Supervisors:

dr hab. Przemysław Grudnik
dr Marta Pabiś (project leader)

Malopolska Centre of Biotechnology (MCB)

Project description:

The project is designed to uncover the mechanism of action of selected human pluripotent stem cell (PSC)-specific lncRNAs. Although over 170 000 human lncRNAs transcripts are reported in most recent releases of databases (e.g. NONCODE), only a part of those RNAs have been attributed a biological function based on specific experimental studies reported in literature. Moreover, their interaction with binding partners (e.g. proteins) and mechanisms of action underlying their cellular functions are still far from being well understood. There is also a shortage of experimental data concerning lncRNA structure. The PhD student will apply structural biology and biochemical approaches to address these unknowns and work in close collaboration with the Postdoctoral researcher who will focus on lncRNA mechanisms of action on the cellular level. The planned scope of the PhD student work is the following:

• Determination of two-dimensional structures and identification of structural modules of the selected lncRNAs using bioinformatic and chemical probing approaches
• Confirmation of direct interactions with protein binding partners reported in literature and identified within our studies, as well as their biochemical characterization in vitro
• Identification of the localization of protein binding sites on the lncRNAs, both in vitro and in cells (the later in collaboration with the Postdoctoral researcher)
• Three-dimensional structural analysis of largest stable fragments of studied lncRNAs with and without protein-binding partners by cryo-EM and crystallography
• Validation of structural data in cells (in collaboration with the Postdoctoral researcher)

Candidate profile:

• MSc or equivalent degree in biology, biotechnology, chemistry or other relevant field
• Interest in RNA biology and structural biology
• Basic experience in molecular biology and biochemistry
• Previous experience in structural biology techniques is not required but is a plus
• Very good knowledge of English (written and spoken)
• Very good presentation and communication skills
• High motivation and engagement in research work, reasonable level of independence at work, positive attitude, good organizational skills, ability of multitasking