Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators
- Lauren R. Polstein1,
- Pablo Perez-Pinera1,7,
- D. Dewran Kocak1,
- Christopher M. Vockley2,3,
- Peggy Bledsoe2,
- Lingyun Song2,
- Alexias Safi2,
- Gregory E. Crawford2,4,
- Timothy E. Reddy2,5 and
- Charles A. Gersbach1,2,6
- 1Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA;
- 2Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA;
- 3Department of Cell Biology, Duke University Medical Center, Durham, North Carolina 27710, USA;
- 4Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina 27710, USA;
- 5Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina 27710, USA;
- 6Department of Orthopaedic Surgery, Duke University Medical Center, Durham, North Carolina 27710, USA
- Corresponding authors: greg.crawford{at}duke.edu, tim.reddy{at}duke.edu, charles.gersbach{at}duke.edu
Abstract
Genome engineering technologies based on the CRISPR/Cas9 and TALE systems are enabling new approaches in science and biotechnology. However, the specificity of these tools in complex genomes and the role of chromatin structure in determining DNA binding are not well understood. We analyzed the genome-wide effects of TALE- and CRISPR-based transcriptional activators in human cells using ChIP-seq to assess DNA-binding specificity and RNA-seq to measure the specificity of perturbing the transcriptome. Additionally, DNase-seq was used to assess genome-wide chromatin remodeling that occurs as a result of their action. Our results show that these transcription factors are highly specific in both DNA binding and gene regulation and are able to open targeted regions of closed chromatin independent of gene activation. Collectively, these results underscore the potential for these technologies to make precise changes to gene expression for gene and cell therapies or fundamental studies of gene function.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.179044.114.
- Received May 29, 2014.
- Accepted May 27, 2015.
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
