Department of RNA Structural Genomics

 


 

Head:
Prof. Elżbieta Kierzek

 

 

 


Staff:

Dr Elżbieta Lenartowicz,

Dr Ewa Biała

 


 

PhD Students:


Paula Michalak, MSc Eng;

Julita Piasecka, MSc;

Barbara Szutkowska, MSc

 


 

Rys.1


 

Rys.2


 

Rys.3


 

 

 

 

Key words

RNA structural genomics, RNA viruses, isoenergetic microarrays, modified microarray probes, nucleic acids thermodynamics of nucleic acids, modified oligonucleotides, RNA structure, RNA interactions, pathogenic RNA

 

Research profile

The research of Department of RNA Structural Genomics focus on studies of RNA secondary and tertiary structures as well as complexes of RNA with functional proteins, other RNA or small molecule ligands. Goal of these research is not only to determine RNA structure, but also to use this knowledge to modulate RNA functional activities, including pathogenic RNAs involved with human diseases. The tools for study of RNA structures and interactions are beside others chemical mapping and  microarrays mapping based on application of isoenergetic microarrays. One of the main goals of the Department is to improve microarrays mapping applicability for the study of the structure and interactions of RNA. At present moment, the Department research objects are RNA of influenza virus. The goal is to determine secondary structures of selected influenza virus segments and functional crucial structural motifs of vRNA(-) and RNA(+).The Department’s research also includes selection and application of short modified oligonucleotides and their bioconjugats as functional and structural probes tested in vitro and in cell lines toward inhibition of influenza virus proliferation.

 

Actual research

  • RNA structural genomics of influenza virus, influence of RNA structure on virus replication
  • Study of structure and interactions of selected segments of influenza virus vRNA(-) and RNA(+) and important for function structural motifs of virus RNA in vitro and in vivo.
  • Determination in the RNA of influenza virus the regions of modified oligonucleotides and ligands strong binding with application of isoenergetic and small molecule microarrays (collaboration with Mathews D. Disney, The Scripps Research Institute, USA).
  • Selection and optimization of modified oligonucleotides and ligands as potential inhibitors of influenza virus life cycle.
  • Study of structures and interactions of complexes of influenza virus vRNA(-) and virus nucleoprotein (NP).
  • Inhibition and regulation of influenza virus proliferation.
  • Modified oligonucleotides – antisense and microarrays strategies.
  • Improving microarrays mapping method with isoenergetic microarrays (collaboration with Department of Structural Chemistry and Biology of Nucleic Acids from IChB PAN and prof. Douglas H. Turner from Department of Chemistry, University of Rochester, USA)
  • Thermodynamic and comparison analysis of studied RNA, prediction of RNA secondary structure.

 

Main research achievement

  • Defining thermodynamic rules of isoenergetic microarrays hybridization and determining the microarrays mapping methodology based on model RNAs such as: 5S rRNA from Escherisia coli, tRNAPhe from Saccharomyces cerevisiae, tRNAiMetand tRNAmMet from Lupinus Luteus (Department of RNA Structural Genomics and Department of Structural Chemistry and Biology of Nucleic Acids). Defining the rules of isoenergetic modified probes binding to model RNA structural motifs.
  • Microarrays mapping method was successfully applied to study structure, function and interactions of several natural RNAs, such as five homological retrotransposon R2 5'RNAs from Bombyx mori (323 nt.), Saturnia pyri (329 nt.), Callosamia promethea (336 nt.), Coscinocera hercules (330 nt.) and Samia cynthia (339 nt.). Theirs secondary structures were determined and common for all these RNAs structural motifs, including pseudoknot, were found.
  • Isoenergetic microarrays can also be used as alternative method to study interactions of RNA in complexes RNA1/RNA2, RNA/protein and RNA1/RNA2/protein. Studies were performed on regulatory RNA (OxyS RNA and DsrA RNA from E. coli) and theirs complexes with fragments of the target mRNA (rpoS and fhlA, respectively) and parent protein Hfq.
  • Also it was shown that chimeric LNA-DNA primers are substrates for reverse transcriptase and in comparison to DNA primers make possible chemical mapping of thermodynamic stable fragments of target RNAs.
  • Chemical, enzymatic and microarray mapping revealed equilibrium between pseudoknot and hairpin structures for 63-nucleotide region of influenza A segment 7 mRNA, containing 3’ splice site. Probably it is regulatory element in virus mRNA splicing.
  • Conserved structure motif in segment 7 mRNA of influenza A virus was identified. The motif contains sequence coding for influenza essential proteins, M1 and M2, also contains M4 mRNA 5’ splice site. Biochemical structural mapping, mutagenesis, and NMR confirms the predicted three-way multibranch structure. The defined secondary structure motif is involved in regulation of segment 7 splicing.
  • Conserved structural motif in segment 5 mRNA of influenza A was identified. Results with modified oligonucleotides showed that it could be good target in antisense strategies leading to inhibition of virus proliferation.
  • Secondary structure of segment 8 vRNA of influenza virus type A was determined (875 nt) based on chemical mapping, thermodynamic rules, bioinformatics analysis and hybridization on isoenergetic microarrays. This was first publication about secondary structure of entire influenza virus RNA segment. Base pairs conservation of the determined structure is 83.6% for type A influenza.
  • Effective antisense oligonucleotides in inhibition of influenza virus proliferation were designed based on segment 8 vRNA secondary structure. The most effective three oligonucleotides significantly inhibit virus proliferation: 25, 20 and 16 times. Antisense oligonucleotides were specific for type A and not influence the proliferation of strain B type of virus.
  • Secondary structure of segment 7 vRNA of influenza virus type A (1027 nt) was determined based on chemical mapping, sequence-structure analysis and microarray mapping. High thermodynamic stability and conservation of its structural motifs for type A could suggest their important function, for example in packaging process of influenza virion. RNA Structural motifs could influence on proteins binding, RNA editing, regulation of virus replication or transcription.

 

Actual research project

  • Conserved RNA structural motifs in influenza virus: toward revealing viral RNA functions, (NCN, Harmonia)
  • Folding RNA: From AIDS to the Human Genome, subaward, National Institutes of Health (NIH, USA)
  • In vivo and in vitro structure of influenza virus RNA. The structural determinants behind the inhibition of influenza virus proliferation with modified antisense oligonucleotides, siRNAs and small molecule ligands, (NCN, Opus)

Wybrane publikacje

E. Kierzek, R. Kierzek, W.N. Moss, S.M. Christensen, T.H. Eickbush, D.H. Turner
Isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an RNA element orchestrating R2 retrotransposon protein function.Nucleic Acids Research, 36, 1770-1782 (2008).

E. Kierzek, S.M. Christensen; T.H. Eickbush, R. Kierzek; D.H. Turner, W.N.Moss
Secondary structures for 5' regions of R2 retrotransposon RNAs reveal a novel conserved pseudoknot and regions that evolve under different constraints.Journal of Molecular Biology, 390, 428-442 (2009).

E. Kierzek
Binding of short oligonucleotides to RNA: Studies of binding of common RNA structural motifs to isoenergetic microarrays.Biochemistry, 48, 11344-11356 (2009).

A. Fratczak, R. Kierzek, E. Kierzek
Isoenergetic microarrays to study the structure and interactions of DsrA and OxyS RNAs in two- and three-component complexes.
Biochemistry, 50, 7647-7665 (2011).

W.N. Moss, L.I. Dela-Moss, E. Kierzek, R. Kierzek, S.F. Priore, D.H. Turner
The 3 ' splice site of influenza A segment 7 mRNA can exist in two conformations: a pseudoknot and a hairpin. PLOS One, 7, e38323, (2012).

S.F. Priore, E. Kierzek, R. Kierzek, J.R. Baman, W.N. Moss, L.I. Dela-Moss, D.H. Turner
Secondary structure of a conserved domain in the intron of influenza A NS1 mRNA.
PLOS One, 8, e70615 (2013).

Y. Zhou, E. Kierzek, Z.P. Loo, M. Antonio, Y.H. Yau, Y.W. Chuah, S. Geifman-Shochat, R. Kierzek, G. Chen
Recognition of RNA duplexes by chemically modified triplex-forming oligonucleotides.
Nucleic Acids Research, 41, 6664–6673 (2013).

E. Kierzek, M. Malgowska, J. Lisowiec, D.H Turner, Z. Gdaniec, R. Kierzek
The contribution of pseudouridine to stabilities and structure of RNAs.
Nucleic Acids Research, 42, 3492–3501 (2014).

T. Jiang, S.D. Kennedy, W.N. Moss, E. Kierzek, D.H. Turner,
Secondary Structure of a Conserved Domain in an Intron of Influenza A M1 mRNA.
Biochemistry, 53, 5236-5248 (2014).

I. Yildirim, E. Kierzek, R. Kierzek, G.C. Schatz
Interplay of LNA and 2ʹ-O-methyl RNA in the structure and thermodynamics of RNA hybrid systems: A
molecular dynamics study using revised AMBER force field and comparison to experimental results.
The Journal of Physical Chemistry B, 118, 14177-14187 (2014).

R. Kierzek, D.H. Turner, E. Kierzek
Microarrays for identifying binding sites and probing structure of RNAs.
Nucleic Acids Research, 43, 1-12 (2015).

J. Lisowiec, M. Magner, E. Kierzek, E. Lenartowicz, R. Kierzek
Structural determinants for alternative splicing regulation of the MAPT pre-mRNA.
RNA Biology, 12, 330-342, (2015).

M. Soszynska-Jozwiak, P. Michalak, W.N. Moss, R. Kierzek, E. Kierzek, A Conserved Secondary Structural Element in the Coding Region of the Influenza A Virus Nucleoprotein (NP) mRNA Is Important for the Regulation of Viral Proliferation.
PloS One, 10, e0141132 (2015).

E. Lenartowicz, J. Kęsy, A. Ruszkowska, M. Soszynska-Jozwiak, P. Michalak, W.N. Moss, D.H. Turner, R. Kierzek, E. Kierzek, Self-Folding of Naked Segment 8 Genomic RNA of Influenza A Virus.
PloS One, 11, e0148281 (2016).

E. Lenartowicz, A. Nogales, E. Kierzek, R. Kierzek, L. Martinez-Sobrido, D.H. Turner,
Antisense Oligonucleotides Targeting Influenza A Segment 8 Genomic RNA Inhibit Viral Replication.
Nucleic Acid Therapeutics, 26, 277-285 (2016).

A. Ruszkowska, E. Lenartowicz, W. N. Moss, R. Kierzek and E. Kierzek,
Secondary structure model of the naked segment 7 influenza A virus genomic RNA.
Biochemical Journal, 473, 4327-4348 (2016).