Home page of the Genomic Regulation Lab
New positions available within ERC Starting Grant (PhD student, postdoc, technician) – please get in touch if you would like to work with us!
Welcome to the STOP lab
Genomic Regulation – focusing on Gene Ends
Our lab’s aim is to integrate different levels of gene expression regulation – chromatin, transcription and RNA processing – focusing on gene ends.
We want to understand the basic mechanisms of when and how transcription stops (terminates), but also how perturbed termination contributes to disease. Premature termination, called also transcription attenuation, is particularly relevant in the pathological context. Premature termination was known to be an important regulatory mechanism in bacteria and yeast, but overlooked in humans and animals in general. We and others have recently shown that this phenomenon is a very abundant genomic event in metazoa. It has also medical implications, particularly in cancer.
Our main approaches are based on NGS (genomics and nascent transcriptomics), combined with molecular biology, biochemistry and proteomics. The lab’s experimental workhorse are mammalian cell culture models of cancer and neuronal differentiation. We use both experimental and computational approaches.
Update: in our new ERC Starting Grant “Alternative gene ends: the crosstalk of RNA cleavage and transcription termination” we have the following positions available: PhD student in nascent transcriptomics (experimental and computational), postdoc combining protein biochemistry and genomics, postdoc in NGS bioinformatics and microscopy high-throughput screening, technician responsible for protein expression and purification.
Official ads will follow, but if you are interested don’t hesitate to reach out already!
Kinga Kamieniarz-Gdula, PhD, DSc
kinga.kamieniarz-gdula [at] amu.edu.pl
Kinga is an experimental and computational biologist. She finished her undergraduate studies at Adam Mickiewicz University in Poznań. She then did her PhD as well as a short postdoc in the field of Chromatin and Epigenetics with Rob Schneider at the Max-Planck-Institute in Freiburg, Germany. After that she moved to the University of Oxford to join Nick Proudfoot’s lab, supported by a Marie Skłodowska-Curie Fellowship. In Oxford, Kinga started studying the links between transcription termination and RNA processing, and became fascinated by gene ends.
After 13 successful years abroad, Kinga returned to Poznań to set up her own research group in October 2019. Her team is generously supported by NAWA Polish Returns, NCN SONATA BIS, EMBO Installation Grant and ERC Starting Grant.
In her spare time Kinga loves hiking in the local forests with her family.
Agata Stępień, PhD, eng.
Agata received her Engineer and MSc degree in biotechnology from the University of Agriculture in Krakow. She then moved to Poznan for her PhD, and worked in the group of Prof. Jarmolowski and Prof. Szweykowska-Kulinska at Adam Mickiewicz University. Her PhD research was focused on the characterization of the crosstalk between the spliceosome and the microprocessor in plants by molecular biology, microscopic and biochemical techniques. After graduating in 2017, Agata got her first Postdoc position in K. Dorota Raczynska’s group to study the role of U7 snRNA in human cells. In 2019, Agata joined STOP lab to investigate transcription termination changes during cancer progression.
Martyna received her MSc degree in Molecular Biology from Adam Mickiewicz University in Poznań where she continued with PhD research in the group of prof. Hans Bluyssen. She focused on potential strategies to inhibit STAT proteins activity in inflammation during onset and progression of atherosclerosis. Currently she is writing up her PhD thesis and making sure experiments in STOP lab can run smoothly.
Martyna loves cats, dogs and plants and aims to convert our hallway to an exotic greenhouse. In her free time you’ll find her in the bushes watching birds.
Joanna Kwiatkowska, PhD
Asia earned her MSc and PhD degrees in Molecular Biology from the Adam Mickiewicz University. In the Laboratory of RNA Biochemistry, headed by Prof. Mikolaj Olejniczak, she used biochemical approaches to characterize the mechanism of bacterial RNA molecules interaction with chaperone proteins. She joined STOP lab in June 2022 and is interested in biochemical aspects of alternative polyadenylation. She likes non-fiction literature, jogging and sewing.
Magda graduated from the Poznan University of Medical Sciences with a Master’s degree in Medical Biotechnology. During her undergraduate studies she worked on the role of long non-coding RNA molecules in cancer and their potential utility as biomarkers at the Laboratory of Cancer Genetics (Greater Poland Cancer Center). In October 2020 she started her PhD studies in our team and investigates how the chromatin environment influences transcription termination, and vice versa. In her spare time Magda enjoys popular science writing. Together with Martyna they form the green-fingered fraction in the lab, taking loving care of the plants on our floor.
Upasana Saha, PhD
Upasana received her MSc in Biotechnology from Visva-Bharati in India. She continued her PhD in India at Jadavpur University under the supervision of Prof. Biswadip Das. Her research involved understanding mRNA quality control pathways in Saccharomyces cerevisieae, focusing mainly on the nucleus. In 2019, she moved to the lab of Prof. Torben Heick Jensen in Aarhus University, Denmark for her first postdoc position. There she studied the role of the nuclear poly(A) binding protein Nab2p in mRNA homeostasis. She joined STOP lab in October 2021 to investigate the molecular mechanism of premature transcription termination. Upasana loves cooking, shopping and exploring new places.
1) CLP1-dependent premature transcription termination opposes neurodegeneration.
Gdula MR, Kopczyńska M, Saha U, Kamieniarz-Gdula K.
Neuron. 2022 https://doi.org/10.1016/j.neuron.2022.03.012
2) Transcriptional Control by Premature Termination: A Forgotten Mechanism.
Kamieniarz-Gdula K, Proudfoot NJ.
Trends Genet. 2019 https://doi.org/10.1016/j.tig.2019.05.005
3) Selective Roles of Vertebrate PCF11 in Premature and Full-Length Transcript Termination.
Kamieniarz-Gdula K, Gdula MR, Panser K, Nojima T, Monks J, Wiśniewski JR, Riepsaame J, Brockdorff N, Pauli A, Proudfoot NJ.
Mol Cell. 2019 https://doi.org/10.1016/j.molcel.2019.01.027
4) WNK1 kinase and the termination factor PCF11 connect nuclear mRNA export with transcription.
Volanakis A, Kamieniarz-Gdula K [joint-first & co-corresponding author], Schlackow M, Proudfoot NJ.
Genes Dev. 2017 https://doi.org/10.1101/gad.303677.117
5) BRCA1 recruitment to transcriptional pause sites is required for R-loop-driven DNA damage repair.
Hatchi E, Skourti-Stathaki K, Ventz S, Pinello L, Yen A, Kamieniarz-Gdula K, Dimitrov S, Pathania S, McKinney KM, Eaton ML, Kellis M, Hill SJ, Parmigiani G, Proudfoot NJ, Livingston DM.
Mol Cell. 2015 https://doi.org/10.1016/j.molcel.2015.01.011
6) R-loops induce repressive chromatin marks over mammalian gene terminators.
Skourti-Stathaki K, Kamieniarz-Gdula K, Proudfoot NJ.
Nature. 2014 https://doi.org/10.1038/nature13787
7) The genomic landscape of the somatic linker histone subtypes H1.1 to H1.5 in human cells.
Izzo A, Kamieniarz-Gdula K [joint-first author], Ramírez F, Noureen N, Kind J, Manke T, van Steensel B, Schneider R.
Cell Rep. 2013 https://doi.org/10.1016/j.celrep.2013.05.003
8) Regulation of transcription through acetylation of H3K122 on the lateral surface of the histone octamer.
Tropberger P, Pott S, Keller C, Kamieniarz-Gdula K, Caron M, Richter F, Li G, Mittler G, Liu ET, Bühler M, Margueron R, Schneider R.
Cell. 2013 https://doi.org/10.1016/j.cell.2013.01.032
9) A dual role of linker histone H1.4 Lys 34 acetylation in transcriptional activation.
Kamieniarz K, Izzo A, Dundr M, Tropberger P, Ozretic L, Kirfel J, Scheer E, Tropel P, Wisniewski JR, Tora L, Viville S, Buettner R, Schneider R.
Genes Dev. 2012 https://doi.org/10.1101/gad.182014.111
More publications in PubMed.
Prof. Elmar Wahle, MLU, Halle, Germany
Dr Andrea Pauli, IMP, Vienna, Austria
Dr Stephan Hamperl, HMGU, Munich, Germany
Dr Shazia Irshad, University of Oxford, UK
Prof. Hiroshi Kimura, Tokyo Institute of Technology, Japan
YouTube: popular science
We are affiliated with the Institite of Molecular Biology and Biotechnology (IBMiB), Faculty of Biology, Adam Mickiewicz University (AMU) in Poznań. Our laboratory is located in the building of the Center for Advanced Technology, at the Morasko Campus which hosts all Science Faculties of AMU.
Poznań is the capital of the Wielkopolska (Greater Poland) region. It is a vibrant university city, with an urban area population of ~1 million, located only 3 hours away from Warsaw and Berlin. At the same time, it is a paradise for nature lovers, as it is surrounded by beautiful forests & lakes.
Center for Advanced Technology
Uniwersytetu Poznańskiego 10
61-614 Poznań, POLAND
Email: kinga.kamieniarz-gdula [at] amu.edu.pl
Lab members: firstname.lastname@example.org