Thesis supervisor: Dóra Tombácz
Location of studies (in Hungarian): Department of Medical Biology Abbreviation of location of studies: ÁOK
Description of the research topic:
Our aim is to characterize the global transcriptome and epigenome profile of 11 viruses (Human herpesvirus 6, Autographa c. nucleopolyhedrovirus, Vaccinia, Vesicular stomatitis, Mumps, Measles, Rubella, Providence, Zika, Crimian-Congo haemorrhagic fever, Coxackie); to obtain comprehensive knowledge on the various levels of gene expression. We will identify and characterize transcript isoforms, long non-coding (lnc)RNAs, transcriptional overlaps, and their kinetic properties using long-read sequencing (3GS; PacBio, Oxford Nanopore: ONT). We will examine whether the large extent of transcriptional complexity observed in herpesviruses are also present in other viruses.
PolII-ChIP-Seq method will be used for the analysis of transcription 'real-time', while for the analysis of the active, protein-coding genes, the Ribo-Seq method will be carried out. We will generate recombinant Vaccinia, AcMNPV viruses using homologous recombination and CRISPR/Cas9 methods. Genetic modifications will be used for altering the extent of the transcriptional overlaps, etc. They will be analyzed by 3GS. Micro and circular RNAs have been found to regulate gene expression. They will be analyzed both in silico and experimentally in the above mentioned viruses. We will examine the effect of viral infection on the gene expression of Vero cell line.
One of the important forms of the transcription-regulation is the DNA/RNA methylation. Our aim is to characterize the global methylation pattern of viruses (DNA: PacBio, ONT, Illumina-bisulfite-seq; RNA: ONT). We will develop a new algorithm for the base modification detection.
Required language skills: English B2 complex exam Number of students who can be accepted: 2
Deadline for application: 2020-08-14
2024. IV. 17. ODT ülés Az ODT következő ülésére 2024. június 14-én, pénteken 10.00 órakor kerül sor a Semmelweis Egyetem Szenátusi termében (Bp. Üllői út 26. I. emelet).
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