Maaike Moen | Erasmus University Rotterdam (original) (raw)
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Papers by Maaike Moen
Clinical & Experimental Allergy
Translational Psychiatry, 2017
Nature Communications, 2015
The locations of transcriptional enhancers and promoters were recently mapped in many mammalian c... more The locations of transcriptional enhancers and promoters were recently mapped in many mammalian cell types. Proteins that bind those regulatory regions can determine cell identity but have not been systematically identified. Here we purify native enhancers, promoters or heterochromatin from embryonic stem cells by chromatin immunoprecipitations (ChIP) for characteristic histone modifications and identify associated proteins using mass spectrometry (MS). 239 factors are identified and predicted to bind enhancers or promoters with different levels of activity, or heterochromatin. Published genome-wide data indicate a high accuracy of location prediction by ChIP-MS. A quarter of the identified factors are important for pluripotency and includes Oct4, Esrrb, Klf5, Mycn and Dppa2, factors that drive reprogramming to pluripotent stem cells. We determined the genome-wide binding sites of Dppa2 and find that Dppa2 operates outside the classical pluripotency network. Our ChIP-MS method provides a detailed read-out of the transcriptional landscape representative of the investigated cell type.
The HMG-box transcription factor Sox2 plays a role throughout neurogenesis 1 and also acts at oth... more The HMG-box transcription factor Sox2 plays a role throughout neurogenesis 1 and also acts at other stages of development 2 , as illustrated by the multiple organs affected in the anophthalmia syndrome caused by SOX2 mutations 3-5. Here we combined proteomic and genomic approaches to characterize gene regulation by Sox2 in neural stem cells. Chd7, a chromatin remodeling ATPase associated with CHARGE syndrome 6,7 , was identified as a Sox2 transcriptional cofactor. Sox2 and Chd7 physically interact, have overlapping genome-wide binding sites and regulate a set of common target genes including Jag1, Gli3 and Mycn, genes mutated in Alagille, Pallister-Hall and Feingold syndromes, which show malformations also associated with SOX2 anophthalmia syndrome or CHARGE syndrome 8-10. Regulation of disease-associated genes by a Sox2-Chd7 complex provides a plausible explanation for several malformations associated with SOX2 anophthalmia syndrome or CHARGE syndrome. Indeed, we found that Chd7haploinsufficient embryos showed severely reduced expression of Jag1 in the developing inner ear. As a first step to gain more insight into the transcriptional network in which Sox2 operates, we identified Sox2-interacting proteins in neural stem cells (NSCs). Sox2 is essential for the in vivo maintenance of mouse embryonic and adult NSCs and subsequent neurogenesis 1. NSCs are therefore an appropriate cell type in which to study gene regulation by Sox2. NSCs that stably express FLAG-Sox2 (ref. 11) (F-Sox2) have a normal morphology and expressed NSC markers such as Nestin, RC2 (ref. 11) and Pax6 (Supplementary Fig. 1a). To identify interaction partners, we purified F-Sox2 from NSC nuclear extract by a FLAG-affinity-based protocol 12 , separated proteins by polyacrylamide gel (Supplementary Fig. 1b) and analyzed them using mass spectrometry. We identified 50 Sox2-interacting factors that were specifically present in two F-Sox2 purifications (Table 1 and
Nature Communications, 2015
The locations of transcriptional enhancers and promoters were recently mapped in many mammalian c... more The locations of transcriptional enhancers and promoters were recently mapped in many mammalian cell types. Proteins that bind those regulatory regions can determine cell identity but have not been systematically identified. Here we purify native enhancers, promoters or heterochromatin from embryonic stem cells by chromatin immunoprecipitations (ChIP) for characteristic histone modifications and identify associated proteins using mass spectrometry (MS). 239 factors are identified and predicted to bind enhancers or promoters with different levels of activity, or heterochromatin. Published genome-wide data indicate a high accuracy of location prediction by ChIP-MS. A quarter of the identified factors are important for pluripotency and includes Oct4, Esrrb, Klf5, Mycn and Dppa2, factors that drive reprogramming to pluripotent stem cells. We determined the genome-wide binding sites of Dppa2 and find that Dppa2 operates outside the classical pluripotency network. Our ChIP-MS method provides a detailed read-out of the transcriptional landscape representative of the investigated cell type.
Clinical & Experimental Allergy
Translational Psychiatry, 2017
Nature Communications, 2015
The locations of transcriptional enhancers and promoters were recently mapped in many mammalian c... more The locations of transcriptional enhancers and promoters were recently mapped in many mammalian cell types. Proteins that bind those regulatory regions can determine cell identity but have not been systematically identified. Here we purify native enhancers, promoters or heterochromatin from embryonic stem cells by chromatin immunoprecipitations (ChIP) for characteristic histone modifications and identify associated proteins using mass spectrometry (MS). 239 factors are identified and predicted to bind enhancers or promoters with different levels of activity, or heterochromatin. Published genome-wide data indicate a high accuracy of location prediction by ChIP-MS. A quarter of the identified factors are important for pluripotency and includes Oct4, Esrrb, Klf5, Mycn and Dppa2, factors that drive reprogramming to pluripotent stem cells. We determined the genome-wide binding sites of Dppa2 and find that Dppa2 operates outside the classical pluripotency network. Our ChIP-MS method provides a detailed read-out of the transcriptional landscape representative of the investigated cell type.
The HMG-box transcription factor Sox2 plays a role throughout neurogenesis 1 and also acts at oth... more The HMG-box transcription factor Sox2 plays a role throughout neurogenesis 1 and also acts at other stages of development 2 , as illustrated by the multiple organs affected in the anophthalmia syndrome caused by SOX2 mutations 3-5. Here we combined proteomic and genomic approaches to characterize gene regulation by Sox2 in neural stem cells. Chd7, a chromatin remodeling ATPase associated with CHARGE syndrome 6,7 , was identified as a Sox2 transcriptional cofactor. Sox2 and Chd7 physically interact, have overlapping genome-wide binding sites and regulate a set of common target genes including Jag1, Gli3 and Mycn, genes mutated in Alagille, Pallister-Hall and Feingold syndromes, which show malformations also associated with SOX2 anophthalmia syndrome or CHARGE syndrome 8-10. Regulation of disease-associated genes by a Sox2-Chd7 complex provides a plausible explanation for several malformations associated with SOX2 anophthalmia syndrome or CHARGE syndrome. Indeed, we found that Chd7haploinsufficient embryos showed severely reduced expression of Jag1 in the developing inner ear. As a first step to gain more insight into the transcriptional network in which Sox2 operates, we identified Sox2-interacting proteins in neural stem cells (NSCs). Sox2 is essential for the in vivo maintenance of mouse embryonic and adult NSCs and subsequent neurogenesis 1. NSCs are therefore an appropriate cell type in which to study gene regulation by Sox2. NSCs that stably express FLAG-Sox2 (ref. 11) (F-Sox2) have a normal morphology and expressed NSC markers such as Nestin, RC2 (ref. 11) and Pax6 (Supplementary Fig. 1a). To identify interaction partners, we purified F-Sox2 from NSC nuclear extract by a FLAG-affinity-based protocol 12 , separated proteins by polyacrylamide gel (Supplementary Fig. 1b) and analyzed them using mass spectrometry. We identified 50 Sox2-interacting factors that were specifically present in two F-Sox2 purifications (Table 1 and
Nature Communications, 2015
The locations of transcriptional enhancers and promoters were recently mapped in many mammalian c... more The locations of transcriptional enhancers and promoters were recently mapped in many mammalian cell types. Proteins that bind those regulatory regions can determine cell identity but have not been systematically identified. Here we purify native enhancers, promoters or heterochromatin from embryonic stem cells by chromatin immunoprecipitations (ChIP) for characteristic histone modifications and identify associated proteins using mass spectrometry (MS). 239 factors are identified and predicted to bind enhancers or promoters with different levels of activity, or heterochromatin. Published genome-wide data indicate a high accuracy of location prediction by ChIP-MS. A quarter of the identified factors are important for pluripotency and includes Oct4, Esrrb, Klf5, Mycn and Dppa2, factors that drive reprogramming to pluripotent stem cells. We determined the genome-wide binding sites of Dppa2 and find that Dppa2 operates outside the classical pluripotency network. Our ChIP-MS method provides a detailed read-out of the transcriptional landscape representative of the investigated cell type.