A molecular thermometer connects body temperature with alternative splicing

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In higher eukaryotes, alternative splicing plays a fundamental role in increasing the genomes coding capacity and in dynamically regulating protein expression. Activation-induced alternative splicing in response to changing extracellular conditions makes alternative splicing a potential mechanism to regulate day-time dependent changes in gene expression. Therefore, alternative splicing has been hypothesized to be involved in regulating the mammalian circadian clock, but functional evidence is only beginning to emerge and regulatory details are as of yet missing. Following our longstanding interest in the splicing factor U2AF26, we found U2AF26 itself to be alternatively spliced. More recently we could show U2AF26 alternative splicing to be circadian and light-inducible in particular in mouse cerebellum and to play a fundamental role in the molecular clockwork and adaptation to jetlag. A frameshift in the alternative U2AF26 isoform allows translation into the 3-UTR thus generating a protein domain with homology to a central component of the fly circadian clock. Our data lead to a model in which light-induced U2AF26 alternative splicing slows down the adaptation process thus stabilizing the circadian clock against changes in light:dark conditions. Having identified the first functionally important circadian splicing switch in a mammalian system we are now aiming to characterize the signaling module that translates the input light (or circadian time) into the output splicing. We will first characterize the cis-acting RNA-element, which is the sequence within the pre-mRNA, that is necessary and sufficient to regulate this functionally important splicing switch (aim 1). We will then identify trans-acting proteins that bind to this sequence in order to regulate alternative splicing. Furthermore, we will analyze signaling cascades that mediate circadian activity of such proteins (aim 2). These detailed molecular analyses will then allow us to identify coregulated genes on a system-wide scale (aim 3). To this end we will use sequence comparison with the cis-acting element (aim 1), knock-down/RNA-Seq and CLIP with the trans-acting factor (aim 2) and identification of circadian and light-inducible exons in cerebellum using RNA-Seq. Together, our analyses will shed first light on the regulation of circadian and light-inducible alternative splicing. This will be a major contribution towards understanding circadian gene expression and the regulation of signal-induced alternative splicing in circadian settings. As the splicing switch we are analyzing is functionally important, we will also provide new insights into the mechanism of clock-resetting under jetlag conditions in peripheral clocks. Merging the fields of chronobiology and alternative splicing will open new directions in these exciting research areas and will form the basis for further interdisciplinary work and collaborations.