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erlenmyer-research
Research group/lab  |  PI T.S. Barakat, PhD

Non-Coding Genome in Neurodevelopmental Disorders

Our group focuses on deciphering the role of the non-coding genome in gene regulation, specifically addressing human embryonic stem cells and neurodevelopment.

About our research group/lab

Our research

Background information

The non-coding genome is important for gene regulation, but its role in health and disease is still not fully clear. Many disorders of brain development, such as malformations of cortical brain development, have a genetic cause, but current genetic investigations only address protein coding genes. Whether alterations of non-coding genome elements are involved in the development of these disorders needs clarification. The goal of our group is to decipher the non-coding regulatory network of brain development and thereby develop novel tools that can be of value in the genetic diagnosis of patients suffering from neurodevelopmental disorders.

Overall aim

We aim to understand the roles of non-coding regulatory elements, such as enhancers, in normal brain development and disease. We therefore apply state-of-the-art methods such as functional genomics and disease modeling using induced pluripotent stem cells and brain organoids.

Research focus areas

  • Functional genomics, including massively-parallel-reporter assays.
  • Epigenomic characterization of the genome, including ChIP-seq, ATAC-seq, RNA-seq.
  • Disease modeling using patient-derived induced pluripotent stem cells differentiated into brain organoids.

Key Publications

Functional dissection of the enhancer repertoire in human embryonic stem cells.
Barakat TS, Halbritter F, Zhang M, Rendeiro AF, Perenthaler E, Bock C, Chambers I. (2018). Cell Stem Cell. 2018 Aug 2;23(2):276-288.e8.

Dynamics of gene silencing during X inactivation using allele-specific RNA-seq.
Marks H, Kerstens HH, Barakat TS, Splinter E, Dirks RA, van Mierlo G, Joshi O, Wang SY, Babak T, Albers CA, Kalkan T, Smith A, Jouneau A, de Laat W, Gribnau J, Stunnenberg HG. (2015). Genome Biol. 2015 Aug 3;16:149.

X chromosome inactivation and embryonic stem cells.
Barakat TS, Gribnau J. (2010). Adv Exp Med Biol. 2010;695:132-54.

X chromosome inactivation in the cycle of life.
Barakat TS, Gribnau J. (2012). Development. 2012 Jun;139(12):2085-9.

Combined DNA-RNA fluorescent in situ hybridization (FISH) to study X chromosome inactivation in differentiated female mouse embryonic stem cells.
Barakat TS, Gribnau J. (2014). J Vis Exp. 2014 Jun 14;(88).