Bioinformatic pipeline for the analysis of the molecular mechanisms linking alternative splicing to the regulation of circadian rhythms in plants using RNA-Seq

ESTEFANIA MANCINI; R. GUSTAVO SCHLAEN; ARIEL CHERNOMORETZ; MARCELO YANOVSKY

Mendoza

Simposio; VI Latin American Symposium on High Performance Computing HPCLatAm 2013; 2013

High-Performance Computing Latin America Community

Post-transcriptional mechanisms are an important regulatory layer of circadian networks across kingdoms. In plants, many core clock genes are alternatively spliced in a temperature dependent manner, but the proteins modulating this process are not known. There is increasing evidence that alternative splicing (AS) is regulated not only by SR and hnRNP auxiliary factors, but also by changes in the levels or activities of core spliceosomal components or spliceosome assembly factors. In  mammals, spliceosome assembly is controlled by the Survival Motor Neuron (SMN) protein complex. Arabidopsis homologue of GEMIN2, a component of the SMN complex conserved from yeast to humans, display developmental and physiological alterations such as early flowering and period shortening of multiple circadian rhythms.Here we propose a bioinformatic pipeline focused on the discovery of alternative splicing events in Arabidopsis thaliana using RNA-Seq data. This approach revealed that gemin2 phenotypes are associated with changes in a small subset of AS events, including thoseinvolving the core clock genes TOC1 and CCA1.