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.

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. 

I hold first class bachelor's and master's degrees in zoology and molecular biology and biotechnology (MBBT) from Dibrugarh and Tezpur University respectively.

Gosia Milewska, 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.

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.

Ewa Demianiuk, MSc

Administration Officer

I graduated at Faculty of Geology University of Warsaw and studied Environmental Protection at the University Center for Environmental Studies and Sustainable Development.

In 2014, I started my PhD studies program in Interdisciplinary Polar Studies at Centre for Polar Studies, then continued my PhD studies at the Institute of Paleobiology PAS.

I started working at the Dioscuri Centre for Chromatin Biology and Epigenomic in early 2022 as an administrative support.