Details:

Alternative Title:
Nat Commun
Personal Author:
Rogers, Julia M. ; Barrera, Luis A. ; Reyon, Deepak ; Sander, Jeffry D. ; Kellis, Manolis ; ... More +
Rogers, Julia M. ; Barrera, Luis A. ; Reyon, Deepak ; Sander, Jeffry D. ; Kellis, Manolis ; Joung, J. Keith ; Bulyk, Martha L. Less -
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.
Subject:
[+]
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 ; ... More +
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 Less -
Collection(s):
CDC Public Access
Main Document Checksum:
[+]
urn:sha256:92eb033ae5355565f346c449b3dbabc1b044053ac3354e79f90be9041b3526a3
File Type:

Supporting Files

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