PhD project

Supervisor: Monika Gullerova

Genetic information encoded in DNA is constantly exposed to both endogenous and exogenous damaging agents, leading to the occurrence of numerous damaged sites within the genome. Consequently, proficient DNA damage response and repair mechanisms are indispensable for the viability of every living cell. Failure or inaccuracy in DNA repair processes results in the accumulation of DNA damage, adversely impacting cellular viability and contributing to various diseases, notably cancer and aging. Hence, gaining insights into the molecular mechanisms essential for DNA damage repair holds significant importance.

Distinct DNA repair pathways are tailored to address specific types of DNA damage. Among these, double-strand breaks (DSBs) represent the most lethal form of DNA damage due to the physical separation of DNA strands. DSBs are repaired by various proteins through either non-homologous end joining (NHEJ) or homologous recombination (HR) pathways. While DNA repair proteins have been extensively studied for decades, recent attention has turned towards the emerging field of non-coding RNA in the DNA damage response (DDR). We have found that transcripts derived from DSBs are important for efficient DNA repair at multiple levels: they provide a binding platform for DNA repair factors; facilitate the formation of dynamic repair compartments through liquid-liquid phase separation and additionally, they can be modified and processed. Therefore, it is critical to understand the biogenesis and regulation of damage-responsive RNAs.

Drosha is an enzyme that plays a crucial role in the process of microRNA (miRNA) biogenesis, an essential pathway for gene regulation. Specifically, Drosha is a type of ribonuclease III enzyme that is involved in the initial step of converting primary miRNA transcripts (pri-miRNAs) into precursor miRNA (pre-miRNA), which are then processed into mature miRNA molecules that regulate gene expression. Recent research has uncovered a secondary role for Drosha in the DNA damage response, particularly at DSBs. At these breaks, Drosha was proposed to processes RNA transcripts and recruit key repair proteins such as 53BP1 and Rad51. This non-canonical role of Drosha might have a significant implication, as defects in this function could undermine genome stability, potentially leading to mutations or chromosomal abnormalities that contribute to cancer development and aging. However, the exact molecular function of Drosha at DSBs is not known. We propose to investigate novel miRNA-independent role of Drosha in DDR. This research could uncover novel aspects of Drosha’s role in genome stability and reveal potential therapeutic targets in DDR pathways, especially in cancer where DNA repair is often compromised.

Keywords:

Cancer, Molecular Biology

Publications:

1. Bader, A.S., Hawley, B.R., Wilczynska, A. & Bushell, M. The roles of RNA in DNA double-strand break repair. Br J Cancer 122, 613-623 (2020).
2. Michelini, F. et al. From “Cellular” RNA to “Smart” RNA: Multiple Roles of RNA in Genome Stability and Beyond. Chem Rev 118, 4365-4403 (2018).
3. Burger, K., Schlackow, M. & Gullerova, M. Tyrosine kinase c-Abl couples RNA polymerase II transcription to DNA double-strand breaks. Nucleic Acids Res 47, 3467-3484 (2019).
4. Long, Q. et al. The phosphorylated trimeric SOSS1 complex and RNA polymerase II trigger liquid-liquid phase separation at double-strand breaks. Cell Rep 42, 113489 (2023).
5. Gromak, N. et al. Drosha regulates gene expression independently of RNA cleavage function. Cell Rep 5, 1499-1510 (2013).
6. Cabrini, M. et al. DROSHA is recruited to DNA damage sites by the MRN complex to promote non-homologous end joining. J Cell Sci 134 (2021).
7. Francia, S., Cabrini, M., Matti, V., Oldani, A. & d’Adda di Fagagna, F. DICER, DROSHA and DNA damage response RNAs are necessary for the secondary recruitment of DNA damage response factors. J Cell Sci 129, 1468-1476 (2016).
8. Lu, W.T. et al. Drosha drives the formation of DNA:RNA hybrids around DNA break sites to facilitate DNA repair. Nat Commun 9, 532 (2018).
9. Bonath, F., Domingo-Prim, J., Tarbier, M., Friedlander, M.R. & Visa, N. Next-generation sequencing reveals two populations of damage-induced small RNAs at endogenous DNA double-strand breaks. Nucleic Acids Res 46, 11869-11882 (2018).