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Genome Res. 2015 Aug;25(8):1158-69. doi: 10.1101/gr.179044.114. Epub 2015 May 29.

Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators.

Author information

1
Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA;
2
Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA; Department of Cell Biology, Duke University Medical Center, Durham, North Carolina 27710, USA;
3
Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA;
4
Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA; Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina 27710, USA;
5
Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA; Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina 27710, USA;
6
Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA; Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA; Department of Orthopaedic Surgery, Duke University Medical Center, Durham, North Carolina 27710, USA.

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.

PMID:
26025803
PMCID:
PMC4510000
DOI:
10.1101/gr.179044.114
[Indexed for MEDLINE]
Free PMC Article

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