Slicing Up Complex Alternative Splicing

Slicing Up Complex Alternative Splicing 03/09/2016 [from BioTechniques] By Kelly Rae Chi http://www.biotechniques.com/news/biotechniquesNews/biotechniques-363551.html#.Vt79QH0rJaQ

Studies of alternative splicing events just got easier and more comprehensive, thanks to a new computational tool. Read more... Messenger RNA can be spliced in multiple ways, altering how a gene functions in a cell in ways that affect health and development. Yet even with today’s state-of-the-art RNA-sequencing methods, it is still challenging to define splice variants or determine how abundant those variants are. Now in the journal eLife, researchers describe a new method for mapping RNA variations in better detail, exposing not only more fundamental splicing events but also some of the so-called “dark matter” of the transcriptome: previously unidentified complex alternative splicing events. Using more than 30 RNA-Seq data sets from a range of species, Yoseph Barash and his team at the University of Pennsylvania created a new, freely available software program called MAJIQ (Modeling Alternative Junction Inclusion Quantification) for detecting and quantifying alternative splicing forms, as well as a companion application, VOILA, for visualizing the variations. Barash’s group used MAJIQ to compare isoforms of CAMK2, a gene well known for its role in promoting neuronal connections, in RNA-Seq data sets of healthy brain tissue and tissue ravaged by Alzheimer’s disease (AD). Looking broadly, the team found ~200 cases of altered splicing in AD in two independent data sets. One isoform of one gene was 40% percent less prevalent in brains affected by AD. This and other examples suggest that many complex cases of splicing hold some sort of function. In other words, they don’t seem to be a result of transcriptional noise. One big lesson from the study is that splicing is much more complex than anyone had realized. How molecular machinery decides to splice is often not a yes-or-no question but instead part of a 3- or 4-way decision between different RNA segments. In human samples, for instance, ~37% of the transcriptome variations are complex. Complex splicing events have not been given much attention in the field, said Gene Yeo, an associate professor of cellular and molecular medicine at the University of California, San Diego, who was not involved with the present work. The new tool, which he plans to use, will “alter the vocabulary of how we think about alternative splicing control.”

Reference Vaquero-Garcia J, Barrera A, Gazzara MR, González-Vallinas J, Lahens NF, Hogenesch JB, Lynch KW, Barash Y. A new view of transcriptome complexity and regulation through the lens of local splicing variations. Elife. 2016 Feb 1;5. pii: e11752. [Epub ahead of print]