RNA-binding proteins in transcription and genome integrity

For decades, it was believed that RNA was merely an intermediate step between DNA and protein effectors. It is now appreciated that RNA is an extremely versatile molecule that affects almost every aspect inside a cell. Most often RNA exerts its functions together with RNA binding proteins, or RBPs, in a partnership that promotes different behaviors according to the situation. Given their critical role in maintaining cell homeostasis, it is not surprising that RBPs malfunction underlies the onset of many diseases. In paper I, we find that WRAP53β, an RBP involved in telomere biogenesis, Cajal body formation and DNA repair, is downregulated in epithelial ovarian cancers, and that this correlates with poor prognosis of the patients. At the molecular level, this results in defective DNA damage signaling and repair, establishing WRAP53β expression as a potential biomarker for the prediction of drug response of epithelial ovarian cancer. In paper II, we show that ongoing splicing is required for proper DNA damage signaling and repair. Using small molecules to block spliceosome assembly, or by knocking-down various splicing factors, we demonstrate that the mechanism underlying the regulation of DNA repair by splicing involves downregulation of the E3 ubiquitin ligase RNF8. Re-introduction of this protein into splicing-deficient cells completely restores DNA repair signaling. Accordingly, altered DNA repair may be the underlying cause of various diseases associated with deregulation of splicing factors. In paper III, we show that dyskerin and the associated H/ACA complex localize to splicing speckles and associate with RNAPII-transcribed genes genome-wide. Moreover, we demonstrate that this complex carries out pseudouridylation of mRNAs cotranscriptionally, affecting their translation efficiency in cells. Collectively, the results presented in this thesis corroborate the pervasive involvement of RBPs and RNA metabolism in gene expression and DNA repair, and, moreover, highlight new targets and possibilities for treating disease.

List of scientific papers

I. Hedström E, Pederiva C, Farnebo J, Nodin B, Jirström K, Brennan DJ, Farnebo M. Downregulation of the cancer susceptibility protein WRAP53β in epithelial ovarian cancer leads to defective DNA repair and poor clinical outcome. Cell Death Dis. 2015;6(10):e1892.
https://doi.org/10.1038/cddis.2015.250

II. Pederiva C*, Böhm S*, Julner A, Farnebo M. Splicing controls the ubiquitin response during DNA double-strand break repair. Cell Death Differ. 2016;23(10):1648-57. *These authors contributed equally to this work.
https://doi.org/10.1038/cdd.2016.58

III. Pederiva C, Trevisan DM, Chen S, Larsson O, Ule J, Baranello L, Agostini F, Farnebo M. Co-transcriptional pseudouridylation of mRNAs by the H/ACA complex controls translational efficiency. [Manuscript]