Hi-C analysis: from data generation to integration

Computational Biology Solutions to Identify Enhancers-target Gene Pairs

Enhancers are non-coding regulatory elements that are distant from their target gene. Their characterization still remains elusive especially due to challenges in achieving a comprehensive pairing of enhancers and target genes. A number of computational biology solutions have been proposed to address this problem leveraging the increasing availability of functional genomics data and the improved mechanistic understanding of enhancer action. In this review we focus on computational methods for genome-wide definition of enhancer-target gene pairs. We outline the different classes of methods, as well as their main advantages and limitations. The types of information integrated by each method, along with details on their applicability are presented and discussed. We especially highlight the technical challenges that are still unresolved and hamper the effective achievement of a satisfactory and comprehensive solution. We expect this field will keep evolving in the coming years due to the ever-growing availability of data and increasing insights into enhancers crucial role in regulating genome functionality.