Poor understanding of the spliceosomal mechanisms to select intronic 3' ends (3'ss) is a major obstacle to deciphering eukaryotic genomes. Here, we discern the rules for global 3'ss selection in yeast. We show that, in contrast to the uniformity of yeast splicing, the spliceosome uses all available 3'ss within a distance window from the intronic branch site (BS), and that in 70% of all possible 3'ss this is likely to be mediated by pre-mRNA structures. Our results reveal that one of these RNA folds acts as an RNA thermosensor, modulating alternative splicing in response to heat shock by controlling alternate 3'ss availability. Thus, our data point to a deeper role for the pre-mRNA in the control of its own fate, and to a simple mechanism for some alternative splicing.

We thank C. Query, J. Valcárcel, and J. Warner for helpful discussions and comments on the manuscript. This research has been supported by the Spanish Ministry of Science (BIO2008-01091 and 363), MC #510183, EURASNET (LSHG-CT-2005-518238), CSIC (200920I195), and Agaur. M. M. is supported in part by a Training of Researchers (FI) fellowship (Agaur) and M. P. by a Carlos III PhD fellowship.