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

Publication ,  Journal Article
Polstein, LR; Perez-Pinera, P; Kocak, DD; Vockley, CM; Bledsoe, P; Song, L; Safi, A; Crawford, GE; Reddy, TE; Gersbach, CA
Published in: Genome Res
August 2015

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.

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Published In

Genome Res

DOI

EISSN

1549-5469

Publication Date

August 2015

Volume

25

Issue

8

Start / End Page

1158 / 1169

Location

United States

Related Subject Headings

  • Transcription Factors
  • Sequence Analysis, RNA
  • Sequence Analysis, DNA
  • Humans
  • HEK293 Cells
  • Genome, Human
  • Genetic Engineering
  • Gene Expression Regulation
  • DNA-Binding Proteins
  • DNA
 

Citation

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Chicago
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MLA
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Polstein, L. R., Perez-Pinera, P., Kocak, D. D., Vockley, C. M., Bledsoe, P., Song, L., … Gersbach, C. A. (2015). Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators. Genome Res, 25(8), 1158–1169. https://doi.org/10.1101/gr.179044.114
Polstein, Lauren R., Pablo Perez-Pinera, D Dewran Kocak, Christopher M. Vockley, Peggy Bledsoe, Lingyun Song, Alexias Safi, Gregory E. Crawford, Timothy E. Reddy, and Charles A. Gersbach. “Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators.Genome Res 25, no. 8 (August 2015): 1158–69. https://doi.org/10.1101/gr.179044.114.
Polstein LR, Perez-Pinera P, Kocak DD, Vockley CM, Bledsoe P, Song L, et al. Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators. Genome Res. 2015 Aug;25(8):1158–69.
Polstein, Lauren R., et al. “Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators.Genome Res, vol. 25, no. 8, Aug. 2015, pp. 1158–69. Pubmed, doi:10.1101/gr.179044.114.
Polstein LR, Perez-Pinera P, Kocak DD, Vockley CM, Bledsoe P, Song L, Safi A, Crawford GE, Reddy TE, Gersbach CA. Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators. Genome Res. 2015 Aug;25(8):1158–1169.

Published In

Genome Res

DOI

EISSN

1549-5469

Publication Date

August 2015

Volume

25

Issue

8

Start / End Page

1158 / 1169

Location

United States

Related Subject Headings

  • Transcription Factors
  • Sequence Analysis, RNA
  • Sequence Analysis, DNA
  • Humans
  • HEK293 Cells
  • Genome, Human
  • Genetic Engineering
  • Gene Expression Regulation
  • DNA-Binding Proteins
  • DNA