Dioscuri Centre for Chromatin Biology and Epigenomics
Our team
Aleksandra Pękowska, PhD
PRINCIPAL INVESTIGATOR
Head of the Lab
I graduated from the University of Lodz with a MS in biology (spec. biophysics, lab of Prof. Grzegorz Bartosz, Dept. of Molecular Biophysics) in 2006. For my Ph.D., I joined the lab of Dr. Pierre Ferrier at the CIML in Marseilles. Combining a variety of high throughput genome analysis approaches (including ChIP-seq, RNA-seq, and microarray-based assays) and computational biology tools, we discovered a chromatin signature allowing to distinguish active from poised enhancers (Pękowska A. et al., 2011, EMBO Journal). In a purely in silico study, we show for the first time, that tissue-specific genes display a unique pattern of histone modifications (Pękowska A. et al., 2010 Genome Research).
In 2011, I obtained the EIPOD fellowship (EMBL/Marie Curie actions) and joined groups of Dr. Wolfgang Huber, Dr. Lars Steinmetz, and Dr. Paul Bertone at EMBL/EBI for an interdisciplinary postdoc. My goal was to define the relationship between cellular plasticity and chromatin topology. Using stem cell models and in-situ Hi-C, we revealed that differentiation of pluripotent stem cells to neuronal lineage coincides with a genome-wide buildup of chromatin loops and strengthening of chromatin boundaries (Pękowska A. et al., Cell Systems).
In 2016, I joined the team of Dr. Rafael Casellas at NIAMS (NIH) in Bethesda, US. In a recent paper, we described architectural stripes - specialized chromatin structures frequently involving super-enhancers (Vian L.#, Pękowska A.# et al. 2018 Cell, # equal contribution). Combining CRISPR-Cas9, Hi-C and ChIP-seq, we show that stripes rely on the action of CTCF and cohesins; and that their formation requires constant energy input.
In my spare time, I enjoy astronomy, history, and hiking.
Katarzyna Ciuba, PhD
PostDoc
I have graduated as a MSc of Biochemistry at Jagiellonian University in Cracow. Then, I joined Pekka Lappalainen’s lab at the University of Helsinki as a PhD student. I took advantage of a wide range of cell biology, microscopy and biochemistry methods to unravel mechanisms regulating assembly and function of contractile actin-based structures in non-muscle cells.
Currently, I am interested in functional genomics of astrocytes. Taking advantage of genome editing methods accompanied by broad molecular biology and microscopy techniques, I aim to decipher the role of certain astrocyte genes in functional and evolutionary context.
In my spare time I experiment with coffee and travels.
Anna Stroynowska-Czerwińska, PhD
PostDoc
While studying biotechnology at the University of Life Sciences in Poznan, I became fascinated by how cells function at the molecular level. Especially I was impressed by the variety of epigenetic mechanisms that are responsible for the proper functioning of the whole organism. In the meantime, I have been awarded the “Diamond Grant”, which I carried out under the supervision of prof. dr hab. Wlodziemierz Krzyzosiak at the Institute of Bioorganic Chemistry Polish Academy of Sciences (IChB PAS). During this time, I aimed to understand the mechanistic features of allele-specific silencing provided by miRNA-like siRNA, which is used as a potential therapeutic treatment for incurable polyglutamine diseases. Afterwards, I joined the laboratory of prof. dr hab. Matthias Bochtler at the International Institute of Molecular and Cell Biology (IIMCB). There I have defended my PhD thesis on the binding properties of chromatin-reading domains of KMT2/MLL proteins.
In May 2023 I joined the Dioscuri Centre of dr Aleksanda Pekowska. I would like to contribute to a better understanding of the regulation of gene expression by enhancer-promoter interactions in the context of chromatin structure and cell differentiation.
After work I sing in a choir, dance Lindy Hop, go hiking and travel.
Monika Mielnicka, PhD
PostDoc
I have graduated with MSci in Biotechnology (with Applied Molecular Biology) at University of Aberdeen in Scotland. I have then moved to Napoli in Italy to work on a yearlong project involving genome editing in sea urchin in Maria Ina Arnone lab at Stazione Zoologica. After that position I have moved to EMBL Rome to do my PhD in Matthieu Boulard group to work on study understanding the biological function of TRIM66 protein in reproduction and spermiogenesis.
Currently I am working on molecular evolution and function of interlaminar astrocytes. To address this question I am using mouse and in-vitro tissue culture models to look for differences to profile for transcriptome changes between different primate species using single-cell sequencing methods.
In my spare time I like to try out new recipes, do yoga and play video games.
Debadeep Chaudhury, MSc
PhD student
I obtained my M.Sc. Degree from the Institute of Bioinformatics and Applied Biotechnology, Bangalore University, Bangalore, India specialising in Bioinformatics and Biotechnology. For my M.Sc. project, I investigated the possible role of epigenetic markers in inheritance of memory. I briefly worked as a Bioinformatician at the Jawaharlal Nehru Center for Advanced Science, Bangalore, India.
Currently, I'm working on a project to understand the evolution of regulatory networks in Astrocytes. I'm interested to learn the development and evolution of our brain and possibly the evolution of memory. I have tons of hobbies notably reading, travelling, video games and DIY projects.
Bondita Dehingia, MSc
PhD student
I'm working with Dr Aleksandra Pekowska's group since Fall 2020. My research is centred around understanding the role of transcription factors that help define the outstanding biology of human astrocytes across evolution. I aim to divulge the Gene regulatory network of human astrocyte by a combinatorial approach of cell reprogramming, CRISPR-Cas9 mediated gene editing, sequencing technology (ChIP-seq, RNA-seq and ATAC-seq) and bioinformatics.
Prior to joining Dioscuri Centre, I worked at Jubilant Biosys Ltd and then at the Indian Institute of Science (IISc) in Bengaluru for a duration of two years in the field of cancer therapeutics. I also did a nine-month stint at the National Institute of Mental Health and Neurosciences (NIMHANS), also in Bengaluru, where my work concentrated on stem cell biology.
Gosia Milewska-Puchała, MSc
PhD student
In 2019 I graduated from Warsaw University of Life Sciences with a Master’s degree majoring in Molecular Biology. During my MSc studies, I worked on the detection of protein-protein interaction using a two-hybrid system. I determined a potential function of a few parasite antigens which have a significant role during Toxocara canis invasion in the human organism.
Currently I participate in a project on the regulation of chromatin topology. I am interested in the three-dimensional structure of the genome and the regulation of gene expression during development. Using high-throughput sequencing technologies, I would like to answer the question of how the factors associated with the CTCF influence cell development. In my spare time, I am a big fan of good cuisine and long walks.
Eryk Duński, MSc
PhD student
I completed a Bachelor in Science with specialisation in Molecular Genetics at the University of Edinburgh and a Master degree in Biology-Biotechnology at the University of Copenhagen. In my master thesis I was developing a transcriptional biosensor for detection of adipic acid. I also worked for two years in a molecular diagnostics start-up Sense Biodetection.
Currently, I am interested in finding the evolutionary basis for human-specific traits in astrocytes. To achieve that, I am developing and employing functional screens coupled with bioinformatic analyses. Outside of the lab, I am interested in biotechnological entrepreneurship.
Misbah Abbas, MPhil
PhD student
I obtained my MPhil degree from National Centre for BioInformatics, Quaid-i-Azam University Islamabad, Pakistan. During my MPhil studies, I worked on Population Genomics Analysis of Whole Genome Sequencing (WGS) Data in Dogs. I did internship at Lahore University of Management Sciences (LUMS) Lahore, Pakistan, involved in Biomedical Informatics Research Laboratory, Department of Biology. Prior to joining Dioscuri Centre, I worked as Lecturer in Government University Faisalabad, Pakistan affiliated campus.
I recently joined the Dioscuri Centre for Chromatin Biology and Epigenomics, I am involved in computational analysis of the data generated in the lab. Currently, my major focus is on molecular mechanisms of the regulation of gene expression.
Sajjad Iqbal, MSc
PhD student
In 2020 I completed my post-graduation majoring in Biosciences from Jamia Millia Islamia. During my M.Sc studies I worked on establishing therapeutics efficacy of Saponins in cancer. Then for a short period of time I worked as a Junior Research Fellow at Institute of Bioinformatics and Biotechnology, Bengaluru where my project was to establish the epithelial to mesenchymal transitioning in colorectal cancer cell lines.
I recently joined Dr Pekowska's lab on December, 2022 as a Ph.D. Since then I have been working with Dr Aleksandra Pekowska on a project to understand the non-canonical functions of ATP and how does it effects the chromatin organization in mouse embryonic stem cells. Apart from lab, I enjoy taking pictures, experimenting with new recipes, and doing sports.
Ola Piotrowska, MSc
Research Technician
I am interested in the molecular bases of inheritance, in particular, in how epigenetics shapes the identity of a cell.
In 2019, I obtained a Master’s Degree in Molecular Biotechnology at the University of Warsaw. My project was aimed at the development of molecular biology methods to diagnose chosen rare genetic disorders.
I joined the Dioscuri Centre for Chromatin Biology and Epigenomics in Fall 2019. I derive and maintain induced pluripotent stem cell lines from mammals (mouse, primates, and humans). I am still learning about their needs and moods. I am also responsible for the technical infrastructure in the lab.
Besides my implication in the lab, I study bioethics at the University of Warsaw. I am interested in ethical aspects of biotechnology in particular, the moral implications of the use of human ES cells and of human genome editing.
Ewelina Borsuk, MSc
Research Technician
I obtained my MSc diploma from the Faculty of Biology at Warsaw University as a Biotechnologist. My master studies and the next few years I spent in Prof Barbara Tudek’s lab in the IBB PAS in Warsaw. I was exploring the dark depths of DNA damage response pathway in Fanconi anemia patients’ cells to understand the etiology of this rare disease.
Iconsider myself as a cell biologist with a heart for microcope imaging.
I have joined the group at the end of February 2023. I have started with moody but cute IPS cells and trying some gene modifications on them. I am learning how to work with mice too.
In my free time I enjoy sourdough baking, reading and playing outside with kids.
Agatha Iwanek, BA
Administration Officer
I graduated at Faculty of Industrial Design at the Academy of Fine Arts in Warsaw.
After completing one year of Master Course at Faculty of Big Data Analysis at the Warsaw School of Economics. I took and graduated an intense course of UX/UI Design at Spanish IT School Ironhack.
I started working at the Dioscuri Centre for Chromatin Biology and Epigenomic in February 2023 as an administration officer. I'm doing my best to support other lab members in non-scientific tasks.
My leisure time is spent on outdoor activities and arts & crafts.
