"In other words, every transcript that we could predict as a Nova-regulated alternatively spliced RNA fit the prediction of this map," says Darnell. "Half of them were inhibited by Nova and half were enhanced in their exon use by Nova, and every one very cleanly fit the pattern."
The researchers also simulated alternative splicing in the test tube, mixing purified RNA and a splicing extract. When purified Nova was added to the extracts, it bound to the mRNA clusters, altering the outcome of the how the splicing machinery was able to assemble in a manner that again conformed to the predictions of the RNA map. In one case Nova blocked specific components of the splicing machinery, in another it enhanced the ability of this machinery to assemble the right way and use an alternatively spliced site that is otherwise poorly utilized.
By offering a global understanding of how alternative splicing works across the genome, the map has implications for the treatment of a growing list of human neurologic diseases in which RNA regulation, and particularly RNA splicing, has been implicated as the primary cause, including certain types of cancer and a number of brain and muscle disorders.
"Given that the complexity of the brain is orders and orders of magnitude more complex than the number of genes we have, one of the intriguing things about alternative splicing is that a relatively small number of regulatory splicing factors acting in concert on a single transcript can potentially generate a large number of different protein variants," says Darnell.
"There is a converging set of observations indicating that as neurologic diseases are better understood, alternative splicing is going to play an important role in generation of disease and therefore an important role in normal generation of cognitive function," he adds. "Our new