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2014 ; 69
(2
): 121-7
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Tools for TAL effector design and target prediction
#MMPMID24981075
Booher NJ
; Bogdanove AJ
Methods
2014[Sep]; 69
(2
): 121-7
PMID24981075
show ga
TAL effectors are transcription factors injected into plant cells by pathogenic
bacteria during infection. They find their specific DNA targets via a string of
contiguous, structural repeats that individually recognize single nucleotides
(with some degeneracy) by virtue of polymorphisms at residue 13. The number of
repeats and sequence of the amino acids at position 13 determine the nucleotide
sequence of the DNA target. Due to this modularity, TAL effectors are readily
engineered and have been used alone or as molecular fusions for targeted gene
activation, gene repression, chromatin modification, chromatin tagging, and most
broadly, for genome editing as TAL effector nucleases (TALENs). Several moderate
and high-throughput cloning methods are in place for assembling TAL
effector-based genetic constructs. Targeting is complicated to an extent by a
general requirement for thymine to precede the DNA target, a requirement of
TALENs to bind paired opposing sites separated by a defined range of distances,
differential contributions of different repeat types to overall affinity, and a
polarity to mismatch tolerance. Several computational tools are available online
to aid in design and the identification of candidate off-target binding sites, as
well as assembly and implementation. These tools vary in their approaches,
capabilities, and relative utility for different types of TAL effector
applications. Accuracy of off-target prediction is not well characterized yet for
any of the tools and will require a better understanding of the qualitative and
quantitative variation in the nucleotide preferences of individual repeats.
free
free
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