# Shadow enhancer

Shadow enhancers are groups of DNA regulatory sequences that function alongside primary enhancers to regulate gene expression. They play a important role in stabilizing gene expression against genetic and environmental fluctuations. Originally discovered in Drosophila, shadow enhancers have since been identified in a wide range of organisms, including insects, plants, and mammals. They can act at a great distance from their target gene to minimize variability in gene expression and ensure developmental processes proceed correctly, even under variable environmental conditions or genetic perturbations. Shadow enhancers play a crucial role in development and early embryogenesis by maintaining stable expression of a variety of genes.

## Discovery

Shadow enhancers were first described in 2008 by Michael Levine and his research group at the University of California, Berkeley. Their research in Drosophila investigated the transcription factor Dorsal and its target genes. Through characterization of enhancers, other than the primary enhancer, they found that these enhancers appeared to produce gene expression patterns that overlap with those produced by the primary enhancer. Initially, shadow enhancers were believed to act redundantly to the function of the primary enhancer to ensure proper gene expression, despite environmental or genetic variability.

## Function

Shadow enhancers are regulatory DNA elements that play a critical role in stabilizing gene expression and minimizing variability. They work alongside primary enhancers to ensure robust and consistent transcriptional activity, even under fluctuating environmental conditions or genetic perturbations. One of their primary functions is to provide a backup mechanism for gene regulation; if a primary enhancer is mutated or damaged, shadow enhancers can compensate and maintain proper gene expression patterns. Shadow enhancers work in a similar pattern to primary enhancers, in the sense that they both tend to bind the same transcription factors, and other trans regulatory elements.

## Characteristics
### Location

Shadow enhancers can be positioned at various distances from their target genes, often farther away compared to primary enhancers. They may reside within intronic regions or beyond adjacent genes, exerting their regulatory influence over a broader genomic range. Although both shadow and primary enhancers contribute to gene expression, shadow enhancers tend to operate from more distal genomic locations.

### Redundancy

A key characteristic of shadow enhancers is their functional redundancy, which arises from their ability to overlap with primary enhancers in controlling gene expression. This redundancy enhances the robustness of gene regulation by ensuring that multiple enhancers contribute to the expression of a single gene. If a gene is regulated not only by a primary enhancer but also by two or more shadow enhancers, then the gene has additional protection against the failure of a single regulatory element. In contrast, genes regulated solely by a primary enhancer lack this redundancy, making them more vulnerable to regulatory disruptions.

## Role in development

Shadow enhancers play a critical role in embryogenesis, particularly in defining body patterning. By modulating transcriptional activation strength, timing, and location, they ensure precise control of gene expression during development. Their ability to fine-tune gene expression levels helps maintain stability, allowing organisms to grow and develop properly despite environmental stresses. Research has shown that shadow enhancers can compensate for mutations in primary enhancers, acting as a buffer against genetic and environmental fluctuations. This buffering capacity ensures consistent and precise gene expression patterns, which are crucial for proper body development and overall developmental stability. Shadow enhancers are important in the regulation of many genes involved in development and have been well characterized in Drosophila.

### Twin of eyeless regulation in Drosophila

Shadow enhancers are important in the regulation of the twin of eyeless (toy) gene in Drosophila. The toy gene is crucial for eye development, therefore these shadow enhancers work together to drive toy expression during early embryogenesis. Their overlapping yet distinct expression patterns ensures consistent toy expression during critical developmental processes.

### snail regulation in Drosophila

Shadow enhancers play a crucial role in regulation of the snail gene during Drosophila embryogenesis. The snail gene encodes a transcription factor that is essential for epithelial-mesenchymal transitions in many developmental processes. Shadow enhancers maintain snail expression under environmental and genetic disturbances in order to ensure proper gastrulation.

### Krüppel regulation in Drosophila

Shadow enhancers are important in the regulation of the Krüppel (Kr) gene in Drosophila. The Krüppel gene is involved in early segmentation and creates precise patterning along the anterior-posterior axis of the Drosophila embryo. Shadow enhancers are crucial in facilitating Kr expression, ultimately ensuring accurate spacial and temporal expression of Krüppel. Shadow enhancers are important in fine-tuning gene expression patterns during critical developmental stages.

### Sonic hedgehog regulation in mice

Two shadow enhancers have been identified to be involved in the regulation of the sonic hedgehog (SHH) gene in mice. In vertebrates, Shh is important in forming the ventral midline of the central nervous system. Without shadow enhancers to ensure proper expression of Shh, the brain can become malformed. Therefore, shadow enhancers are crucial to ensuring proper development by stabilizing gene expression of important developmental genes, like Shh.