Characterization of cis-acting elements that control oscillating alternative splicing. Issue 8 (3rd August 2018)

• Record Type: Journal Article
• Authors: Goldammer, Gesine; Neumann, Alexander; Strauch, Miriam; Müller-McNicoll, Michaela; Heyd, Florian; Preußner, Marco
• Is Part Of: RNA biology. Volume 15:Issue 8(2018)
• Page Start: 1081
• Page End: 1092
• Publication Date: 2018-08-03
• Subjects: Alternative splicing -- circadian clock -- SR proteins -- minigene -- body temperature cycle -- phosphorylation -- iCLIP -- splicing network; RNA -- Periodicals; Molecular biology -- Periodicals; Molecular biology; RNA; Periodicals; 572.8805
• DOI: 10.1080/15476286.2018.1502587
• Languages: English
• ISSNs: 1547-6286

Abstract

ABSTRACT: Alternative splicing (AS) in response to changing external conditions often requires alterations in the ability of sequence-specific RNA-binding proteins to bind to cis- acting sequences in their target pre -mRNA. While daily oscillations in AS events have been described in several organisms, cis -acting sequences that control time of the day-dependent AS remain largely elusive. Here we define cis -regulatory RNA elements that control body-temperature driven rhythmic AS using the mouse U2af26 gene as a model system. We identify a complex network of cis -regulatory sequences that regulate AS of U2af26, and show that the activity of two enhancer elements is necessary for oscillating AS. A minigene comprising these U2af26 regions recapitulates rhythmic splicing of the endogenous gene, which is controlled through temperature-regulated SR protein phosphorylation. Mutagenesis of the minigene delineates the ci s-acting enhancer element for SRSF2 within exon 6 to single nucleotide resolution and reveals that the combined activity of SRSF2 and SRSF7 is required for oscillating U2af26 AS. By combining RNA-Seq with an siRNA screen and individual-nucleotide resolution cross-linking and immunoprecipitation (iCLIP), we identify a complex network of SR proteins that globally controls temperature-dependent rhythmic AS, with the direction of splicing depending on the position of the cis -acting elements. Together, we provide detailed insights into the sequence requirements that allow trans -acting factors to generate daily rhythms in AS.