Context Influences on TALE-DNA Binding Revealed by Quantitative Profiling

Details

• Alternative Title:
  Nat Commun
• Personal Author:
  Rogers, Julia M. ; Barrera, Luis A. ; Reyon, Deepak ; Sander, Jeffry D. ; Kellis, Manolis ; Joung, J. Keith ; Bulyk, Martha L.
• Description:
  Transcription activator-like effector (TALE) proteins recognize DNA using a seemingly simple DNA-binding code, which makes them attractive for use in genome engineering technologies that require precise targeting. Although this code is used successfully to design TALEs to target specific sequences, off-target binding has been observed and is difficult to predict. Here we explore TALE-DNA interactions comprehensively by quantitatively assaying the DNA-binding specificities of 21 representative TALEs to ∼5,000-20,000 unique DNA sequences per protein using custom-designed protein-binding microarrays (PBMs). We find that protein context features exert significant influences on binding. Thus, the canonical recognition code does not fully capture the complexity of TALE-DNA binding. We used the PBM data to develop a computational model, Specificity Inference For TAL-Effector Design (SIFTED), to predict the DNA-binding specificity of any TALE. We provide SIFTED as a publicly available web tool that predicts potential genomic off-target sites for improved TALE design.
• Subjects:
  Article Base Sequence DNA DNA-Binding Proteins Models, Molecular Protein Array Analysis Protein Binding
• Source:
  Nat Commun. 6:7440
• Pubmed ID:
  26067805
• Pubmed Central ID:
  PMC4467457
• Document Type:
  Journal Article
• Funding:
  DP1 GM105378/GM/NIGMS NIH HHS/United States ; R01 GM113708/GM/NIGMS NIH HHS/United States ; R01 HG004037/HG/NHGRI NIH HHS/United States ; R21 HG007573/HG/NHGRI NIH HHS/United States ; T32 HG002295/HG/NHGRI NIH HHS/United States ; DP1 GM105378/DP/NCCDPHP CDC HHS/United States
• Volume:
  6
• Collection(s):
  CDC Public Access
• Main Document Checksum:
  urn:sha256:92eb033ae5355565f346c449b3dbabc1b044053ac3354e79f90be9041b3526a3
• Download URL:
  https://stacks.cdc.gov/view/cdc/32847/cdc_32847_DS1.pdf
• File Type:
  [PDF - 923.03 KB ]