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Research subject

Role of transcription factors and chromatin modifiers in establishing normal cognitive ability

Group leader: Raymond Poot

Group members:
Marti Quevedo (PhD student), Lize Meert (PhD student), Mike Dekker (Research assistant), Eva Niggl (Master student)


Gene expression is mostly regulated at the level of gene transcription into mRNA. Transcription is regulated by sequence-specific transcription factors, helped by chromatin modifiers. Chromatin modifiers also regulate other DNA-related processes such a DNA repair and mRNA splicing. My group aims to address both fundamental and more applied questions such as:
1) How do transcription factors and chromatin modifiers at enhancers and promoters regulate transcription?
2) Why and how do mutations in chromatin modifiers and transcription factors often cause cognitive disabilities, such as autism.

We try to answer these questions using embryonic stem cells and neural stem cells as model systems. In the past we used neural stem cells to show that Sox2 (mutated in patients with SOX2 anophtalmia syndrome) interacts with chromatin remodeling factor Chd7 (mutated in patients with CHARGE syndrome) and together they regulate a set of common target genes. Intriguingly, SOX2 syndrome and CHARGE syndrome have overlapping features that are also observed in patients that have mutations in some of the Sox2-Chd7 target genes (see Figure 1 and Engelen et al. 2011 for details). Our analysis of interaction partners and target genes of disease-associated transcription factors can therefore provide insight in the relationships of different human syndromes.  


Figure 1. Hypothetical model for mechanistic links between shared malformations in different human syndromes. Syndromes are in gray lettering, haploinsufficiency for the gene associated with the syndrome is in black lettering, associated malformations or defects are indicated by black arrows, transcriptional regulation of genes by Sox2+Chd7 in NSCs are indicated by dashed red arrows and shared malformations or defects are indicated in blue. (Details see Engelen et al. 2011)

We set-up a method to ChIP DNA marked by certain histone modifications and identify the proteins bound to these types of chromatin (ChIP-MS) and used this to identify transcription and chromatin factors that bind to highly active enhancers and promoters (see Figure 2 and Engelen, Brandsma et al. 2015 for details).


Figure 2. ChIP-MS predicts protein factors at active enhancers, active promoters and heterochromatin. (Details see Engelen, Brandsma et al. 2015)

Recently it has emerged that chromatin modifier genes represent nearly half of the high confidence autism genes ( This high enrichment has sparked our interest to understand how mutations in chromatin modifier genes cause autism. We have purified transcription factors from (mouse) neural stem cells and identified their interaction partners by mass spectroscopy. The resulting protein interaction network is enriched for proteins whose genes are mutated in patients with intellectual disability, autism or schizophrenia (see Figure 3, and Moen et al 2017 for details). Interestingly, mutations in network protein genes are often loss-of-function in patients with autism with low IQ, but harbour missense mutations in patients with autism and normal IQ or patients with schizophrenia, suggesting that the severity of disruption of the same protein network correlates with the severity of the cognitive disability (see Moen et al 2017 for details).


Figure 3. Protein interaction network in neural stem cells. Interaction network represents proteins present in two or more purifications of FLAG-tagged Tcf4, Olig2, Npas3 or Sox2 from neural stem cells. Protein complexes are larger circles, thickness of the edges (black lines) gives an indication of protein quantity in the purified samples. Colouring according to protein/gene mutated in patients with ID, ASD-normIQ, ASD-lowIQ or schizophrenia. ID; intellectual disability, ASD-normIQ; autism with normal IQ (>90). ASD-lowIQ; autism with low IQ (≤90). (details see Moen et al., 2017)

We now use human neural stem cells with mutations in autism-related chromatin modifiers and purification of autism-related chromatin modifiers from human neural stem cells to better understand what these chromatin modifiers do in human neural stem cells and what molecular pathways are affected when they are mutated. Aberrant human neural stem cell proliferation is implied in early post-natal excess brain growth and the resulting temporal or permanent macrocephaly associated with autism, making human neural stem cells an excellent model system to identify autism-related molecular pathways.

Positions for PhD students, post-docs and master students become available on a regular basis. If you are interested, please send your CV to