Remote regulators of gene expression ? a potential cause of disease?

Gene enhancers light up in distinctive patterns in different cell types in a fruit fly. Image: Olga Mikhaylichenko and Eileen Furlong/European Molecular Biology Laboratory

In many genetic disorders, mutations in the genes themselves cause an abnormal protein to be produced. These mutated proteins have altered functionality with the potential to cause wide-reaching and catastrophic complications, such as in sickle cell anaemia where a mutated gene produces improperly shaped haemoglobin, reducing red blood cells’ oxygen-carrying capacity.

In recent years, scientists have begun to think more about whether the over- or under-expression of healthy normal genes at the wrong time and in the wrong tissue could be the cause of disease. The instructions to switch genes on and off come from DNA segments called enhancers, located far away from the genes they control. Babies can be born without a pancreas because of a mutation in an enhancer gene tens of thousands of DNA bases away. These enhancer mutations are increasingly being linked with conditions such as type 2 diabetes, congenital heart disease and certain cancers.

A recently published study by Karen Adelman, professor of biological chemistry and molecular pharmacology at Harvard Medical School, used the Start-seq tool to generate maps of active enhancers in a given disease, tissue type or environment. “How do enhancers give the right instructions in embryonic development and go wrong in cancer?” she said. “Not only is this stuff fascinating to explore, but we also need to answer these questions if we ever want to alter enhancers, such as to treat disease.” Start-seq is a technique used to isolate and characterise short RNA sequences.

Previously it was thought that enhances simply send transcriptional machinery to the genes they want to activate. This switches the gene on, transcribing DNA to mRNA, ultimately producing protein. In 2010, researchers discovered that enhancers also produce tiny, short-lived RNAs when active that don’t encode for proteins. Adelman and colleagues decided to exploit the unique nature of this DNA by developing the Start-seq to identify them when they’re still stuck to their enhancer.

The first step of the Start-seq process is to take cell samples and wash away the long RNAs, maintaining the ones still stuck to the genome. They then selected the short RNAs that have a chemical tag indicative of RNA-construction material found at genes and enhancers. These RNAs were sequenced to determine where on the genome they originated.

The resultant list contained the enhancers that were active at the time of sampling. They found that 95% of enhancers make RNA and Start-seq returned fewer false positives and negatives than other techniques. “This means transcription at enhancers and protein-coding genes have much more in common than we appreciated,” said Adelman. “Philosophically it makes sense ? and it helps explain why protein-coding genes can act as enhancers ? but it still turns things on their head quite a bit.”