Genome editing with programmable nucleases using transcription activator-like effector nucleases (TALENs) or RNA-guided clustered regularly interspersed short palindromic repeat (CRISPR) associated protein (Cas9) have become popular and important technologies.
These systems can be modified to carry other functional protein domains such that transcription activators like VP64 or repressors like KRAB (Krueppel-associated box) repressor domains to create “designed transcription factors”.
Perturbing patterns of gene expression is a powerful functional genomics tool – transcription repression or mis-activation coupled with phenotype analysis.
Given the availability of TALE-based or nuclease-defective Cas9 (dCas9)-based designed transcription factor systems, which is ‘better’?
Gao et al (2014) publish their investigations into this problem in Nucleic Acids Research in the context of mouse embryonic fibroblast cells in vitro.
Using a number of gene expression metrics including luciferase assays, endogenous gene expression measurements and induction pluripotent stem cells Gao et al. found each system had their own characteristics
Clearly CRISPR/Cas9 was more cost effective, scalable and capable of trageting multiple loci but ‘the TALE system has the advantage of customizable length of DNA binding domain.’ (from Gao et al.)
Performance of these two systems was also distinguishable with dCas9-Activators consistently less effective than TALE-Acitvators of transcription while, on the other hand, dCas9-Repressors were as good or better than TALE-Repressors of transcription. The authors report that binding of dCas9 resulted in physical interference of other transcription factors and this may have contributed to its effectiveness when designed to be a repressor.
There has been a great deal of excitement about genome editing systems recently, and rightfully so. In this excitement a less nuanced understanding of the systems may lead one to believe that TALEs are obsolete and should be shelved, while CRISPR/Cas9 is going to solve all of our functional genomics problems quickly, easily and cheaply. Gao et al (2014) like a number of others who have made meaningful comparisons of the systems find that they are different and each with their own pros and cons. Understanding the capabilities of each system, their limitations and differences are clearly important. You want to pick the right tool for the job.
Gao et al think that their “results provided the scientific justification of a combined TALE/dCas9 approach for efficient simulataneous genetic activation and repression of independent loci”
Gao X, Tsang JCH, Gaba F, Wu D, Lu L, Liu P (2014) Comparison of TALE designer transcription factors and the CRISPR/dCas9 in regulation of gene expression by targeting enhancers. Nucleic Acids Res 10.1093/nar/gku836
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