During development, each of the tissues in an organism exhibits spatially precise and perfectly timed gene expression patterns, like musicians in an orchestra playing a well-rehearsed symphony. But in the case of directing gene expression, the conductors work behind the scenes.

Gene expression in the cell is triggered by the binding of transcription factors to a gene's regulatory sequences. Some of these regulatory sequences, also called enhancers, can be located hundreds of thousands of base pairs away from the promoters of their target genes, and often multiple enhancers control the expression of a given gene at once. Despite the critical role of enhancers in processes such as development, there is relatively little known about where exactly in the genome these sequences are located and when and where they are active in the organism.

Enhancers exhibiting different activity patterns in the developing brain. Image courtesy of A. Visel.

Through the collaborative work of a team of functional genomics experts, developmental neuroscientists and computational biologists, the first high-resolution atlas of enhancer activity in the developing mammalian forebrain (a region comprising the cortex and the basal ganglia) has been released. The atlas includes the spatial patterns of activation of hundreds of enhancers during a critical time of brain development.

To generate this resource, the researchers, lead by Axel Visel and members of his laboratory at the Genomics Division of the Lawrence Berkeley National Laboratory, used several different techniques. They first performed chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) using an antibody for the enhancer-associated protein p300 from embryonic day 11.5 mouse brain tissue. p300 binds active tissue-specific enhancers. From the list of candidates, the researchers selected noncoding DNA sequences that were located far from transcription initiation sites, and this gave them 4,425 enhancer candidates.

Because not all the enhancers active in a tissue may be bound to p300 at a given time, they also performed computational analysis of genomic sequences based on high conservation between mouse and human and vicinity to genes known to be involved in forebrain development and function, which added 231 more sequences to the list of candidates.

The researchers then selected 329 candidate sequences, amplified them from human DNA, cloned them into an enhancer reporter vector and generated transgenic reporter mice. Of the 329 sequences, 105 exhibited reproducible activation patterns, and they analyzed these sequences in detail. The result was a vast collection of images showing spatially confined and beautifully defined enhancer activation patterns.

“When one looks at the diversity of patterns in the images it is pretty remarkable,” says Visel, “in many cases they don't really match any single transcription factor expression pattern that we know.” The tens of thousands of high-resolution images in the collection can be explored through a dedicated website (http://enhancer.lbl.gov/).

There are several immediate applications of this resource. For one, it provides molecular tools of practical value to many researchers interested in targeting gene expression to subregions of the developing brain. The web-based accessible data also allow analysis of the biological properties of enhancers in more detail. Analysis of the sequences contained in these enhancers and their relation to the gene expression patterns they control will teach us the rules behind orchestrated genetic patterns that drive a tissue through development.