title: Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators.
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.
authors.affiliation: Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA;
authors.forename: Lauren R
authors.initials: LR
authors.lastname: Polstein
authors.affiliation: Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA;
authors.forename: Pablo
authors.initials: P
authors.lastname: Perez-Pinera
authors.affiliation: Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA;
authors.forename: D Dewran
authors.initials: DD
authors.lastname: Kocak
authors.affiliation: 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;
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Vockley
authors.affiliation: Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA;
authors.forename: Peggy
authors.initials: P
authors.lastname: Bledsoe
authors.affiliation: Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA;
authors.forename: Lingyun
authors.initials: L
authors.lastname: Song
authors.affiliation: Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA;
authors.forename: Alexias
authors.initials: A
authors.lastname: Safi
authors.affiliation: 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;
authors.forename: Gregory E
authors.initials: GE
authors.lastname: Crawford
authors.affiliation: 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;
authors.forename: Timothy E
authors.initials: TE
authors.lastname: Reddy
authors.affiliation: 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.
authors.forename: Charles A
authors.initials: CA
authors.lastname: Gersbach
mesh_terms: D001665:Binding Sites; D064113:CRISPR-Cas Systems; D002843:Chromatin / Q000737:chemistry*; D042002:Chromatin Assembly and Disassembly; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism*; D005786:Gene Expression Regulation; D005818:Genetic Engineering / Q000379:methods; D015894:Genome, Human; D057809:HEK293 Cells; D006801:Humans; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA; D014157:Transcription Factors / Q000737:chemistry / Q000378:metabolism*
chemical_list: D002843:Chromatin; D004268:DNA-Binding Proteins; D014157:Transcription Factors; D004247:DNA