Wojciech Siwek, PhD

Doctor in Biological Sciences in the field of Biochemistry

Principal Investigator –  Identification of transcriptional memory maintenance factors through a cell selection strategy (IMMUNE-GENEMEMO)/ Horizon 2020 Marie Skłodowska-Curie Action Individual Fellowship

Main research focus: gene control, epigenetics, chromatin, structural biology

e-mail: wojciech.siwek@ug.edu.pl


Academic career:

From the early steps of my scientific career, I have been striving for independence. During my MSc studies at the University of Warsaw, PL I worked in a laboratory that enabled me to pursue my own project. During this time, I became fascinated by molecular mechanisms of gene regulation and have been following this path ever since. Moreover, I completed an international internship at a world-renowned research institute, the Sainsbury Laboratory, UK and co-organized a laboratory training workshop for high school students with the Centre for Innovative Bioscience Education, PL.

To gain deeper understanding of gene regulation, during my PhD studies at the International Institute of Molecular and Cell Biology, PL I focused my efforts on structural biology of protein-DNA interactions. I designed my own research project, persuaded my PhD advisor to follow this path and secured a scholarship and research funding, as a principal investigator, for this work. This resulted in the discovery of a mechanism underlying specific recognition of methylated DNA by proteins. The research gave rise to two high impact publications (among others) in an international peer-reviewed journal on which I am the first and for the second one also the corresponding author. Within the time of my PhD project, I kick started a long-standing collaboration with a mass spectrometry laboratory and the results of that partnership became part of the published work, as well as my thesis. I wrote the manuscripts resulting from my work and advised my younger colleagues. Moreover, in that time, I completed postgraduate studies in analytical chemistry at the University of Warsaw, PL, created a scientific discussion club and organized several high-profile, scientific events with Nobel Prize laureates.

For my postdoctoral training, initially at Instituto Gulbenkian de Ciência, PT and later at the Department of Biochemistry, University of Oxford, UK, both with Lars Jansen, I decided to expand and consolidate my interests in gene regulation above structural biology to a more physiological model system. In the lab, I spearheaded a novel theme centered on gene regulation in mammalian cells that went above and beyond the host laboratory established expertise. I discovered a mechanism by which transcriptional memory is established in human cells. On that work, I am the first and corresponding author. I was also a co-advisor to a PhD student, on this publication, I am a corresponding author. Additionally, I developed a novel method to measure nucleosome dynamics that resulted in a first author, publication. For my postdoctoral training, I secured a fellowship and as a co-PI with my advisor, a research grant from the Portuguese state funding agency. I was also a lecturer for the PhD program and a member of the postdoctoral committee at the Instituto Gulbenkian de Ciência, PT.

Achievements from my postdoc, as well as the tools and assays I developed during that time, allowed me to secure a Marie Skłodowska-Curie global fellowship to continue my work, on transcriptional memory, as an independent research fellow at the Massachusetts General Hospital (MGH), Harvard Medical School, USA in partnership with the International Centre for Cancer Vaccine Science (ICCVS) at the University of Gdańsk, PL. More recently, I secured an assistant professor position at the ICCVS, together with a start-up package. Aside from the research I have been conducting at the MGH, I also completed an intensive, nine-month long course on Leadership in Research offered by Harvard University. This training consolidated my expertise in laboratory management and gave me the necessary tools to establish a successful research group at the ICCVS in the field of epigenetics and innate immunity.



publications from post-doctoral work:

  • Sahar S.H. Tehrani, Pawel Mikulski, Izma Abdul-Zani, João F. Mata, Wojciech Siwek*, Lars E.T. Jansen*. (2023) STAT1 is required to establish but not maintain interferon-γ-induced transcriptional memory. EMBO J. e112259

*Corresponding authors

Summary and contribution:

STAT1 is the key transcription factor in IFNγ signaling. In this work, we showed that STAT1 is required to establish but not maintain IFNγ transcriptional memory. Additionally, we demonstrated that transcription of a memory gene is not sufficient to establish memory. Moreover, we showed that STAT1 and IRF1 are recruited more rapidly to chromatin of memory genes upon restimulation but the degree of activation and nuclear import of STAT1 is not changed.


  • Wojciech Siwek*, Sahar S.H. Tehrani, João F. Mata and Lars E.T. Jansen*. (2020) Activation of clustered IFNγ target genes drives cohesin-controlled transcriptional memory. Molecular Cell. 80(3):396-409.e6

*Corresponding authors

Summary and contribution:

Transcriptional memory is a process during which cells induced with a cue show increased rates of gene expression after subsequent re-stimulation. In this publication, we explored the nature of establishment and maintenance of IFNγ-induced transcriptional memory in human cells that is relevant for the physiological phenomenon of trained immunity. We discovered GBPs as novel genes showing strong transcriptional memory. We found that cells can remember previous cytokine exposure through at least 14 cell division cycles. We determined the stochastic nature of the process by a single cell RNA-seq. Finally, we discovered that strongly memorized genes tend to reside in genomic clusters and uncovered a cohesin-based regulatory mechanism controlling establishment of transcriptional memory.

The work was highlighted by Science Immunology: “A cytokine to remember me by” and covered by national media, Science in Poland (scienceinpoland.pap.pl): “How do cells memorize information? A new lead.”


publications from PhD work:

  • Honorata Czapinska, Wojciech Siwek, Roman H. Szczepanowski, Janusz M. Bujnicki, Matthias Bochtler and Krzysztof J. Skowronek. (2019) Crystal structure and directed evolution of specificity of NlaIV restriction endonuclease. Journal of Molecular Biology. 431(11):2082-2094

Summary and contribution:

Protein engineering can enhance enzyme function for the benefit of a selected biotechnology process. In this work, we used advanced protein engineering and directed evolution methods to create a restriction enzyme with novel sequence specificity. We developed a compartmentalization-based selection strategy for direct evolution of NlaIV restriction endonuclease. We obtained new variants of the protein with altered sequence specificity. We determined the kinetic properties of those variants. Finally, we solved the structure of the NlaIV restriction endonuclease in the apo form and computationally modelled the DNA into the structure.


  • Marta Szychowska(1), Wojciech Siwek(1), Damian Pawolski, Asgar Abbas Kazrani, Krzysztof Pyrc and Matthias Bochtler. (2016) Type III CRISPR complexes from Thermus thermophilus. Acta Biochim Pol. 63(2):377-86
  • Equal contribution

Summary and contribution:

The CRISPR system is a bacteriophage defense strategy that revolutionized molecular biology. In this work we purified CRISPR complexes from a native source of Thermus thermophilus by multistep chromatography combined with northern blot monitoring of specific gRNAs. Next, we determined the mass of the complexes by size exclusion chromatography and demonstrated that the biogenesis or stability of the gRNAs is dependent on the complex components.


  • Karolina Mierzejewska(1), Wojciech Siwek(1)*, Honorata Czapinska(1), Magdalena Kaus-Drobek, Monika Radlinska, Krzysztof Skowronek, Janusz M. Bujnicki, Michal Dadlez and Matthias Bochtler*. (2014) Structural basis of the methylation specificity of R.DpnI. Nucleic Acids Research. 42(13):8745-54
  • Equal contribution, *Corresponding authors

Summary and contribution:

DNA modifications can maintain gene expression states. Here, we discovered that R.DpnI, a modification specific restriction enzyme, selects for the modified DNA by indirect readout. The methyl groups on separate strands in the substrate DNA are adjacent to each other in 3D. This proximity enforces a conformational change in the DNA that is selected for by the enzyme. We obtained a DNA co-crystal structure of R.DpnI with both protein domains binding DNA molecules. Next, we validated the structure with biochemical means. Finally, we performed hydrogen-deuterium exchange MS assays to gain insights into dynamics of the complex.


  • Wojciech Siwek, Honorata Czapinska, Matthias Bochtler, Janusz M. Bujnicki and Krzysztof Skowronek. (2012) Crystal structure and mechanism of action of the N6-methyladenine-dependent type IIM restriction endonuclease R.DpnI. Nucleic Acids Research. 40(15):7563-72.

Summary and contribution:

DNA modifications can maintain gene expression states. In this work, we established a modification-dependent restriction endonuclease R.DpnI as a structural model to study how proteins read and act upon DNA modifications. We performed extensive biochemical analysis and obtained a high resolution DNA co-crystal structure of R.DpnI. We discovered that the enzyme is composed of two domains which both can independently bind DNA in a sequence- and methylation-sensitive manner. We concluded that independent readout of DNA sequence and methylation by the two domains contributes to the enzyme’s exceptional specificity and helps the monomeric enzyme to cut the second strand after introducing a nick.


book chapter:

  • Wojciech Siwek(1), Mariluz Gómez-Rodríguez(1), Daniel Sobral, Ivan R. Corrêa Jr and Lars E.T. Jansen. (2018) time-ChIP: a method to determine long-term locus-specific nucleosome inheritance. Methods in Molecular Biology. 1832:131-158
  • Equal contribution

Summary and contribution:

Chromatin modifications and dynamics are essential for maintenance of gene expression states. In this work, we developed a novel approach to measure histone turnover at high resolution across long timescales – called time-ChIP. This is a SNAP-tag, pulse-chase-based method that in combination with high throughput sequencing can trace long-term fate of a chromatin bound histone pool, genome wide. We developed novel biotin-based SNAP-tag substrates. We showed that the H3 histone variants are locally retained in chromatin during the cell cycle but exchange rapidly on active parts of the genome.


Research projects:

role as principal investigator:

  1. Apr 2023 (results pending), EMBO installation grant, EU (250000 €) “Mechanisms for Maintenance of Transcriptional Memory.”
  2. June 2023, granted, start date under negotiation, (2022/47/D/NZ1/01883), National Science Centre, PL (665000 €) “Mechanisms for Establishment of Transcriptional Memory.”
  3. Feb 2022 – Dec 2023, (1220/junG/1/2022), University of Gdansk, PL (44000 €), “Junior Research Group Leader Programme UG – junG, start-up grant.”
  4. Jun 2021–May 2024, Marie Skłodowska-Curie GF (101025900), the European Commission (250000 €), “Identification of transcriptional memory maintenance factors through a cell selection strategy.”
  5. May 2018 (not initiated), Co-principal investigator with Lars Jansen (02/SAICT/2017), Fundação para a Ciência e Tecnologia, PT (235000 €), “Determining chromatin-based mechanisms and biological relevance of long-term transcriptional memory during innate immune response.”
  6. Jan 2013 – Jan 2015, (UMO-2012/05/N/NZ1/01912), National Science Centre, PL, (24000 €), “Structural basis of the recognition of postreplicative DNA modifications”


role as team member:

  1. Jan 2018–Aug 2020, (210645/Z/18/Z), principal investigator: Lars Jansen, Wellcome Trust, UK (1800000 £) “Determining the mechanisms underlying epigenetic inheritance of chromosome structure and gene expression states.”
  2. Jan 2015–May 2019, (ERC-2013-CoG-615638), principal investigator: Lars Jansen, European Research Council (1600000 €) “Mechanisms of Chromatin-based Epigenetic Inheritance”
  3. Jun 2011–Dec 2014, (N N302 654640), principal investigator: Matthias Bochtler, Ministry of Science and Higher Education, PL (95000 €) “Is there a “universal” RNA-guided DNA endonuclease?”


Fellowships and awards:

  1. Nov 2021, Award on the Horizon, scholarship (516254/PnH2/2021), funded by the Ministry of Education and Science, PL (55000 €)
  2. Jun 2021–May 2024, Marie Skłodowska-Curie global fellowship (101025900), funded by the European Commission (250000 €), “Identification of transcriptional memory maintenance factors through a cell selection strategy.”
  3. Apr 2017–Mar 2020, Postdoctoral fellowship (SFRH/BPD/117179/2016), funded by Fundação para a Ciência e Tecnologia, PT (53000 €), “Mechanisms of chromatin-based transcriptional memory.”
  4. 2015–2017, Multiple Travel Grants, funded by EMBO, EU
  5. 2010, Travel Grant, funded by Federation of European Biochemical Societies (FEBS), EU
  6. 2009, PhD scholarship, funded by Mazovian Voivodship, Warsaw, PL