Regulation of alternative splicing in Arabidopsis thaliana - a combined RNA-Seq and RIP-Seq approach
Final Report Abstract
Understanding the regulation of alternative splicing in Arabidopsis thaliana requires a novel combination of experimental approaches such as RNA sequencing (RNA-seq) and RNA immunoprecipitation sequencing (RIP-seq) with computational approaches. These computational approaches include – but are not limited to – approaches for (i) the analysis of RNA-seq data, (ii) the analysis of RIP-seq data, (iii) the prediction of rhythmically expressed transcripts, (iv) the prediction of differentially used transcripts, (v) the prediction of alternatively spliced genes, and (vi) the visualization of these predictions. The goal of the bioinformatics sub-project of DFG project Regulation of alternative splicing in Arabidopsis thaliana – a combined RNA-Seq and RIP-Seq approach conducted at the Chair of Bioinformatics at the Institute of Computer Science at Martin Luther University Halle-Wittenberg was (i) to develop, to optimize, and to evaluate bioinformatics pipelines for these six tasks, (ii) to apply these six bioinformatics pipelines to the wet-lab data generated by our project partners to perform the above-mentioned predictions, and (iii) to analyse and to interpret the results of these computational predictions. All of this work (i) - (iii) was performed jointly in close collaboration with our project partners at the Chair of RNA Biology and Molecular Physiology at University Bielefeld lead by Prof. Dr. Dorothee Staiger and our lab members at the Chair of Bioinformatics at the Institute of Computer Science at Martin Luther University Halle- Wittenberg.
Publications
- (2014) Regulation of pri-miRNA processing by the hnRNP-like protein AtGRP7 in Arabidopsis. Nucleic Acids Research 42, 9925-9936
Köster T, Meyer K, Weinholdt C, Smith LS, Lummer M, Speth C, Grosse I, Weigel D, Staiger D
(See online at https://doi.org/10.1093/nar/gku716) - (2017) Adaptation of iCLIP to plants determines the binding landscape of the clock-regulated RNA- binding protein AtGRP7. Genome Biology 18, 204
Meyer K, Köster T, Nolte C, Weinholdt C, Lewinski M, Grosse I, Staiger D
(See online at https://doi.org/10.1186/s13059-017-1332-x)
