Applying CRISPR–Cas9 tools to identify and characterize transcriptional enhancers

CRISPR–Cas9-based genome editing tools have been developed recently to study non-coding transcriptional regulatory elements, enabling the characterization of enhancers in their endogenous context. The applications, current limitations and future development of such CRISPR–Cas9 tools are discussed, with emphasis on identifying and characterizing enhancer elements in a high-throughput manner. The development of the CRISPR–Cas9 system triggered a revolution in the field of genome engineering. Initially, the use of this system was focused on the study of protein-coding genes but, recently, a number of CRISPR–Cas9-based tools have been developed to study non-coding transcriptional regulatory elements. These technological advances offer unprecedented opportunities for elucidating the functions of enhancers in their endogenous context. Here, we discuss the application, current limitations and future development of CRISPR–Cas9 systems to identify and characterize enhancer elements in a high-throughput manner.