PHD Student

Updated: 5 months ago
Job Type: FullTime
Deadline: 31 Jul 2022

KEY WORDS: long noncoding RNAs, subcellular localization, synteny, lncRNA orthologues

Principal Investigator: Dr. Barbara Uszczynska-Ratajczak

Research topic: Identification of positionally conserved lncRNAs across human and mouse genomes at subcellular resolution

I. Project description

Vertebrate genomes produce tens of thousands of long noncoding RNAs (lncRNAs) that do not encode for functional proteins. Although lncRNAs have been proven to be functionally important, their sequences evolve much more rapidly than most mRNAs and only <100 lncRNAs have a detectable sequence conservation between human and zebrafish. At the same time, thousands of lncRNAs appear to have conserved positions in vertebrate genomes without almost any sequence conservation. This fact imposes an important question about the functional meaning of positional conservation, in particular of sequence-divergent syntenic orthologues. Moreover, it has been recently shown that lncRNA orthologues undergo distinct cellular processing and exhibit diverse subcellular localizations and biological functions.

The main goal of this project is to study positionally conserved lncRNAs between human and mouse at subcellular resolution. To increase the power of this analysis we will employ our newly developed software – ConnectOR to detect novel, uncatalogued, positionally conserved lncRNAs in human and mouse genomes. To annotate and study them at subcellular resolution, we will develop a new approach – CLS-SF (Capture Long-read Sequencing in Subcellular Fractions). Proposed cutting-edge experimental methodology will allow to study lncRNA orthologues at subcellular resolution with so far unprecedented accuracy and throughput.

Additional information:

  • Research and doctoral theses shall be carried out within the SONATA BIS 11 Grant 2021/42/E/NZ2/00434, entitled “ Functional or not functional? Studying positionally conserved vertebrate lncRNA orthologues at subcellular resolution”, funded by the Polish National Science Centre.
  • PhD students shall receive a stipend in the gross amount of ca 4 300 PLN (3 800 PLN net), for the period of 45 months with possible extension.
  • PhD students shall be subject to social insurance, pursuant to article. 6 section 1 passage 7b of the act of October 13th, 1998 on the social insurance system (Journal of Laws of 2019, item 300, 303 and 730).

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