Technological Convergence: Highlighting the Power of CRISPR Single-Cell Perturbation Toolkit for Functional Interrogation of Enhancers

Simple Summary Enhancers serve as logic gates of the regulatory mechanism of gene expression, and their malfunction is associated with numerous diseases. Therefore, the functional validation of enhancer elements is of great importance in genomics research. Recent technological advancements have enabled the perturbation of enhancers and the examination of their impact on the expression of nearby genes. Here, we review the progress made in experimental and computational methods, which have equipped researchers with a promising arsenal to uncover relationships between enhancers and phenotypes, providing mechanistic insights into diseases. Higher eukaryotic enhancers, as a major class of regulatory elements, play a crucial role in the regulation of gene expression. Over the last decade, the development of sequencing technologies has flooded researchers with transcriptome-phenotype data alongside emerging candidate regulatory elements. Since most methods can only provide hints about enhancer function, there have been attempts to develop experimental and computational approaches that can bridge the gap in the causal relationship between regulatory regions and phenotypes. The coupling of two state-of-the-art technologies, also referred to as crisprQTL, has emerged as a promising high-throughput toolkit for addressing this question. This review provides an overview of the importance of studying enhancers, the core molecular foundation of crisprQTL, and recent studies utilizing crisprQTL to interrogate enhancer-phenotype correlations. Additionally, we discuss computational methods currently employed for crisprQTL data analysis. We conclude by pointing out common challenges, making recommendations, and looking at future prospects, with the aim of providing researchers with an overview of crisprQTL as an important toolkit for studying enhancers.