Department of Molecular and Systems Biology


 

Head:
Prof. Marek Figlerowicz

 

 


Staff:
Dr. Paulina Jackowiak,

Dr. Anna Philips,

Dr. Magdalena Alejska,

Dr. Eng. Antonina Lorenz

Post-doctoral position:
Dr. Lucyna Budźko

 


PhD students:
Anna Hojka-Osińska,

Natalia Koralewska,

Katarzyna Kozłowska,

Małgorzata Marszałek-Zeńczak,

Michał Stelmaszczuk,

Ireneusz Stolarek,

Aleksander Strugała,

Michał Zeńczak,

Magdalena Zielińska


 

 

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Two laboratories are affiliated to Department

Laboratory of Genomics

Head: Dr. Luiza Handschuh  

Research Technicians: Dr. Jan Podkowiński, Dr. Paweł Wojciechowski, Dr. Agnieszka Żmieńko

Laboratory of Cell and Tissue Cultures

Head: Dr. Paweł Stróżycki

Research Technicians: Hanna Glapiak, Nelli Malinowska, Dr. Mariola Piślewska-Bednarek

 

Key words:

complex intracellular systems, structural genomics, DNA copy number polymorphism, archaeogenomics, regulatory RNA, RNA degradome, circular RNA, RNA-binding proteins, ribonuclease

 

Research area:

A long-term goal of our research is to elucidate the molecular mechanisms that underlie the formation and functioning of complex intracellular systems. In particular, our studies are focused on the systems whose main components are nucleic acids, both DNA and RNA. In case of DNA, an example of such system is a genome. Thus, we try to identify and get to know the factors that determine genome structure and influence its functioning. The main research objects are model eukaryotic genomes, i.e. Arabidopsis thaliana and human genomes.

In case of RNA, we especially concentrate on its regulatory potential. Accordingly, we are interested in the processes giving rise to complex regulatory RNA-based systems and the mechanisms that allow these systems to function. Initially our studies were mainly focused on RNA viruses. At present, we use model plant organisms and human cell lines, just as in case of the studies on eukaryotic genomes. Another important field of our investigation is a search for new regulatory RNAs. In order to identify such molecules, we apply both the traditional method of in vitro selection of RNA molecules as well as the innovative bioinformatic methods. Moreover, we elaborate the methods to design short molecules regulating miRNA biogenesis, translation or replication of viral RNAs. Recently, we have also begun the studies of RNA degradome. There are several lines of evidence that stable intermediates of RNA degradation (the so-called RNA fragments) have regulatory function in eukaryotic cells. One of our goals is to recognize the role of RNA fragments in virus-host interactions. We not only focus on regulatory RNAs that are encoded in the host genome, but also on viral genome-derived RNA fragments. It seems that RNA degradome may also be a source of biomarkers. Another recently launched project concerns identification and analysis of the functional potential of circular RNAs.

 

Current research activity: 

1. Copy number polymorphism in plant genomes

- factors inducing copy number variation

- mechanisms underlying copy number polymorphism

- functional gene clusters

2. Archaeogenomics

- population inhabiting contemporary Great Poland territory in 1st Millennium CE

- archaeogenomics of microorganisms

3. RNA as a regulator of cell processes

- RNA involvement in regulation of miRNA/siRNA biogenesis

- RNA degradome as a source of regulatory RNAs (biogenesis and functioning of RNA fragments)

- evolution of regulatory RNAs

- circular RNAs in plants and human

 

Most important research achievements:

  • Elaboration of an effective method for the analysis of copy number variation in plants, particularly A. thaliana.
  • Identification of nonallelic homologous recombination as an important mechanism underlying natural variability of the A. thaliana genome.
  • Identification of the genes that both encode proteins which belong to the hepatitis C virus interactome and are located in the regions that show copy number polymorphism. A change in gene copy number may influence HCV infection and the result of antiviral therapy.
  • Identification of microorganisms accompanying 1000-2000-year-old human remains.
  • Revealing a new activity of human ribonuclease Dicer DUF283 domain. The DUF283 and thus Dicer support the process of base-pairing of complementary DNA/RNA. The data collected indicate that Dicer may act as chaperone proteins. 
  • Elaboration of a method for designing short RNA molecules which selectively control the maturation of miRNAs, in vitro and in vivo.
  • Elaboration of a method for regulation of human ribonuclease Dicer with RNA aptamers.
  • Elaboration of an effective method for the analysis of high-copy number, stable intermediates of RNA degradation by two-dimensional polyacrylamide gel electrophoresis.
  • Discovery of a relationship between HCV population structure (genetic polymorphism of HCV quasispecies) and the efficiency of combined interferon-ribavirin treatment of chronic hepatitis C in children.

 

Current projects:

  • Establishment of a novel scientific workshop enabling complex analysis of RNA degradome - elaboration of innovative methods for the identification of RNA degradants and the assessment of their functional potential; National Science Centre project 2012/05/D/NZ2/02238; period: 01.03.2013-31.08.2016; PI: Paulina Jackowiak,
  • Identification of circular RNAs and protein factors involved in their biogenesis in a model plant, Arabidopsis thaliana; National Science Centre project 2014/15/D/NZ2/02305; period: 21.07.2015-20.07.2018; PI: Anna Philips
  • Elucidation of the mechanisms that induce copy number polymorphism of large genome fragments and of the relations between this phenomenon and metabolic gene cluster formation and evolution in plants; National Science Centre project 2014/13/B/NZ2/03837; period: 26.02.2015-25.02.2018; PI: Marek Figlerowicz
  • Dynasty and population of the Piast State in view of the integrated historical, anthropological and genomic studies; National Science Centre project 2014/12/W/NZ2/00466; period: 10.12.2014-09.12.2019; PI: Marek Figlerowicz

 

Selected papers:

1. P. Jackowiak, M. Nowacka, P. M. Stróżycki, M. Figlerowicz.
RNA degradome - its biogenesis and functions.
2011 Nucleic Acids Research 39(17), 7361-7370

2. A. Tyczewska, A. Kurzyńska-Kokorniak, N. Koralewska, A. Szopa, A. M. Kietrys, J. Wrzesiński, T. Twardowski, M. Figlerowicz
Selection of RNA oligonucleotides that can modulate human Dicer activity in vitro
2011 Nucleic Acid Therapeutics 21(5): 333-346

3. J. Sztuba-Solińska, A. Urbanowicz, M. Figlerowicz, J. J. Bujarski
RNA-RNA Recombination in Plant Virus Replication and Evolution
2011 Annual Review of Phytopathology 49: 415-443

4. M. Nowacka, P. Jackowiak, A. Rybarczyk, T. Magacz, P. M. Stróżycki, J. Barciszewski, M. Figlerowicz
2D-PAGE as an effective method of RNA degradome analysis
2012 Molecular Biology Reports 39(1): 139-146

5. A. Kurzynska-Kokorniak, N. Koralewska, A. Tyczewska, T. Twardowski, M. Figlerowicz
A new short oligonucleotide-based strategy for the precursor-specific regulation of microRNA processing by Dicer
2013, PLoS One, 8(10):e77703. DOI 10.1371/journal.pone.0077703.

6. M. Nowacka, P. M. Strozycki, P. Jackowiak, A. Hojka-Osinska, M. Szymanski, M. Figlerowicz
Identification of stable, high copy number, medium-sized RNA degradation intermediates that accumulate in plants under non-stress conditions
2013, Plant Molecular Biology, 83(3):191-204

7. A. Zmieńko, A. Samelak, P. Kozłowski, M. Figlerowicz
Copy number polymorphism in plant genomes.
2014, Theor Appl Genet. 127: 1-18

8. P. Jackowiak, K. Kuls, L. Budźko, A. Mania, M. Figlerowicz, M. Figlerowicz
Phylogeny and molecular evolution of the hepatitis C virus.
2014, Infection, Genetics and Evolution 21, 67–82                                                                                                                            

9. Kurzynska-Kokorniak A, Koralewska N, Pokornowska M, Urbanowicz A, Tworak A, Mickiewicz A, Figlerowicz M.
The many faces of Dicer: the complexity of the mechanisms regulating Dicer gene expression and enzyme activities.
2015, Nucleic Acids Res. 43(9):4365-80

10. Zmienko A, Samelak-Czajka A, Goralski M, Sobieszczuk-Nowicka E, Kozlowski P, Figlerowicz M.
Selection of reference genes for qPCR- and ddPCR-based analyses of gene expression in senescing barley leaves.
2015, PLoS One. 10(2):e0118226.

11. Budzko L, Marcinkowska-Swojak M, Jackowiak P, Kozlowski P, Figlerowicz M.
Copy number variation of genes involved in the hepatitis C virus-human interactome.
2016, Scientific Reports 11;6:31340.

12. Kurzynska-Kokorniak A, Pokornowska M, Koralewska N, Hoffmann W, Bienkowska-Szewczyk K, Figlerowicz M.
Revealing a new activity of the human Dicer DUF283 domain in vitro.
2016, Scientific Reports 5;6:23989.

13. Tworak A, Urbanowicz A, Podkowinski J, Kurzynska-Kokorniak A, Koralewska N, Figlerowicz M.
Six Medicago truncatula Dicer-like protein genes are expressed in plant cells and upregulated in nodules.
2016, Plant Cell Rep. May;35(5):1043-52.

14. Penzkofer T, Jäger M, Figlerowicz M, Badge R, Mundlos S, Robinson PN, Zemojtel T.
L1Base 2: more retrotransposition-active LINE-1s, more mammalian genomes.
2016, Nucleic Acids Res. Oct 18, doi:10.1093/nar/gkw925.

15. Zmienko A, Samelak-Czajka A, Kozlowski P, Szymanska M, Figlerowicz M.
Arabidopsis thaliana population analysis reveals high plasticity of the genomic region spanning MSH2, AT3G18530 and AT3G18535 genes and provides evidence for NAHR-driven recurrent CNV events occurring in this location.
2016, BMC Genomics 8;17(1):893.