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Article ; Online: The Rules of Successful Speed Dating Are Complex, Even for Super-Enhancers.

Poot, Raymond

2018 Volume 22, Issue 4, Page(s) 477–478

Abstract: Super-enhancers (SEs) are important for regulating cell identity genes and oncogenes, but correctly assigning target genes to SEs is difficult. Recently in Cell Reports, Lopes Novo et al. (2018) map interactions between SEs and promoters and observe a ... ...

Abstract	Super-enhancers (SEs) are important for regulating cell identity genes and oncogenes, but correctly assigning target genes to SEs is difficult. Recently in Cell Reports, Lopes Novo et al. (2018) map interactions between SEs and promoters and observe a significant rewiring of complex SE-promoter networks between different pluripotent states.
MeSH term(s)	Animals ; Enhancer Elements, Genetic ; Mice ; Mouse Embryonic Stem Cells
Language	English
Publishing date	2018-04-05
Publishing country	United States
Document type	Journal Article ; Comment
ZDB-ID	2375354-7
ISSN	1875-9777 ; 1934-5909
ISSN (online)	1875-9777
ISSN	1934-5909
DOI	10.1016/j.stem.2018.03.001
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Zs.A 6589: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Compartmentalization of androgen receptors at endogenous genes in living cells.

Yavuz, Selçuk / Kabbech, Hélène / van Staalduinen, Jente / Linder, Simon / van Cappellen, Wiggert A / Nigg, Alex L / Abraham, Tsion E / Slotman, Johan A / Quevedo, Marti / Poot, Raymond A / Zwart, Wilbert / van Royen, Martin E / Grosveld, Frank G / Smal, Ihor / Houtsmuller, Adriaan B

Nucleic acids research

2023 Volume 51, Issue 20, Page(s) 10992–11009

Abstract: A wide range of nuclear proteins are involved in the spatio-temporal organization of the genome through diverse biological processes such as gene transcription and DNA replication. Upon stimulation by testosterone and translocation to the nucleus, ... ...

Abstract	A wide range of nuclear proteins are involved in the spatio-temporal organization of the genome through diverse biological processes such as gene transcription and DNA replication. Upon stimulation by testosterone and translocation to the nucleus, multiple androgen receptors (ARs) accumulate in microscopically discernable foci which are irregularly distributed in the nucleus. Here, we investigated the formation and physical nature of these foci, by combining novel fluorescent labeling techniques to visualize a defined chromatin locus of AR-regulated genes-PTPRN2 or BANP-simultaneously with either AR foci or individual AR molecules. Quantitative colocalization analysis showed evidence of AR foci formation induced by R1881 at both PTPRN2 and BANP loci. Furthermore, single-particle tracking (SPT) revealed three distinct subdiffusive fractional Brownian motion (fBm) states: immobilized ARs were observed near the labeled genes likely as a consequence of DNA-binding, while the intermediate confined state showed a similar spatial behavior but with larger displacements, suggesting compartmentalization by liquid-liquid phase separation (LLPS), while freely mobile ARs were diffusing in the nuclear environment. All together, we show for the first time in living cells the presence of AR-regulated genes in AR foci.
MeSH term(s)	Animals ; Cell Nucleus/genetics ; Cell Nucleus/metabolism ; Nuclear Proteins/metabolism ; Receptors, Androgen/metabolism ; Humans ; Mice ; Cell Line, Tumor
Chemical Substances	Nuclear Proteins ; Receptors, Androgen
Language	English
Publishing date	2023-10-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkad803
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Article ; Online: Characterization of the TBR1 interactome: variants associated with neurodevelopmental disorders disrupt novel protein interactions.

Sollis, Elliot / den Hoed, Joery / Quevedo, Marti / Estruch, Sara B / Vino, Arianna / Dekkers, Dick H W / Demmers, Jeroen A A / Poot, Raymond / Deriziotis, Pelagia / Fisher, Simon E

Human molecular genetics

2022 Volume 32, Issue 9, Page(s) 1497–1510

Abstract: TBR1 is a neuron-specific transcription factor involved in brain development and implicated in a neurodevelopmental disorder (NDD) combining features of autism spectrum disorder (ASD), intellectual disability (ID) and speech delay. TBR1 has been ... ...

Abstract	TBR1 is a neuron-specific transcription factor involved in brain development and implicated in a neurodevelopmental disorder (NDD) combining features of autism spectrum disorder (ASD), intellectual disability (ID) and speech delay. TBR1 has been previously shown to interact with a small number of transcription factors and co-factors also involved in NDDs (including CASK, FOXP1/2/4 and BCL11A), suggesting that the wider TBR1 interactome may have a significant bearing on normal and abnormal brain development. Here, we have identified approximately 250 putative TBR1-interaction partners by affinity purification coupled to mass spectrometry. As well as known TBR1-interactors such as CASK, the identified partners include transcription factors and chromatin modifiers, along with ASD- and ID-related proteins. Five interaction candidates were independently validated using bioluminescence resonance energy transfer assays. We went on to test the interaction of these candidates with TBR1 protein variants implicated in cases of NDD. The assays uncovered disturbed interactions for NDD-associated variants and identified two distinct protein-binding domains of TBR1 that have essential roles in protein-protein interaction.
MeSH term(s)	Humans ; Autism Spectrum Disorder/genetics ; Autism Spectrum Disorder/metabolism ; Forkhead Transcription Factors/genetics ; Forkhead Transcription Factors/metabolism ; Intellectual Disability/genetics ; Intellectual Disability/metabolism ; Neurodevelopmental Disorders/genetics ; Neurodevelopmental Disorders/metabolism ; Protein Binding/genetics ; Protein Binding/physiology ; Proteins/genetics ; Proteins/metabolism ; Repressor Proteins/genetics ; Repressor Proteins/metabolism ; T-Box Domain Proteins/genetics ; T-Box Domain Proteins/metabolism ; Transcription Factors/genetics ; Transcription Factors/metabolism
Chemical Substances	Forkhead Transcription Factors ; FOXP1 protein, human ; Proteins ; Repressor Proteins ; T-Box Domain Proteins ; TBR1 protein, human ; Transcription Factors
Language	English
Publishing date	2022-11-18
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1108742-0
ISSN	1460-2083 ; 0964-6906
ISSN (online)	1460-2083
ISSN	0964-6906
DOI	10.1093/hmg/ddac311
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Article: Identification of SOX2 Interacting Proteins in the Developing Mouse Lung With Potential Implications for Congenital Diaphragmatic Hernia.

Schilders, Kim A A / Edel, Gabriëla G / Eenjes, Evelien / Oresta, Bianca / Birkhoff, Judith / Boerema-de Munck, Anne / Buscop-van Kempen, Marjon / Liakopoulos, Panagiotis / Kolovos, Petros / Demmers, Jeroen A A / Poot, Raymond / Wijnen, Rene M H / Tibboel, Dick / Rottier, Robbert J

Frontiers in pediatrics

2022 Volume 10, Page(s) 881287

Abstract: Congenital diaphragmatic hernia is a structural birth defect of the diaphragm, with lung hypoplasia and persistent pulmonary hypertension. Aside from vascular defects, the lungs show a disturbed balance of differentiated airway epithelial cells. The Sry ... ...

Abstract	Congenital diaphragmatic hernia is a structural birth defect of the diaphragm, with lung hypoplasia and persistent pulmonary hypertension. Aside from vascular defects, the lungs show a disturbed balance of differentiated airway epithelial cells. The Sry related HMG box protein SOX2 is an important transcription factor for proper differentiation of the lung epithelium. The transcriptional activity of SOX2 depends on interaction with other proteins and the identification of SOX2-associating factors may reveal important complexes involved in the disturbed differentiation in CDH. To identify SOX2-associating proteins, we purified SOX2 complexes from embryonic mouse lungs at 18.5 days of gestation. Mass spectrometry analysis of SOX2-associated proteins identified several potential candidates, among which were the Chromodomain Helicase DNA binding protein 4 (CHD4), Cut-Like Homeobox1 (CUX1), and the Forkhead box proteins FOXP2 and FOXP4. We analyzed the expression patterns of FOXP2, FOXP4, CHD4, and CUX1 in lung during development and showed co-localization with SOX2. Co-immunoprecipitations validated the interactions of these four transcription factors with SOX2, and large-scale chromatin immunoprecipitation (ChIP) data indicated that SOX2 and CHD4 bound to unique sites in the genome, but also co-occupied identical regions, suggesting that these complexes could be involved in co-regulation of genes involved in the respiratory system.
Language	English
Publishing date	2022-05-09
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2711999-3
ISSN	2296-2360
ISSN	2296-2360
DOI	10.3389/fped.2022.881287
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Article ; Online: SMPD4 regulates mitotic nuclear envelope dynamics and its loss causes microcephaly and diabetes.

Smits, Daphne J / Schot, Rachel / Krusy, Nathalie / Wiegmann, Katja / Utermöhlen, Olaf / Mulder, Monique T / den Hoedt, Sandra / Yoon, Grace / Deshwar, Ashish R / Kresge, Christina / Pletcher, Beth / van Mook, Maura / Ferreira, Marta Serio / Poot, Raymond A / Slotman, Johan A / Kremers, Gert-Jan / Ahmad, Abeer / Albash, Buthaina / Bastaki, Laila /

Marafi, Dana / Dekker, Jordy / van Ham, Tjakko J / Nguyen, Laurent / Mancini, Grazia M S

Brain : a journal of neurology

2023 Volume 146, Issue 8, Page(s) 3528–3541

Abstract: Biallelic loss-of-function variants in SMPD4 cause a rare and severe neurodevelopmental disorder with progressive congenital microcephaly and early death. SMPD4 encodes a sphingomyelinase that hydrolyses sphingomyelin into ceramide at neutral pH and can ... ...

Abstract	Biallelic loss-of-function variants in SMPD4 cause a rare and severe neurodevelopmental disorder with progressive congenital microcephaly and early death. SMPD4 encodes a sphingomyelinase that hydrolyses sphingomyelin into ceramide at neutral pH and can thereby affect membrane lipid homeostasis. SMPD4 localizes to the membranes of the endoplasmic reticulum and nuclear envelope and interacts with nuclear pore complexes (NPC). We refine the clinical phenotype of loss-of-function SMPD4 variants by describing five individuals from three unrelated families with longitudinal data due to prolonged survival. All individuals surviving beyond infancy developed insulin-dependent diabetes, besides presenting with a severe neurodevelopmental disorder and microcephaly, making diabetes one of the most frequent age-dependent non-cerebral abnormalities. We studied the function of SMPD4 at the cellular and organ levels. Knock-down of SMPD4 in human neural stem cells causes reduced proliferation rates and prolonged mitosis. Moreover, SMPD4 depletion results in abnormal nuclear envelope breakdown and reassembly during mitosis and decreased post-mitotic NPC insertion. Fibroblasts from affected individuals show deficient SMPD4-specific neutral sphingomyelinase activity, without changing (sub)cellular lipidome fractions, which suggests a local function of SMPD4 on the nuclear envelope. In embryonic mouse brain, knockdown of Smpd4 impairs cortical progenitor proliferation and induces premature differentiation by altering the balance between neurogenic and proliferative progenitor cell divisions. We hypothesize that, in individuals with SMPD4-related disease, nuclear envelope bending, which is needed to insert NPCs in the nuclear envelope, is impaired in the absence of SMPD4 and interferes with cerebral corticogenesis and survival of pancreatic beta cells.
MeSH term(s)	Humans ; Animals ; Mice ; Nuclear Envelope/chemistry ; Nuclear Envelope/metabolism ; Microcephaly/genetics ; Microcephaly/metabolism ; Sphingomyelin Phosphodiesterase/analysis ; Sphingomyelin Phosphodiesterase/genetics ; Sphingomyelin Phosphodiesterase/metabolism ; Nuclear Pore/metabolism ; Mitosis ; Diabetes Mellitus/metabolism
Chemical Substances	Sphingomyelin Phosphodiesterase (EC 3.1.4.12)
Language	English
Publishing date	2023-02-22
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80072-7
ISSN	1460-2156 ; 0006-8950
ISSN (online)	1460-2156
ISSN	0006-8950
DOI	10.1093/brain/awad033
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Article ; Online: Publisher Correction: Mediator complex interaction partners organize the transcriptional network that defines neural stem cells.

Quevedo, Marti / Meert, Lize / Dekker, Mike R / Dekkers, Dick H W / Brandsma, Johannes H / van den Berg, Debbie L C / Ozgür, Zeliha / van IJcken, Wilfred F J / Demmers, Jeroen / Fornerod, Maarten / Poot, Raymond A

Nature communications

2019 Volume 10, Issue 1, Page(s) 3318

Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

Abstract	An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Language	English
Publishing date	2019-07-22
Publishing country	England
Document type	Published Erratum
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-019-11254-1
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Article ; Online: Epigenetic regulation: DNA confers identity but is not enough to maintain it.

Poot, Raymond A / Festenstein, Richard

Genome biology

2006 Volume 7, Issue 1, Page(s) 302

MeSH term(s)	Animals ; Chromosomes/genetics ; Chromosomes/metabolism ; DNA/genetics ; DNA/metabolism ; Epigenesis, Genetic ; Evolution, Molecular ; Histones/genetics ; Histones/metabolism ; Humans
Chemical Substances	Histones ; DNA (9007-49-2)
Language	English
Publishing date	2006-01-27
Publishing country	England
Document type	Congress
ZDB-ID	2040529-7
ISSN	1474-760X ; 1474-760X
ISSN (online)	1474-760X
ISSN	1474-760X
DOI	10.1186/gb-2006-7-1-302
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Article ; Online: Proteomic analysis of FOXP proteins reveals interactions between cortical transcription factors associated with neurodevelopmental disorders.

Estruch, Sara B / Graham, Sarah A / Quevedo, Martí / Vino, Arianna / Dekkers, Dick H W / Deriziotis, Pelagia / Sollis, Elliot / Demmers, Jeroen / Poot, Raymond A / Fisher, Simon E

Human molecular genetics

2018

Language	English
Publishing date	2018-06-26
Publishing country	England
Document type	Journal Article
ZDB-ID	1108742-0
ISSN	1460-2083 ; 0964-6906
ISSN (online)	1460-2083
ISSN	0964-6906
DOI	10.1093/hmg/ddy230
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Article ; Online: Mediator complex interaction partners organize the transcriptional network that defines neural stem cells.

Nature communications

2019 Volume 10, Issue 1, Page(s) 2669

Abstract: The Mediator complex regulates transcription by connecting enhancers to promoters. High Mediator binding density defines super enhancers, which regulate cell-identity genes and oncogenes. Protein interactions of Mediator may explain its role in these ... ...

Abstract	The Mediator complex regulates transcription by connecting enhancers to promoters. High Mediator binding density defines super enhancers, which regulate cell-identity genes and oncogenes. Protein interactions of Mediator may explain its role in these processes but have not been identified comprehensively. Here, we purify Mediator from neural stem cells (NSCs) and identify 75 protein-protein interaction partners. We identify super enhancers in NSCs and show that Mediator-interacting chromatin modifiers colocalize with Mediator at enhancers and super enhancers. Transcription factor families with high affinity for Mediator dominate enhancers and super enhancers and can explain genome-wide Mediator localization. We identify E-box transcription factor Tcf4 as a key regulator of NSCs. Tcf4 interacts with Mediator, colocalizes with Mediator at super enhancers and regulates neurogenic transcription factor genes with super enhancers and broad H3K4me3 domains. Our data suggest that high binding-affinity for Mediator is an important organizing feature in the transcriptional network that determines NSC identity.
MeSH term(s)	Cell Line ; Enhancer Elements, Genetic/genetics ; Gene Expression Regulation, Developmental/physiology ; Gene Regulatory Networks/physiology ; Histones/metabolism ; Humans ; Jumonji Domain-Containing Histone Demethylases/metabolism ; Mediator Complex/metabolism ; Neural Stem Cells/physiology ; Neurogenesis/genetics ; Oxidoreductases, N-Demethylating/metabolism ; Promoter Regions, Genetic/genetics ; Protein Interaction Mapping ; Protein Interaction Maps/genetics ; Protein-Arginine N-Methyltransferases/metabolism ; Transcription Factor 4/metabolism ; Transcription, Genetic/physiology
Chemical Substances	Histones ; Mediator Complex ; TCF4 protein, human ; Transcription Factor 4 ; histone H3 trimethyl Lys4 ; JMJD1C protein, human (EC 1.14.11.-) ; Jumonji Domain-Containing Histone Demethylases (EC 1.14.11.-) ; Oxidoreductases, N-Demethylating (EC 1.5.-) ; Protein-Arginine N-Methyltransferases (EC 2.1.1.319) ; coactivator-associated arginine methyltransferase 1 (EC 2.1.1.319)
Language	English
Publishing date	2019-06-17
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-019-10502-8
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Article ; Online: Proteomic analysis of FOXP proteins reveals interactions between cortical transcription factors associated with neurodevelopmental disorders.

Estruch, Sara B / Graham, Sarah A / Quevedo, Martí / Vino, Arianna / Dekkers, Dick H W / Deriziotis, Pelagia / Sollis, Elliot / Demmers, Jeroen / Poot, Raymond A / Fisher, Simon E

Human molecular genetics

2018 Volume 27, Issue 7, Page(s) 1212–1227

Abstract: FOXP transcription factors play important roles in neurodevelopment, but little is known about how their transcriptional activity is regulated. FOXP proteins cooperatively regulate gene expression by forming homo- and hetero-dimers with each other. ... ...

Abstract	FOXP transcription factors play important roles in neurodevelopment, but little is known about how their transcriptional activity is regulated. FOXP proteins cooperatively regulate gene expression by forming homo- and hetero-dimers with each other. Physical associations with other transcription factors might also modulate the functions of FOXP proteins. However, few FOXP-interacting transcription factors have been identified so far. Therefore, we sought to discover additional transcription factors that interact with the brain-expressed FOXP proteins, FOXP1, FOXP2 and FOXP4, through affinity-purifications of protein complexes followed by mass spectrometry. We identified seven novel FOXP-interacting transcription factors (NR2F1, NR2F2, SATB1, SATB2, SOX5, YY1 and ZMYM2), five of which have well-estabslished roles in cortical development. Accordingly, we found that these transcription factors are co-expressed with FoxP2 in the deep layers of the cerebral cortex and also in the Purkinje cells of the cerebellum, suggesting that they may cooperate with the FoxPs to regulate neural gene expression in vivo. Moreover, we demonstrated that etiological mutations of FOXP1 and FOXP2, known to cause neurodevelopmental disorders, severely disrupted the interactions with FOXP-interacting transcription factors. Additionally, we pinpointed specific regions within FOXP2 sequence involved in mediating these interactions. Thus, by expanding the FOXP interactome we have uncovered part of a broader neural transcription factor network involved in cortical development, providing novel molecular insights into the transcriptional architecture underlying brain development and neurodevelopmental disorders.
MeSH term(s)	Forkhead Transcription Factors/genetics ; Forkhead Transcription Factors/metabolism ; Gene Expression Regulation ; HEK293 Cells ; Humans ; Neurodevelopmental Disorders/genetics ; Neurodevelopmental Disorders/metabolism ; Neurodevelopmental Disorders/pathology ; Purkinje Cells/metabolism ; Purkinje Cells/pathology ; Repressor Proteins/genetics ; Repressor Proteins/metabolism ; Transcription Factors/genetics ; Transcription Factors/metabolism
Chemical Substances	FOXP1 protein, human ; FOXP2 protein, human ; Forkhead Transcription Factors ; Repressor Proteins ; Transcription Factors
Language	English
Publishing date	2018-01-24
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1108742-0
ISSN	1460-2083 ; 0964-6906
ISSN (online)	1460-2083
ISSN	0964-6906
DOI	10.1093/hmg/ddy035
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