Research Interests

Our group aims to dissect how chromatin modifications and enhancer-gene networks affect cell differentiation and contributes to cardiovascular and neurodevelopmental disorders

The main goal of our future research is to advance our understanding of the epigenetic and gene regulatory mechanisms and cellular pathways controlling stem cell differentiation and how perturbations of these pathways leads to cardiovascular and neurodevelopmental disorders.

As a model system we use human induced pluripotent stem cells (hiPSCs) and derived from them differentiated cells (cardiomyocytes, neurons, neuron-microglia co-cultures) and 3D cell cultures.

Our expertise lies in combination of wet- and dry-lab technologies and state-of-the-art omics data integration. Our group uses a systemic approach integrating several "omics" assays both in bulk and in single cells, profiling gene expression, chromatin accessibility and TF binding, together with advanced computational tools for downstream analyses such as constructing enhancer-driven gene regulatory networks to dissect the molecular pathways perturbed in cardiovascular and neurodevelopmental diseases and to find novel treatment strategies.

Our group is part of Berlin Center for Translational Vascular Biomedicine and by combining wet- and dry-lab methods contributes to the interdisciplinary research aiming to ultimately develop new personalised approaches for diagnostics and treatment of vascular diseases. Find out more about our research here...

Publications

Relevant recent publications:

• Bunina D†, Germain PL, Lopez Tobon A, Fernandez-Novel Marx N, Arnold C, Ahern A, Claringbould A, Lai MC, Rangasamy S, Narayanan V, Lorentzen P, Park KM, Testa G, Zaugg JB†, Noh KM†, "Pathological LSD1 mutations cause HDAC-mediated aberrant gene repression during early cell differentiation" bioRxiv 2021 https://doi.org/10.1101/2021.08.11.455900
• Bunina D*, Abazova N*, Diaz N, Noh KM, Krijgsveld J, Zaugg JB. Genomic Rewiring of SOX2 Chromatin Interaction Network during Differentiation of ESCs to Postmitotic Neurons. Cell Syst. 2020;10(6):480-494.e8. doi:10.1016/j.cels.2020.05.003 
• Gehre M, Bunina D, Sidoli S, et al. Lysine 4 of histone H3.3 is required for embryonic stem cell differentiation, histone enrichment at regulatory regions and transcription accuracy. Nat Genet. 2020;52(3):273-282. doi:10.1038/s41588-020-0586-5
• Kim KP, Li C*, Bunina D*, Jeong HW, Ghelman J, Kwak TH, Yoon J, Shin B, Park H, Han DW, Zaugg JB, Kim J, Kuhlmann T, Adams RH, Noh KM, Goldman SA, Schöler, HR. (2021) Donor-cell Memory Confers Metastable State of Directly Converted Cells, Cell Stem Cell, doi: 10.1016/j.stem.2021.02.023

We are hiring!

Our group starts at the MDC in July 2022 and we are hiring PhD students with experimental and/or computational background. If you found some aspects of our research interesting do not hesitate to apply via the MDC PhD Program!