Cajal body functions in the post-transcriptional regulation of gene expression in plantcells under physiological and abiotic stress condition

We are seeking a motivated PhD student for participation in 3-year project: Cajal body functions in the post-transcriptional regulation of gene expression in plant cells under physiological and abiotic stress condition.

Short project description:
Cajal bodies (CBs) are known as nuclear domains participating in maturation of non-coding RNAs,mainly snRNA and snoRNA. Our last research project (Niedojadło et all. 2014, 2016) revealed thepresence of poly(A) RNA, including mRNA in Cajal bodies of eukaryote somatic cells. It was also established that CBs are not places of transcription and splicing, as they lack newly synthesised RNA, RNA polymerase II and SR-proteins (spliceosome elements). Next, it was shown that during oxygen deficiency stress, there is a strong increase in the amount of poly(A) RNA in Cajal bodies. Ncb-1 mutants of Arabidopsis thaliana, which completely lack CBs, die faster under hypoxia than WT plants. Based on this data, we have hypothesized that Cajal Bodies are involved in the posttranscriptional regulation of gene expression in plant cells under physiological conditions and under abiotic stress.


To test this hypothesis, we will perform the following:
a) sequence and compare the transcriptomes of Cajal bodies, cell nuclei and whole plant cells.
b) compare the transcriptome of plants’ Cajal bodies and nucleus under physiological conditions and hypoxic stress.
c) study the location of transcripts and their speed of movement and retention time in CBs and in
the nucleus under physiological conditions and during hypoxic stress.
d) analysis transcripts’ route and rate of RNA accumulation in the double mutants, such as
ncb-1 mutants with mutants of other proteins involved in the exosome or NMD pathway

We will use the subcellular sequencing technique, which involves the analysis of RNA obtained from cell fragments (laser capture microdissections). Next, in situ hybridisation of live cells will be used to detect RNAs that accumulate and do not accumulate in CBs. We will also conduct intracellular localisation and measure the amount of RNA residing in CBs, nucleus, and cytoplasm under physiological conditions, during oxygen deficiency stress, and after reoxygenation.

Stress in plants is one of the main reasons for loss of yields in agriculture. According to forecasts, the frequency of droughts, which are the main cause of oxygen deficiency in plants, will greatly increase throughout the whole planet, including parts of Europe. The findings of the project will reveal some ways plants respond to hypoxia and the potential of new methods of regulating abiotic stress.

Criteria for evaluating candidates
The successful candidate will have a background in working with RNA.
Experience with RNA sequencing, qPCR, crossing A. thaliana and microscopy techniques will be a plus.

Applications including a copy of master’s degree related to the subject area of the project, cover letter, CV, summary of scientific
interests and contact details for two referees should be made to dr hab. Janusz Niedojadło (e-mail: [Email Address Removed])

Fully funded 3-year PhD scholarship grant (2500 PLN / 550 euro). Scholarship allows full financial support in Poland.
Deadline for application is June 10th 2017.