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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 ; Online: 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) 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: Publisher Correction: Mediator complex interaction partners organize the transcriptional network that defines neural stem cells.

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: 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: 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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Article ; Online: The non-canonical Wnt/PKC pathway regulates mitochondrial dynamics through degradation of the arm-like domain-containing protein Alex3.

Serrat, Román / López-Doménech, Guillermo / Mirra, Serena / Quevedo, Martí / Garcia-Fernàndez, Jordi / Ulloa, Fausto / Burgaya, Ferrán / Soriano, Eduardo

PloS one

2013 Volume 8, Issue 7, Page(s) e67773

Abstract: The regulation of mitochondrial dynamics is vital in complex cell types, such as neurons, that transport and localize mitochondria in high energy-demanding cell domains. The Armcx3 gene encodes a mitochondrial-targeted protein (Alex3) that contains ... ...

Abstract	The regulation of mitochondrial dynamics is vital in complex cell types, such as neurons, that transport and localize mitochondria in high energy-demanding cell domains. The Armcx3 gene encodes a mitochondrial-targeted protein (Alex3) that contains several arm-like domains. In a previous study we showed that Alex3 protein regulates mitochondrial aggregation and trafficking. Here we studied the contribution of Wnt proteins to the mitochondrial aggregation and dynamics regulated by Alex3. Overexpression of Alex3 in HEK293 cells caused a marked aggregation of mitochondria, which was attenuated by treatment with several Wnts. We also found that this decrease was caused by Alex3 degradation induced by Wnts. While the Wnt canonical pathway did not alter the pattern of mitochondrial aggregation induced by Alex3, we observed that the Wnt/PKC non-canonical pathway regulated both mitochondrial aggregation and Alex3 protein levels, thereby rendering a mitochondrial phenotype and distribution similar to control patterns. Our data suggest that the Wnt pathway regulates mitochondrial distribution and dynamics through Alex3 protein degradation.
MeSH term(s)	Amino Acid Motifs ; Armadillo Domain Proteins/genetics ; Armadillo Domain Proteins/metabolism ; Gene Expression Regulation ; Genes, Reporter ; Green Fluorescent Proteins/genetics ; Green Fluorescent Proteins/metabolism ; HEK293 Cells ; Humans ; Mitochondria/genetics ; Mitochondria/metabolism ; Mitochondrial Dynamics/genetics ; Mitochondrial Proteins/genetics ; Mitochondrial Proteins/metabolism ; Molecular Sequence Data ; Naphthalenes/pharmacology ; Protein Kinase C/genetics ; Protein Kinase C/metabolism ; Protein Kinase Inhibitors/pharmacology ; Protein Stability ; Protein Structure, Tertiary ; Proteolysis ; Wnt Proteins/genetics ; Wnt Proteins/metabolism ; Wnt Signaling Pathway
Chemical Substances	Armadillo Domain Proteins ; ARMCX3 protein, human ; Mitochondrial Proteins ; Naphthalenes ; Protein Kinase Inhibitors ; Wnt Proteins ; Green Fluorescent Proteins (147336-22-9) ; Protein Kinase C (EC 2.7.11.13) ; calphostin C (I271P23G24)
Language	English
Publishing date	2013-07-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0067773
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Article ; Online: The mixture of "ecstasy" and its metabolites impairs mitochondrial fusion/fission equilibrium and trafficking in hippocampal neurons, at in vivo relevant concentrations.

Barbosa, Daniel José / Serrat, Romàn / Mirra, Serena / Quevedo, Martí / de Barreda, Elena Goméz / Àvila, Jesús / Ferreira, Luísa Maria / Branco, Paula Sério / Fernandes, Eduarda / Lourdes Bastos, Maria de / Capela, João Paulo / Soriano, Eduardo / Carvalho, Félix

Toxicological sciences : an official journal of the Society of Toxicology

2014 Volume 139, Issue 2, Page(s) 407–420

Abstract: 3,4-Methylenedioxymethamphetamine (MDMA; "ecstasy") is a potentially neurotoxic recreational drug of abuse. Though the mechanisms involved are still not completely understood, formation of reactive metabolites and mitochondrial dysfunction contribute to ... ...

Abstract	3,4-Methylenedioxymethamphetamine (MDMA; "ecstasy") is a potentially neurotoxic recreational drug of abuse. Though the mechanisms involved are still not completely understood, formation of reactive metabolites and mitochondrial dysfunction contribute to MDMA-related neurotoxicity. Neuronal mitochondrial trafficking, and their targeting to synapses, is essential for proper neuronal function and survival, rendering neurons particularly vulnerable to mitochondrial dysfunction. Indeed, MDMA-associated disruption of Ca(2+) homeostasis and ATP depletion have been described in neurons, thus suggesting possible MDMA interference on mitochondrial dynamics. In this study, we performed real-time functional experiments of mitochondrial trafficking to explore the role of in situ mitochondrial dysfunction in MDMA's neurotoxic actions. We show that the mixture of MDMA and six of its major in vivo metabolites, each compound at 10μM, impaired mitochondrial trafficking and increased the fragmentation of axonal mitochondria in cultured hippocampal neurons. Furthermore, the overexpression of mitofusin 2 (Mfn2) or dynamin-related protein 1 (Drp1) K38A constructs almost completely rescued the trafficking deficits caused by this mixture. Finally, in hippocampal neurons overexpressing a Mfn2 mutant, Mfn2 R94Q, with impaired fusion and transport properties, it was confirmed that a dysregulation of mitochondrial fission/fusion events greatly contributed to the reported trafficking phenotype. In conclusion, our study demonstrated, for the first time, that the mixture of MDMA and its metabolites, at concentrations relevant to the in vivo scenario, impaired mitochondrial trafficking and increased mitochondrial fragmentation in hippocampal neurons, thus providing a new insight in the context of "ecstasy"-induced neuronal injury.
MeSH term(s)	Adenosine Triphosphate/metabolism ; Animals ; Axonal Transport/drug effects ; Calcium/metabolism ; Cell Survival/drug effects ; Cells, Cultured ; Dose-Response Relationship, Drug ; GTP Phosphohydrolases/metabolism ; Hippocampus/drug effects ; Hippocampus/metabolism ; Mice ; Mitochondrial Dynamics/drug effects ; N-Methyl-3,4-methylenedioxyamphetamine/metabolism ; N-Methyl-3,4-methylenedioxyamphetamine/toxicity ; Neurons/drug effects ; Neurons/metabolism ; Neurotoxicity Syndromes/etiology ; Neurotoxicity Syndromes/metabolism ; Rats
Chemical Substances	Adenosine Triphosphate (8L70Q75FXE) ; GTP Phosphohydrolases (EC 3.6.1.-) ; Mfn2 protein, mouse (EC 3.6.1.-) ; N-Methyl-3,4-methylenedioxyamphetamine (KE1SEN21RM) ; Calcium (SY7Q814VUP)
Language	English
Publishing date	2014-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1420885-4
ISSN	1096-0929 ; 1096-6080
ISSN (online)	1096-0929
ISSN	1096-6080
DOI	10.1093/toxsci/kfu042
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Article ; Online: MDMA impairs mitochondrial neuronal trafficking in a Tau- and Mitofusin2/Drp1-dependent manner.

Barbosa, Daniel José / Serrat, Román / Mirra, Serena / Quevedo, Martí / Gómez de Barreda, Elena / Avila, Jesús / Fernandes, Eduarda / Bastos, Maria de Lourdes / Capela, João Paulo / Carvalho, Félix / Soriano, Eduardo

Archives of toxicology

2014 Volume 88, Issue 8, Page(s) 1561–1572

Abstract: Identification of the mechanisms by which drugs of abuse cause neuronal dysfunction is essential for understanding the biological bases of their acute and long-lasting effects in the brain. Here, we performed real-time functional experiments of axonal ... ...

Abstract	Identification of the mechanisms by which drugs of abuse cause neuronal dysfunction is essential for understanding the biological bases of their acute and long-lasting effects in the brain. Here, we performed real-time functional experiments of axonal transport of mitochondria to explore the role of in situ mitochondrial dysfunction in 3,4-methylenedioxymethamphetamine (MDMA; "ecstasy")-related brain actions. We showed that MDMA dramatically reduced mitochondrial trafficking in hippocampal neurons in a Tau-dependent manner, in which glycogen synthase kinase 3β activity was implicated. Furthermore, we found that these trafficking abnormalities were rescued by over-expression of Mitofusin2 and dynamin-related protein 1, but not of Miro1. Given the relevance of mitochondrial targeting for neuronal function and neurotransmission, our data underscore a novel mechanism of action of MDMA that may contribute to our understanding of how this drug of abuse alters neuronal functioning.
MeSH term(s)	Animals ; Axonal Transport/drug effects ; Calcium/metabolism ; Cells, Cultured ; Dynamins/metabolism ; GTP Phosphohydrolases/metabolism ; Hippocampus/cytology ; Hippocampus/drug effects ; Hippocampus/embryology ; Mice, Inbred C57BL ; Mitochondria/drug effects ; Mitochondria/metabolism ; Mitochondrial Dynamics/drug effects ; N-Methyl-3,4-methylenedioxyamphetamine/toxicity ; Neurons/drug effects ; Neurons/metabolism ; Phosphorylation ; tau Proteins/metabolism
Chemical Substances	Mapt protein, mouse ; tau Proteins ; GTP Phosphohydrolases (EC 3.6.1.-) ; Mfn2 protein, mouse (EC 3.6.1.-) ; Dnm1l protein, mouse (EC 3.6.5.5) ; Dynamins (EC 3.6.5.5) ; N-Methyl-3,4-methylenedioxyamphetamine (KE1SEN21RM) ; Calcium (SY7Q814VUP)
Language	English
Publishing date	2014-08
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	124992-7
ISSN	1432-0738 ; 0340-5761
ISSN (online)	1432-0738
ISSN	0340-5761
DOI	10.1007/s00204-014-1209-7
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