PhD Topics

1. The role RNA modifications in DNA replication and repair

Supervisor: assoc.prof. Mgr. Štěpánka Vaňáčová, Ph.D.

Annotation:

The internal and terminal RNA modifications play crucial roles in a number of essential processes of eukaryotic organisms. They regulate the production of germ cells, cellular differentiation, response to stress, and defects in this pathway have been linked to a number of human diseases. The aim of this project is to study in details how specific terminal RNA modifications regulate and interconnect with DNA replication and repair. The student will master number of diverse methodical approaches, such as human cell culture manipulations (cultivation, RNAi, CRISPR/Cas9, etc.), fluorescence microscopy, protein expression and purification, RNA small scale and high-throughput analyses and/or enzymatic assays.

She/he will have the opportunity to work in a dynamic lively team, attend prestigious international conferences and collaborate with experts at other European institutes. Students from Vanacova group typically continue in their carrier at highly prestigious institutes after accomplishing their theses, such as Yale, Stanford, FMI in Basel, ETH Zurich, Columbia University in New York, etc.

Prospective student should ideally have done masters in molecular biology/biochemistry and have a laboratory experience in nucleic acids and/or protein purification and analysis. The most highly valued feature will however be excitement for science and strong drive in tackling important biological questions.

The applicant must have good English language skills – both spoken and written. The PhD candidate must have a Masters degree.

Recommended literature:

Abakir A, et al. N6-methyladenosine regulates the stability of RNA:DNA hybrids in human cells. Nat Genet. 2020 Jan;52(1):48-55. doi: 10.1038/s41588-019-0549-x. 2019.PMID: 31844323

Marnef A, Legube G.Nat Genet. m(6)A RNA modification as a new player in R-loop regulation. 2020 Jan;52(1):27-28. doi: 10.1038/s41588-019-0563-z.

Santos-Pereira JM, Aguilera A.Nat Rev Genet. R loops: new modulators of genome dynamics and function.2015 Oct;16(10):583-97. doi: 10.1038/nrg3961. Epub 2015 Sep 15.PMID: 26370899 

Covelo-Molares, H., Bartosovic, M., Vanacova S. 2018 RNA methylation in nuclear pre-mRNA processing, WIRES RNA, DOI: 10.1002/wrna.1489

Keywords: epitranscriptomics, DNA replication, posttranscriptional RNA modifications, RNA