Department of RNA Biochemistry


 

Head:
Prof. Jerzy Ciesiołka

 

 


Staff:
Prof. Jan Wrzesiński;

Prof. Mariola Dutkiewicz;

Agata Świątkowska, PhD;

Paulina Żydowicz-Machtel, PhD;

Damian Janecki, PhD;

Martyna Kabacińska, MSc Eng.


PhD Students:
Joanna Szpotkowska, MSc;

Marek Kazimierczyk, MSc Eng.

 


 

Fig. 1.


 

Mapowanie miejsc dostępnych do hybrydyzacji komplementarnych oligonukleotydów w obrębie regionu terminalnego 5? mRNA p53 oraz obniżenie poziomu białka p53 w komórkach MCF-7 w obecności oligonukleotydów antysensowych typu 2?-OMe i GAP.

Fig. 2.


 

Struktura drugorzędowa 5' UTR wirusa coxackie B3 z zaznaczonymi na kolorowo regionami hybrydyzacji oligomerów:  pomocniczych 2?- O-metylo-16-merów (ome No) oraz siRNA (si No) (panel na lewo). Wyciszanie ekspresji konstruktu reporterowego  hrGFP-5?UTRcvb3 za pomocą siRNA działających bez oraz w obecności pomocniczych oligonukleotydów antysensowych (panel na prawo).

Fig. 3.


 

Fig. 4.


Key words:

mRNA, p53, non-coding RNA region, UTR, translation regulation, IRES-dependent translation, coxsackievirus B3, CVB-3, antisense oligonucleotides, siRNA, Sus scrofa, gametogenesis, small non-coding RNA, piRNA biogenesis, catalytic nucleic acids, in vitro selection

 

Research profile:

Currently, in our Department there are three major fields of research activity:

First one is focused on structural and functional characterization of the conserved, non-coding regions of cellular mRNA and viral RNA. Particularly, the laboratory is interested in RNAs which contain IRES element (Internal Ribosome Entry Site). It has been proposed that IRES elements play crucial role in cell as an additional level of the proteins expression regulation when cap-dependent translation is strongly reduced, particularly during the cell phase transition, differentiation or stress. One of the ongoing projects concerns the 5' untranslated region (5'UTR) of p53 mRNA and its function in the translation process. The structural analysis of coding and non-coding regions of coxsackievirus B3 aims at a design of effective nucleic acid-based antiviral agents such as siRNAs and antisense oligonucleotides.

The second research direction is to clarify the role of small non-coding RNAs (miRNAs, piRNA and tRF) in the mechanisms of gametogenesis using as mammalian model - the domestic pig (Sus scrofa). We intend to characterize the most numerous group of sncRNA, which are the piRNA molecules and to determine their role in male and female gonads. In addition, we plan to characterize the shared fraction of sncRNA occurring in both gonads and learn about its role in gametogenesis.

The third direction of research aims on application of HDV ribozymes and other catalytic nucleic acids as biosensors which will be capable to detect toxic metal ions or small molecule metabolites. Additionally, HDV ribozyme derived from hepatitis delta virus is used as a potential antiviral target and we search for low-molecular-weight compounds such as antibiotics that can inhibit the ribozyme activity.

 

Current research activity:

  • elucidation of the role of the 5'-terminus of p53 mRNA sequence variants in translation regulation
  • modulation of synthesis efficiency of p53 isoforms by antisense oligonucleotides targeting of the 5'-terminal region of p53 mRNA
  • elucidation of the secondary structure of RNA genome of CVB-3
  • targeting of viral RNA of CVB-3 with oligonucleotide tools
  • elucidation of the role of small non-coding RNA in mammalian organism development
  • characteristics of piRNAs and Piwi proteins present in S. scrofa gonads and their participation in gametogenesis
  • HDV ribozymes as potential antiviral targets
  • application of nucleic acids for construction of biosensors 

 

Major recent results:

  • Characterization of secondary structure of sequence variants of the 5'-terminal region of p53 mRNA, which are synthesized from various transcription promoters and which use alternative translation initiation sites in generating p53 protein isoforms.
  • Determining the impact of different sequence variants of the 5'-terminal region of p53 mRNA on translation initiation in vitro as well as in HeLa and MCF-7 cells.
  • Application of antisense oligomers targeting the 5'-terminal region of p53 mRNA for translation inhibition of the full-length p53 and Δ40p53 isoform in vitro and in MCF-7 cells. One of the tested oligomers seems to be a good candidate to be used as a support treatment in radiotherapy.
  • Finding that the structure of the 5'-terminal region of p53 mRNA, which acts as an IRES element, plays an important role in translation regulation of the full-length p53 and Δ40p53 isoform under stress conditions.
  • Induction new sites accessible for hybridization of complementary oligonucleotide tools in the 5'UTR of CVB-3 by means of 16-mers 2'-O-methyl-RNA in order to increase the efficiency of targeting this region with siRNA.
  • Identifying a number of sncRNA molecules occuring in the S. scrofa gonads and determining their genomic location. Finding that the piRNA sequences correspond to different non-coding regions of the S. scrofa genome.
  • Determining that the mechanism of piRNA biogenesis in the S. scrofa gonads is different from that proposed in the literature for D. melanogaster "ping pong" mechanism.
  • Finding the occurrence in piRNA molecules at their 3' end post-transcriptional modifications as methylation 2'-O-ribose group.
  • Mapping binding sites for neomycin B, amikacin and actinomycin D to the HDV ribozyme with a set of RNA structural probing methods and molecular modeling. Possible mechanisms by which these antibiotics can impact on the catalytic activity of the HDV ribozyme was evaluated.
  • Discovery of nucleolytic properties of antibiotic bacitracin. Particularly effective degradation occurs in the case of RNA molecules, most likely via hydrolytic mechanism.
  • Using in vitro selection methodology to obtain several DNazymes active in the presence of Cd2+ and some other divalent metal ions, which turn out to be variants of earlier known DNAzyme 8-17.
  • Characterization of efficient RNA-cleaving DNAzymes which show the highest catalytic efficiency at pH 4.0 – 4.5 and are completely inactive at pH higher than 5.0. Importantly, these DNAzymes do not require any divalent metal as cofactors for catalysis.
  • Characterization of secondary structure of the 3' terminal region of coxsackievirus B3 replicative strand. This region consists of structural domains that fold independently.
  • Mapping the sites accessible to hybridization of complementary oligonucleotides in the highly structured RNA regions of coxsackievirus B3.

 

Current research projects:

  • The role of the 5' non-coding regions of p53 mRNA transcripts, which are synthesized from various transcription promoters and which use alternative translation initiation sites in generating p53 protein isoforms (National Science Centre OPUS) /2014-2017/
  • The role of protein factors that bind to the 5' non-coding region of human p53 mRNA in regulation of p53 expression at the translational level (National Science Centre OPUS) /2017-2020/
  • Impact of noncoding RNAs on renal cell development and carcinogenesis (National Science Centre OPUS) /2017-2020/

 

Selected publications:

A. Górska, L. Błaszczyk, M. Dutkiewicz, and J. Ciesiołka
Length variants of the 5′ untranslated region of p53 mRNA and their impact on the efficiency of translation initiation of p53 and its N-truncated isoform ΔNp53.
RNA Biology, 10, 1726-1740 (2013)

A. Górska, A. Swiatkowska, M. Dutkiewicz, and J. Ciesiołka
Modulation of p53 Expression Using Antisense Oligonucleotides Complementary to the 5′-Terminal Region of p53 mRNA In Vitro and in the Living Cells.
PLOS ONE, 8, e78863 (2013)

J. Wrzesinski, L. Błaszczyk, M. Wrońska, A. Kasprowicz, K. Stokowa-Sołtys, J. Nagaj, M. Szafraniec, T. Kuliński, M. Jeżowska-Bojczuk, and J. Ciesiołka
Mapping interactions of selected antibiotics and their copper(II) complexes with antigenomic delta ribozyme.
FEBS Journal, 280, 2652-2664 (2013)

K. Stokowa-Sołtys, N. Gaggelli, J. Nagaj, W. Szczepanik, J. Ciesiołka, J. Wrzesiński, A. Górska, E. Gaggelli, G. Valensin, and M. Jeżowska-Bojczuk
High affinity of copper(II) towards amoxicillin, apramycin and ristomycin. Effect of these complexes on the catalytic activity of HDV ribozyme.
Journal of Inorganic Biochemistry, 124, 26-34 (2013)

M. Dutkiewicz, A. Ojdowska, A. Górska, A. Swiatkowska, J. Ciesiołka
The structural and phylogenetic profile of the 3' terminus of coxsackievirus B3 negative strand.
Virus Research, 188, 81-89 (2014)

D. Kowalczykiewicz, A. Świercz, L. Handschuh, K. Leśniak, M. Figlerowicz, and J. Wrzesiński
Characterization of Sus scrofa small non-coding RNAs present in both female and male gonads.
PLOS ONE, 9, e113249 (2014)

J. Ciesiołka, M. Jeżowska-Bojczuk, J. Wrzesiński, K. Stokowa-Sołtys, J. Nagaj, A. Kasprowicz, L. Błaszczyk, W. Szczepanik
Antibiotic bacitracin induces hydrolytic degradation of nucleic acids.
Biochimica et Biophysica Acta, 1840, 1782-1789 (2014)

K. Stokowa-Sołtys, A. Kasprowicz, J. Wrzesiński,J. Ciesiołka, N. Gaggelli, E. Gaggelli, G. Valensin, and M. Jeżowska-Bojczuk
Impact of Cu2+ ions on the structure of colistin and nucleic acids degradation properties of the antibiotic.
Journal of Inorganic Biochemistry, 151, 67-74 (2015)

L. A. Kirsebom, J. Ciesiolka
Pb+2–induced cleavage of RNA.
In: Handbook of RNA Biochemistry, Second, Completely Revised and Enlarged Edition. Edited by R. K. Hartmann, A. Bindereif, A. Schön, and E. Westhof. WILEY-VCH Verlag, ISBN-13: 9783527327768, pp. 269-284 (2015)

A. Kasprowicz, K. Stokowa-Sołtys, J. Wrzesiński, M. Jeżowska-Bojczuk, and J. Ciesiołka
In vitro selection of deoxyribozymes active with Cd2+ ions resulting in variants of DNAzyme 8-17.
Dalton Transactions, 44, 8138-8149 (2015)

M. Dutkiewicz, A. Ojdowska, J. Kuczyński, V. Lindig, H. Zeichhardt, J. Kurreck, J. Ciesiołka
Targeting Highly Structured RNA by Cooperative Action of siRNAs and Helper Antisense Oligomers in Living Cells.
PLOS ONE, 10, e0136395 (2015)

A. Swiątkowska, P. Żydowicz, A. Górska, J. Suchacka, M. Dutkiewicz, and J. Ciesiołka
The role of structural elements of the 5'-terminal region of p53 mRNA in translation under stress conditions assayed by the antisense oligonucleotide approach.
PLOS ONE, 10, e0141676 (2015)

K. Stokowa-Sołtys, N. A. Barbosa, A. Kasprowicz, R. Wieczorek, N. Gaggelli, E. Gaggelli, G. Valensin, J. Wrzesiński, J. Ciesiołka, T. Kuliński, W. Szczepanik, and M. Jeżowska-Bojczuk
Studies of viomycin, an anti-tuberculosis antibiotic: copper(II) coordination, DNA degradation and the impact on delta ribozyme cleavage activity.
Dalton Trans., 45, 8645–8658 (2016)

M. Dutkiewicz, A. Stachowiak, A. Swiatkowska, and J. Ciesiołka
Structure and function of RNA elements present in enteroviral genomes.
Acta Biochimica Polonica, 63(4), 623-630 (2016)

A. Swiatkowska, P. Zydowicz, J. Sroka, and J. Ciesiołka
The role of the 5' terminal region of p53 mRNA in the p53 gene expression.
Acta Biochimica Polonica, 63(4), 645-651 (2016)

A. Kasprowicz, K. Stokowa-Sołtys, M. Jeżowska-Bojczuk, J. Wrzesiński, and J. Ciesiołka
Characterization of highly efficient RNA-cleaving DNAzymes that function at an acidic pH with no divalent metal ion cofactors.
ChemistryOpen, DOI: 10.1002/open.201600141 (2017)