A Scalable Epitope Tagging Approach for High Throughput ChIP-Seq Analysis

Xiong Xiong, Yanxiao Zhang, Jian Yan, Surbhi Jain, Sora Chee, Bing Ren, Huimin Zhao

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish (US)
Pages (from-to)1034-1042
Number of pages9
JournalACS synthetic biology
Issue number6
StatePublished - Jun 16 2017


  • CRISPR/Cas9
  • ChIP-Seq
  • FLAG tagging
  • genome engineering
  • microhomology mediated end joining

ASJC Scopus subject areas

  • Biomedical Engineering
  • Biochemistry, Genetics and Molecular Biology (miscellaneous)


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