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Institute of Bioorganic Chemistry,
Polish Academy of Sciences
Z. Noskowskiego 12/14
61-704 Poznań
tel centrala: (+48) 61 852 85 03
fax: (+48) 61 852 05 32
e-mail: ibch@ibch.poznan.pl

Sekretariat Dyrektora, tel: 61 852 89 19

Address

Department of Structure and Function of Retrotransposons

Dr. habil. Katarzyna Pachulska-Wieczorek

Head of Department
kasiapw@ibch.poznan.pl
ext.
1193

Angelika Andrzejewska MSc. BEng.
 
PhD student

Małgorzata Zawadzka MSc
PhD student

PhD students:

Julita Gumna MSc 
biologist

Technical Staff:

Dr. Katarzyna Purzycka
adiunkt

Researchers:

Prof. Ryszard W. Adamiak

profesor

Affiliated professors :

  • Andrzejewska A, Zawadzka M, Gumna J, Garfinkel DJ, Pachulska-Wieczorek K. In vivo structure of the Ty1 retrotransposon RNA genome. Nucleic Acids Res. (2021)

  • Gumna J, Zok T, Figurski K, Pachulska-Wieczorek K, Szachniuk M. RNAthor - fast, accurate normalization, visualization and statistical analysis of RNA probing data resolved by capillary electrophoresis. PLoS One., 15(10):e0239287 (2020)

  • Andrzejewska A, Zawadzka M, Pachulska-Wieczorek K. On the Way to Understanding the Interplay between the RNA Structure and Functions in Cells: A Genome-Wide Perspective. Int J Mol Sci., 21(18):6770 (2020)

  • Gumna J, Purzycka KJ, Ahn HW, Garfinkel DJ, Pachulska-Wieczorek K. Retroviral-like determinants and functions required for dimerization of Ty1 retrotransposon RNA. RNA Biol., 16(12):1749-1763 (2019)

  • Zawadzka M, Pachulska-Wieczorek K. Na dobre i na złe: rola endogennych retroelementów u człowieka [For good and for bad: the role of endogenous retroelements in humans]. Postepy Biochem., 65(3):217-223 (2019)

  • Kumari P, Aeschimann F, Gaidatzis D, Keusch JJ, Ghosh P, Neagu A, Pachulska-Wieczorek K, Bujnicki JM, Gut H, Großhans H, Ciosk R. Evolutionary plasticity of the NHL domain underlies distinct solutions to RNA recognition. Nat Commun., 9(1):1549 (2018)

  • Lepeta K, Purzycka KJ, Pachulska-Wieczorek K, Mitjans M, Begemann M, Vafadari B, Bijata K, Adamiak RW, Ehrenreich H, Dziembowska M, Kaczmarek LA normal genetic variation modulates synaptic MMP-9 protein levels and the severity of schizophrenia symptoms.EMBO Molecular Medicine, 9(8):1100-1116 (2017)

  • Z. Miao, R.W. Adamiak, M. Antczak, R.T. Batey, A.J. Becka, M. Biesiada, M.J. Boniecki, J. Bujnicki, S.J. Chen, C.Y. Cheng, F.C. Chou, A.R. Ferré-D’Amaré, R. Das, W.K. Dawson, D. Feng, N.V. Dokholyan, S. Dunin-Horkawicz, C. Geniesse, K. Kappel, W. Kladwang, A. Krokhotin, G.E. Łach, F. Major, T.H. Mann, M. Magnus, K. Pachulska-Wieczorek, D.J. Patel, J.A. Piccirilli, M. Popenda, K.J. Purzycka, A. Ren, G.M. Rice, J.J. Santalucia, J. Sarzynska, M. Szachniuk, M. Tandon, J.J. Trausch, S.Tian, J. Wang, K.M. Weeks, B. Williams, Y. Xiao, X. Xu, D. Zhang, T. Zok, E. WesthofRNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme.RNA, 23(5):655-672 (2017)

  • Błaszczyk L, Biesiada M, Saha A, Garfinkel DJ, Purzycka KJ.Structure of Ty1 Internally Initiated RNA Influences Restriction Factor Expression.Viruses, 9(4). pii: E74 (2017)

  • K. Pachulska-Wieczorek, S.F. Le Grice, K.J. Purzycka Determinants of Genomic RNA Encapsidation in the Saccharomyces cerevisiae Long Terminal Repeat Retrotransposons Ty1 and Ty3.Viruses, 8(7) (2016)

  • M. Biesiada, K. Pachulska-Wieczorek, R.W. Adamiak, K.J. Purzycka RNAComposer and RNA 3D structure prediction for nanotechnology.Methods, 103:120-7 (2016)

  • D.J. Garfinkel, J.M. Tucker, A. Saha, Y. Nishida, K. Pachulska-Wieczorek, L. Błaszczyk, K.J. PurzyckaA self-encoded capsid derivative restricts Ty1 retrotransposition in Saccharomyces.Curr Genet., 62(2):321-9 (2016)

  • K. Pachulska-Wieczorek, L. Błaszczyk, M. Biesiada, R.W. Adamiak, K.J. Purzycka The matrix domain contributes to the nucleic acid chaperone activity of HIV-2 Gag.Retrovirology, 13:18 (2016)

  • Biesiada M, Purzycka KJ, Szachniuk M, Blazewicz J, Adamiak RW,Automated RNA 3D Structure Prediction with RNAComposer.Methods Mol Biol.;1490:199-215 (2016)

  • Y. Nishida, K. Pachulska-Wieczorek, L. Błaszczyk, A. Saha, J. Gumna, D.J. Garfinkel, K.J. Purzycka Ty1 retrovirus-like element Gag contains overlapping restriction factor and nucleic acid chaperone functions.Nucleic Acids Res., 3;43(15):7414-31 (2015)

Selected publications

  • RNA structures and interactions with Gag protein that specify Ty1 RNA functions during retrotransposon replication, NSC SONATA BIS 6

  • Arc as a neuronal Gag. Exploring the viral properties and functions of a master regulator of synaptic plasticity, NSC PRELUDIUM 18

  • Effectors of retrotransposon movement, PI: D.J. Garfinkel, Collaboration: To understand how the retrotransposon restriction factor affects RNA dynamics and structure., NIH

Research activity

  • RNA structure 

  • RNA structure probing methods

  • RNA-protein interactions

  • Structural bioinformatics

  • LTR-retrotransposons (Ty1, Ty3),

  • Retroviruses,

  • Yeast,

  • Gag

  • Arc

  • correlation between RNA structure, function, and stability in the cell

  • RNA structure changes during the RNA lifetime, 

  • RNA structural elements and transitions on both 2D and 3D structure levels that specify RNA function at different stages of Ty1 retrotransposon replication 

  • mechanism of genomic RNA packaging into VLPs and virions

  • RNA binding activity and function of Gag and Gag-like proteins 

  • computational tools for visualization and statistical analysis of RNA structure mapping data (RNAthor)

  • modeling of RNA secondary structure with experimental data (SHAPE, DMS)

  • comparative analysis of RNA 2D models

  • control of retrotransposon movement (collaboration D.J. Garfinkel, UGA USA)

Research area

Keywords

Research activity