; D045744:Cell Line, Tumor; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D004247:DNA / Q000235:genetics* / Q000378:metabolism; D000939:Epitopes / Q000235:genetics* / Q000378:metabolism; D045325:HCT116 Cells; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism
chemical_list: D000939:Epitopes; D014157:Transcription Factors; D004247:DNA
keywords: CRISPR/Cas9; ChIP-Seq; FLAG tagging; genome engineering; microhomology mediated end joining