Every transcription factor deserves its map: Scaling up epitope tagging of proteins to bypass antibody problems

Genome-wide identification of transcription factor binding sites with the ChIP-seq method is an extremely important scientific endeavor − one that should ideally be performed for every transcription factor in as many cell types as possible. A major hurdle on the way to this goal is the necessity for a specific, ChIP-grade antibody for each transcription factor of interest, which is often not available. Here, we describe CETCh-seq, a recently published method utilizing genome engineering with the CRISPR/Cas9 system to circumvent the need for a specific antibody. Using the CETCh-seq method, targeted genomic editing results in an epitope-tagged transcription factor, which is recognized by a well-characterized, standard antibody, efficacious for ChIP-seq. We have used CETCh-seq in human cancer cell lines as well as mouse embryonic stem cells. We find that roughly 60% of transcription factors tagged using CETCh-seq produce a high quality ChIP-seq map, a significant improvement over traditional antibody-based methods.

Transcription factors binding to precise locations in the human genome controls cell identity. Over 1,800 genes in humans encode transcription factors, yet only a minority have been assayed for where they bind. We describe CETCh-seq, a method combining CRISPR/Cas9 and epitope tagging to assay a large fraction of factors with ChIP-seq.

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