Evolutionary Emergence of a Novel Splice Variant with an Opposite Effect on the Cell Cycle

Abstract

Alternative splicing contributes greatly to the diversification of mammalian proteomes, but the molecular basis for the evolutionary emergence of splice variants remains poorly understood. We have recently found a novel class of splicing regulatory elements between the polypyrimidine tract (Py) and 3′ AG (REPA) at intron ends in many human genes, including the multifunctional PRMT5 (for protein arginine methyltransferase 5) gene. The PRMT5 element is comprised of two G tracts that arise in most mammals and accompany significant exon skipping in human transcripts. The G tracts inhibit splicing by recruiting heterogeneous nuclear ribonucleoprotein (hnRNP) H and F (H/F) to reduce U2AF65 binding to the Py, causing exon skipping. The resulting novel shorter variant PRMT5S exhibits a histone H4R3 methylation effect similar to that seen with the original longer PRMT5L isoform but exhibits a distinct localization and preferential control of critical genes for cell cycle arrest at interphase in comparison to PRMT5L. This report thus provides a molecular mechanism for the evolutionary emergence of a novel splice variant with an opposite function in a fundamental cell process. The presence of REPA elements in a large group of genes implies their wider impact on different cellular processes for increased protein diversity in humans.

Supplemental material for this article may be found at http://dx.doi.org/10.1128/MCB.00190-15.

ACKNOWLEDGMENTS

We thank Doug Black for providing polyclonal hnRNP H/F and hnRNP F antibodies for the initial tests and for insightful comments on and editing the manuscript, Vincent Lobo for zebrafish, Niaz Mahmood for help with some of the gene expression experiments, the McGill University and Genome Quebec Innovation Centre, particularly Pascale Marquis, for their RNA-Seq service and gene expression analysis, Mike Myschyshyn and Irene Xie for editing, and Sika Zheng for helpful comments on the manuscript.

This work was supported by a discovery grant from the Natural Science and Engineering Research Council of Canada (NSERC) and in part by a CIHR grant (FRN106608) and a Manitoba Research Chair fund provided to J.X.