Here you can find a summary of the workpackage’s objectives:
WP1: Biogenesis of circRNAs and other unusual splice isoforms
Canonical splicing, including alternative splicing, is catalyzed by the general splicing machinery, the spliceosome. Splice site choice thereby is mainly governed by splice signal sequences in the pre-mRNA and additional regulatory proteins, subsumed under the term ‘splicing code’. This general model most likely also holds for other, recently discovered unusual forms of splicing, in particular for circRNAs. CircRNAs are particularly abundant in the brain, and the specific determinants in their splice code and how this relates to canonical alternative splicing are largely unexplored. WP1 will thus concentrate on the biogenesis of circRNAs, in particular their RNA processing reactions, mechanistic relationships with standard forms of alternative splicing, protein interactions (circRNP assembly), nuclear-cytoplasmic trafficking, and potential release from cells inside of vesicles (exosomes).
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WP2: Molecular mechanisms of circRNA function
For insights into circRNA function, consortium members will perform functional knockdown and overexpression of circRNAs followed by phenotypic analysis. Strategies have been set up for the knockdown of the circular versus linear forms by RNAi. Investigations will be extended to fly models where circRNAs have been downregulated with space and time resolution.
WP3: Role for circRNAs in neurological disease
Deregulation of the expression and function of non-coding RNAs is an important cause of brain disease. Non-coding RNAs such as microRNAs have been linked to pathological mechanisms in diseases such as temporal lobe epilepsy (TLE), amyotrophic lateral sclerosis (ALS) and Parkinson’s disease (PD). However, the role of other classes of non-coding RNAs is less well-understood or remains unexplored. WP3 will further map changes in circRNA expression in neurological disease, to identify molecular pathways affected by these changes, and to understand the functional consequences of disease-associated changes of circRNAs.
WP4: CircRNA as potential biomarkers in human brain and cardiovascular diseases
In analogy to alternative splicing we hypothesize that circRNA expression may also provide specific signatures for human diseases. To address this we will analyse circRNA expression profile in brain tissue, iPS and blood from humans suffering from neurodegenerative diseases including ALS, temporal lobe epilepsy, and Parkinson’s disease.
Since sophisticated NGS and related bioinformatic analysis is hard to use in standard clinical and analytical laboratories an easily accessible detection platform will be established in form of microarrays or, if appropriate, a microtiter plate. The platform will be used to prove circRNA-biomarker detection with popular biosensors alternatively and in comparison to NGS.
