Dr Stefan Barakat

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My lab focusses on deciphering the role of the non-coding genome in gene regulation, with a focus on human embryonic stem cells and neurodevelopment. Despite the fact that we know that the majority of DNA sequences (~98%)  in the human genome do not encode protein-coding genes, our understanding of those sequences and why they are important is still far from complete. An important group of non-coding genome elements are enhancers that are crucial for the proper regulation of spatiotemporal gene expression. Despite the fact that several techniques (e.g. ChIP-seq, chromatin accessibility assays etc.) can predict the identity of enhancers, it is still very challenging to predict the activity of these sequences. During my postdoctoral training, I have developed a new approach which combines chromatin immunoprecipitation with a massively parallel reporter assay that allows generation of comprehensive, genome-wide enhancer activity maps for various cell types. This work has generated one of the largest resources of functionally validated enhancers in human embryonic stem cells existing to date (available at http://hesc-enhancers.computational-epigenetics.org), which will enable further knowledge-based studies to decipher the code underlying the regulation of genes by non-coding sequences. Using these data, we discovered that only a small fraction of genomic regions bound by transcription factors or marked by histone modifications generally believed to be correlated to enhancers, do show measurable enhancer activity in human embryonic stem cells. Active sites show a distinct protein binding profile and enrichment for sequences derived from transposable elements. Enhancer activity changes dramatically upon developmental transitions during differentiation, and only small constituents of “super-enhancers” are responsible for enhancer activity.  
We are now using similar techniques and various other approaches, including induced pluripotent stem cells and cerebral organoids (“mini-brains”), to study the enhancer landscape in cells representing neurodevelopment. As many genetic disorders of brain development can at present not be explained by routine genetic diagnostics, we anticipate that many of these disorders are caused by alterations of non-coding elements, including enhancers. We plan to sequence the enhancers identified through our genome-wide functional enhancer activity assays in patients, to directly test the hypothesis that alterations of non-coding genome regions can be causal in the pathogenesis of brain disorders. We can then apply disease modelling for the patients harboring identified mutations, using patient specific induced pluripotent stem cells and differentiation to cerebral organoids, thereby simulating brain development in a dish. Our studies will facilitate the identification of functional enhancer sequences in the non-coding genome, and will allow novel innovative approaches for patient diagnostics using functional genomics.

Dr Barakat is Co-leader of Neuro-Mig Network Work Group 1 (WG4).

Home page: https://www.erasmusmc.nl/klinische_genetica/research/introduction/stefan-barakat/