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Brain development​

During CNS development, large numbers of progenitor cells are generated in the ventricular and subventricular zone of the brain. These progenitors commit to differentiation towards large variety of functionally distinct neuronal and glial lineages with specific molecular programs and functions. We are interested in the regulatory principles driving this decision process, mainly the functions of histone modifications, transcription factors, DNA methylation, chromatin architecture and long non-coding RNAs in this process. We want to understand how these chromatin modalities work together and how are they coordinated in time and space to ensure proper gene activation and repression during brain development. We map the normal epigenomic states but also are interested in pathological states in which dysregulation of the epigenome is the causal factor.

UMAP projection of 3-modal single-cell profiling of two histone marks and open chromatin using nano-CUT&Tag.

Single-cell and spatial technologies to map the epigenome

We use cutting edge single-cell and spatial technologies to gain novel insights into the process of brain development. We have previously developed novel technologies to multimodally map several histone marks and open chromatin with single-cell resolution (Bartosovic et al., Nature Biotech., 2021; Bartosovic et al., Nature Biotech., in press) and with high spatial resolution (Deng, Bartosovic et al., Nature, 2022; Deng, Bartosovic et al., Science 2022). We are now applying these technologies in important biological systems and models and uncovering epistatic interactions between regulatory factors in real time. We also use cutting edge CRISPR technologies to manipulate both genome and epigenome to gain novel insights into interplay between genetic variability and chromatin.

Spatial ATAC-seq maping of accessible chromatin in adolescent mouse brain

We are always searching for enthusiastic and motivated students and postdocs. If you are interested in development of new cutting edge single-cell epigenomic technologies, and applying them to the study of nervous system, please send your CV, brief motivation letter and list of publications to

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Chromatin velocity analysis based on the multimodal ATAC/H3K27ac signal in the oligodendrocyte lineage 

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