title: Context influences on TALE-DNA binding revealed by quantitative profiling.
abstract: 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.
authors.affiliation: 1] Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA [2] Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, Massachusetts 02138, USA.
authors.forename: Julia M
authors.initials: JM
authors.lastname: Rogers
authors.affiliation: 1] Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA [2] Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, Massachusetts 02138, USA [3] Harvard-MIT Division of Health Sciences and Technology (HST), Harvard Medical School, Boston, Massachusetts 02115, USA [4] Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, Massachusetts 02139, USA.
authors.forename: Luis A
authors.initials: LA
authors.lastname: Barrera
authors.affiliation: 1] Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA [2] Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA [3] Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA [4] Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Deepak
authors.initials: D
authors.lastname: Reyon
authors.affiliation: 1] Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA [2] Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA [3] Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA [4] Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Jeffry D
authors.initials: JD
authors.lastname: Sander
authors.affiliation: Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, Massachusetts 02139, USA.
authors.forename: Manolis
authors.initials: M
authors.lastname: Kellis
authors.affiliation: 1] Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA [2] Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA [3] Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA [4] Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: J Keith
authors.initials: JK
authors.lastname: Joung
authors.affiliation: 1] Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA [2] Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, Massachusetts 02138, USA [3] Harvard-MIT Division of Health Sciences and Technology (HST), Harvard Medical School, Boston, Massachusetts 02115, USA [4] Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Martha L
authors.initials: ML
authors.lastname: Bulyk
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000378:metabolism*; D008958:Models, Molecular; D040081:Protein Array Analysis; D011485:Protein Binding
chemical_list: D004268:DNA-Binding Proteins; D004247:DNA