Enhancer Interactions in Developmental Gene Regulation

Abstract

When and where a gene is expressed during development is a critical determinant of cell identity and transcriptional mis-regulation is a common driver of diverse disease states. The spatial and temporal expression of animal genes is controlled by enhancers, sequences of DNA that are bound by transcription factors (TFs) and direct the pattern, timing, and level of gene expression. Many developmental genes are surrounded by multiple enhancers, each of which directs a subset of the overall gene expression pattern, allowing the gene to be turned on at different stages or in different tissues throughout the lifetime of the organism. However, it remains unclear how the promoter integrates information from across a gene locus such that select enhancers are active at the right times, in the right cells, and in the right combinations. Enhancers have long been described as “modules” that function independent of distance from and orientation to the promoter and other regulatory sequences. However, there is increasing evidence in the field that interactions between enhancers and other regulatory sequences are more common than initially appreciated. The current challenge is to understand the prevalence and functional consequences of these interactions on gene expression, both at the level of a single locus and at longer genomic scales. We challenged this canonical view of enhancer modularity with computational models and quantitative experiments using two enhancers of the even-skipped locus in Drosophila melanogaster blastoderm embryos. Using controlled molecular biology and high-resolution imaging, we moved enhancers relative to each other in reporter constructs and deleted them from the endogenous locus to demonstrate that interactions between enhancers have functional consequences on gene expression. These results argue that mechanisms of gene regulation operate at the locus-level to control the precise expression of this key developmental gene. The evidence presented herein suggests that the classical model by which enhancers function independently of surrounding sequences is too simplistic and lays the groundwork for future studies that identify the mechanisms by which information from many enhancers is integrated by a single promoter to produce precise and robust gene expression patterns throughout development.