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Stem Cell Transcription Factors

Group leader
Raymond Poot

Group members
Maaike Moen (PhD student), Johan Brandsma (PhD student), Marti Quevedo (PhD student), Mike Dekker (Research assistant), Isa Gordaliza (Master student).


For a cell to remember its identity, the genetic information in the form of DNA is not enough. Each cell has a gene expression program where some genes are “on” and some genes are “off”. Transcriptional activators and repressors often decide on the on/off state of a gene.

Figure 1
Model on how Oct4, Sox2 and Esrrb bind together to the Nanog promoter and regulate Nanog expression. Esrrb localization to the Nanog promoter depends both on DNA sequence and interaction with Oct4 protein (details see: van den Berg et al., 2008)

The cell-identity of embryonic stem (ES) cells is determined by key transcription factors such as Oct4, Nanog and Sox2, while Sox2 is also important for the self-renewal of neural stem cells and is mutated in human disease. These transcription factors are thought to promote stem cell self-renewal by, directly or indirectly, activating stem cell genes and repressing genes expressed in more differentiated cells.

We want to understand better how transcription factors maintain stem cell identity and how they are inter-related. Our approach is to purify transcription factors from embryonic stem cells or neural stem cells and determine their interaction partners by mass spectrometry. These interaction partners are likely functionally relevant for the purified factor. An example is ES cell transcription factor Oct4 and the orphan receptor Esrrb, that we identified as an Oct4-interacting protein. We found that Esrrb is a co-factor of Oct4 in the transcriptional regulation of the Nanog gene (see Figure 1 for model, van den Berg et al. 2008 for details).

Figure 2
Transcription factor interaction network in embryonic stem cells. Yellow indicates important for ES cell self-renewal, large circles indicate complexes with multiple subunits
(details see: van den Berg et al., 2010)

We use chromatin immunoprecipitation and shRNA mediated knock-down to investigate the regulation of (novel) target genes by the purified transcription factors and their identified partners. In this way we want to unravel the transcriptional networks, and their players, that regulate the self-renewal and differentiation of ES cells and neural stem cells. Understanding such networks may facilitate better manipulation of stem cell fate decisions

ES cell transcription factors such as Oct4 are important for reprogramming somatic cells into induced pluripotent (iPS) cells, which have future potential for replacement therapy. We recently purified Oct4 and a number of its interaction partners and established an interaction network of nearly 170 factors in ES cells (Fig. 3, see van den Berg et al. 2010 for details). We are currently trying to understand the functional implications of several of the identified interactions.

In neural stem cells we study transcription factors that are mutated in human disease. We recently found 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 3 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 3
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. 

Positions for Post-Docs, PhD students and Master students are becoming available on a regular basis, both on neural stem cell and ES cell projects. If you are interested, please send your CV and a motivation letter to Raymond Poot (