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

Abstract

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.

DOI: 10.1002/bies.201600028

Cite this paper

@article{Partridge2016EveryTF, title={Every transcription factor deserves its map: Scaling up epitope tagging of proteins to bypass antibody problems.}, author={E. Christopher Partridge and Timley A Watkins and Eric M. Mendenhall}, journal={BioEssays : news and reviews in molecular, cellular and developmental biology}, year={2016}, volume={38 8}, pages={801-11} }