Department of RNA Structure and Function

Dr. habil. Katarzyna Pachulska-Wieczorek, associate professor

Head of Department

kasiapw@ibch.poznan.pl
ext. 1236

Research activity

Research area

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)

Keywords

RNA structure
RNA structure probing methods
RNA-protein interactions
Structural bioinformatics
LTR-retrotransposons (Ty1, Ty3),
Retroviruses,
Yeast,
Gag
Arc

Research Projects

Transcriptome-wide analysis of RNA structure in the cell and across cellular compartments, and identification of the impact of cellular factors on RNA structure in S. cerevisiae, NSC OPUS 20
Exploring Ty3 genomic RNA structure during retrotransposition in yeast, NSC PRELUDIUM 20
Arc as a neuronal Gag. Exploring the viral properties and functions of a master regulator of synaptic plasticity, NSC PRELUDIUM 18
RNA structures and interactions with Gag protein that specify Ty1 RNA functions during retrotransposon replication, NSC SONATA BIS 6
Yeast cell factory for mRNA bioproduction (YSCRIPT), EIC Pathfinder
Effectors of retrotransposon movement, PI: D.J. Garfinkel, Collaboration: To understand how the retrotransposon restriction factor affects RNA dynamics and structure., NIH

Selected publications

Gumna J, Andrzejewska-Romanowska A, Garfinkel DJ, Pachulska-Wieczorek K. RNA binding properties of the Ty1 LTR-retrotransposon Gag protein. Int J Mol Sci., 22(16):9103 (2021)
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)

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Department of RNA Structure and Function

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Research activity

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Department of RNA Structure and Function

Researchers:

PhD students:

Research activity

Research area

Keywords

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Research Projects

Selected publications

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