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...

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Bibliographic Details
Published in:BioEssays 2016-08, Vol.38 (8), p.801-811
Main Authors: Partridge, E. Christopher, Watkins, Timley A., Mendenhall, Eric M.
Format: Article
Language:English
Subjects:
Animals
Binding sites
Chromatin Immunoprecipitation - methods
CRISPR
CRISPR-Cas Systems
DNA - metabolism
Epitopes
gene regulation
Genes
Genome, Human
Genomes
genomics
Genomics - methods
Humans
Mice
Protein Binding
Regulatory Sequences, Nucleic Acid
Sequence Analysis, DNA - methods
Stem cells
Transcription factors
Transcription Factors - immunology
Transcription Factors - metabolism
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Summary: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.
ISSN:0265-9247
1521-1878
DOI:10.1002/bies.201600028