RNA 3′-End Modifications Group

RNA 3′-END MODIFICATIONS GROUP

Research
Our research focuses on understanding the role of RNA 3′-end modifications in post-transcriptional gene regulation, with particular emphasis on RNA uridylation, RNA degradation pathways, and their contribution to cellular adaptation to changing environmental conditions.
RNA uridylation, the addition of non-templated uridine residues to the 3′ ends of RNA molecules, is an important regulatory mechanism influencing RNA stability, turnover, and function. Our previous studies demonstrated that mRNA uridylation is widespread in the fission yeast Schizosaccharomyces pombe and revealed its role in regulating the directionality of mRNA degradation.
Currently, we aim to understand how RNA 3′-end modifications contribute to gene expression regulation under different physiological conditions, particularly during the transition to cellular quiescence.

Main Research Areas
1. RNA Metabolism and Uridylation During Cellular Quiescence
Cellular quiescence (G0) is a reversible, non-proliferative state that plays a crucial role in cell survival, stress adaptation, and long-term viability. Despite its biological importance, the mechanisms controlling RNA stability and degradation during quiescence remain poorly understood.
Using S. pombe as a model organism, we investigate how RNA uridylation and different RNA degradation pathways contribute to transcriptome remodeling during the transition from proliferation to quiescence, long-term maintenance of the G0 state, and subsequent cell cycle re-entry.
2. Terminal uridylyltransferases and post-transcriptional RNA regulation
We investigate the functions of terminal uridylyltransferases (TUTases), enzymes responsible for adding uridine residues to RNA 3′ ends, and their roles in regulating RNA stability and degradation.
As part of our scientific collaborations, we also study the functional specialization of human terminal uridylyltransferases TUT4 and TUT7, with particular emphasis on their involvement in mRNA decay and processing body (P-body) biology.
3. RNA metabolism and cellular responses to neurodegeneration-associated mutations
In collaboration with other research groups, we investigate the molecular consequences of mutations associated with neurodegenerative diseases. Using yeast models and transcriptomic analyses, we aim to identify cellular pathways affected by pathogenic variants and better understand their impact on cellular physiology.

Research Methods
Our group combines molecular biology, yeast genetics, and microbiology with high-throughput sequencing technologies and bioinformatic data analysis.
Our main research approaches include:
Fission yeast (Schizosaccharomyces pombe) as a model organism.
Cellular quiescence and stress-response models.
RNA sequencing (RNA-seq) and transcriptomic analyses.
Transcriptome-wide RNA 3′-end mapping (3′ RACE-based approaches).
Direct RNA sequencing using Oxford Nanopore technology.
Genetic and phenotypic characterization of mutants affecting RNA metabolism.
Bioinformatic and computational analyses of RNA processing and degradation.

Team
Lidia Lipińska-Zubrycka, PhD, Eng. – Group Leader
Shirsha Roy, MSc – PhD Student
Julia Tryc, BSc – MSc Student, Biotechnology (Bachelor’s degree obtained in 2024)
Dominika Burakowska – BSc Student, Biology
Maciej Kowalski – Undergraduate Student, MISMaP
Alumni
Gabriela Kulik, MSc – Master’s thesis (2023)
Jeremi Sputo – Bachelor’s thesis (2026)
Szymon Skierczyński – Bachelor’s thesis (2026)
Here you can find some news from our group:
https://rnatailscom.wordpress.com/

Research Grants
1. Molecular Insights into Cellular Quiescence: The Role of Uridylation and RNA Metabolism
Funding: National Science Centre (NCN), SONATA programme
Duration: 2025–2028
Principal Investigator: Lidia Lipińska-Zubrycka
Status: Ongoing
2. Identification of Substrates of Eukaryotic Uridylation
Funding: National Science Centre (NCN), MINIATURA programme
Duration: 2020–2021
Principal Investigator: Lidia Lipińska-Zubrycka
Status: Completed
Selected Publications
Grochowski M., Lipinska-Zubrycka L., Brzyżek G., Jurkovic B., Swiezewski S., Townsend StJ., Ralser M., Malecki M. (2024). Uridylation regulates mRNA decay directionality in fission yeast. Nature Communications, 15, 8359.
Taracha-Wisniewska A., Parks E., Miller M., Lipinska-Zubrycka L., Dworkin S., Wilanowski T. (2024). Vitamin D Receptor regulates the expression of the Grainyhead-like 1 gene. International Journal of Molecular Sciences, 25(14), 7913.
Lipinska-Zubrycka L., Grochowski M., Bähler J., Malecki M. (2023). Pervasive mRNA uridylation in fission yeast is catalysed by both Cid1 and Cid16 terminal uridyltransferases. PLOS ONE, 18(5), e0285576.

Awards and Distinctions
Lidia Lipińska-Zubrycka
2024 – Individual Rector’s Award, University of Warsaw, for scientific achievements.
2024 – Distinction in the Prof. W. Krzyżosiak Award Competition for outstanding experimental research in nucleic acid biology.
2024 – Team Rector’s Award, University of Warsaw, for a publication in Nature Communications.
2024–2025 – Awardee of the IDUB Mentoring Programme for Young Female Researchers and Educators, University of Warsaw.
2023–2024 – IDUB Microgrants supporting Open Access publications in PLOS ONE and Nature Communications.
2018 – Doctoral Thesis Award, Polmos Żyrardów Foundation.
2018 – Third place in the BioHack Łódź Bioinformatics Competition.
2017 – Elsevier Certificate of Outstanding Contribution in Reviewing for Food Control.
2014–2015 – Best Oral Presentation Awards at biotechnology conferences.
2017 – Travel Grant from the German Association for General and Applied Microbiology (VAAM).