The transcriptional regulation of genes determines the fate of animal cell 
differentiation and subsequent organ development. With the recent progress in 
genome-wide technologies, the genomic landscapes of enhancers have been broadly 
explored in mammalian genomes, which led to the discovery of novel specific 
subsets of enhancers, termed super-enhancers. Super-enhancers are large clusters 
of enhancers covering the long region of regulatory DNA and are densely occupied 
by transcription factors, active histone marks, and co-activators. Accumulating 
evidence points to the critical role that super-enhancers play in cell 
type-specific development and differentiation, as well as in the development of 
various diseases. Here, I provide a comprehensive description of the optimal 
approach for identifying functional units of super-enhancers and their unique 
chromatin features in normal development and in diseases, including cancers. I 
also review the recent updated knowledge on novel approaches of targeting 
super-enhancers for the treatment of specific diseases, such as small-molecule 
inhibitors and potential gene therapy. This review will provide perspectives on 
using super-enhancers as biomarkers to develop novel disease diagnostic tools 
and establish new directions in clinical therapeutic strategies.