155 results on '"Dick, H. W."'
Search Results
2. C. elegans TFIIH subunit GTF-2H5/TTDA is a non-essential transcription factor indispensable for DNA repair
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Karen L. Thijssen, Melanie van der Woude, Carlota Davó-Martínez, Dick H. W. Dekkers, Mariangela Sabatella, Jeroen A. A. Demmers, Wim Vermeulen, and Hannes Lans
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Biology (General) ,QH301-705.5 - Abstract
Hereditary mutations in TTDA/GTF2H5 cause a photosensitive form of the rare developmental disorder trichothiodystrophy, however the development of models has been hampered by mutations being lethal. Thijssen et al. show that deficiency of C. elegans TTDA ortholog GTF-2H5 is, compatible with life, in contrast to depletion of other TFIIH subunits and thus propose that this model could be used for studying the pathogenesis of trichothiodystrophy.
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- 2021
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- View/download PDF
3. C. elegans TFIIH subunit GTF-2H5/TTDA is a non-essential transcription factor indispensable for DNA repair
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Thijssen, Karen L., van der Woude, Melanie, Davó-Martínez, Carlota, Dekkers, Dick H. W., Sabatella, Mariangela, Demmers, Jeroen A. A., Vermeulen, Wim, and Lans, Hannes
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- 2021
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4. Characterization of the TBR1 interactome
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Elliot Sollis, Joery den Hoed, Marti Quevedo, Sara B Estruch, Arianna Vino, Dick H W Dekkers, Jeroen A A Demmers, Raymond Poot, Pelagia Deriziotis, Simon E Fisher, Biochemistry, and Cell biology
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Genetics ,General Medicine ,Molecular Biology ,Genetics (clinical) - 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.
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- 2023
5. Mediator complex interaction partners organize the transcriptional network that defines neural stem cells
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Marti Quevedo, Lize Meert, Mike R. Dekker, Dick H. W. Dekkers, Johannes H. Brandsma, Debbie L. C. van den Berg, Zeliha Ozgür, Wilfred F. J. van IJcken, Jeroen Demmers, Maarten Fornerod, and Raymond A. Poot
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Science - Abstract
The Mediator complex regulates transcription by connecting enhancers to promoters. Here, the authors purify Mediator from neural stem cells (NSCs), identify 75 novel protein-protein interaction partners and characterize the Mediator-interacting network that regulates transcription and establishes NSC identity.
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- 2019
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6. Publisher Correction: Mediator complex interaction partners organize the transcriptional network that defines neural stem cells
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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, and Poot, Raymond A.
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- 2019
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7. Mediator complex interaction partners organize the transcriptional network that defines neural stem cells
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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, and Poot, Raymond A.
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- 2019
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8. Characterization of the TBR1 interactome: variants associated with neurodevelopmental disorders disrupt novel protein interactions
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Sollis, Elliot, primary, den Hoed, Joery, additional, Quevedo, Marti, additional, Estruch, Sara B, additional, Vino, Arianna, additional, Dekkers, Dick H W, additional, Demmers, Jeroen A A, additional, Poot, Raymond, additional, Deriziotis, Pelagia, additional, and Fisher, Simon E, additional
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- 2022
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9. CLEC16A interacts with retromer and TRIM27, and its loss impairs endosomal trafficking and neurodevelopment
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Smits, Daphne J., primary, Dekker, Jordy, additional, Schot, Rachel, additional, Tabarki, Brahim, additional, Alhashem, Amal, additional, Demmers, Jeroen A. A., additional, Dekkers, Dick H. W., additional, Romito, Antonio, additional, van der Spek, Peter J., additional, van Ham, Tjakko J., additional, Bertoli-Avella, Aida M., additional, and Mancini, Grazia M. S., additional
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- 2022
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10. USP7 regulates the ncPRC1 Polycomb axis to stimulate genomic H2AK119ub1 deposition uncoupled from H3K27me3
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Sijm, Ayestha, primary, Atlasi, Yaser, additional, van der Knaap, Jan A., additional, Wolf van der Meer, Joyce, additional, Chalkley, Gillian E., additional, Bezstarosti, Karel, additional, Dekkers, Dick H. W., additional, Doff, Wouter A. S., additional, Ozgur, Zeliha, additional, van IJcken, Wilfred F. J., additional, Demmers, Jeroen A. A., additional, and Verrijzer, C. Peter, additional
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- 2022
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11. USP7 regulates the ncPRC1 Polycomb axis to stimulate genomic H2AK119ub1 deposition uncoupled from H3K27me3
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Ayestha Sijm, Yaser Atlasi, Jan A. van der Knaap, Joyce Wolf van der Meer, Gillian E. Chalkley, Karel Bezstarosti, Dick H. W. Dekkers, Wouter A. S. Doff, Zeliha Ozgur, Wilfred F. J. van IJcken, Jeroen A. A. Demmers, C. Peter Verrijzer, Biochemistry, and Cell biology
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Multidisciplinary ,SDG 3 - Good Health and Well-being ,General - Abstract
Ubiquitin-specific protease 7 (USP7) has been implicated in cancer progression and neurodevelopment. However, its molecular targets remain poorly characterized. We combined quantitative proteomics, transcriptomics, and epigenomics to define the core USP7 network. Our multi-omics analysis reveals USP7 as a control hub that links genome regulation, tumor suppression, and histone H2A ubiquitylation (H2AK119ub1) by noncanonical Polycomb-repressive complexes (ncPRC1s). USP7 strongly stabilizes ncPRC1.6 and, to a lesser extent, ncPRC1.1. Moreover, USP7 represses expression of AUTS2, which suppresses H2A ubiquitylation by ncPRC1.3/5. Collectively, these USP7 activities promote the genomic deposition of H2AK119ub1 by ncPRC1, especially at transcriptionally repressed loci. Notably, USP7-dependent changes in H2AK119ub1 levels are uncoupled from H3K27me3. Even complete loss of the PRC1 catalytic core and H2AK119ub1 has only a limited effect on H3K27me3. Besides defining the USP7 regulome, our results reveal that H2AK119ub1 dosage is largely disconnected from H3K27me3.
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- 2022
12. Identification of Full-Length Wild-Type and Mutant Huntingtin Interacting Proteins by Crosslinking Immunoprecipitation in Mice Brain Cortex
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Aleksandra E. Bury, Eric Reits, Karen A. Sap, Arzu Tugce Guler, Dick H. W. Dekkers, Jeroen Demmers, and Biochemistry
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0301 basic medicine ,Research Report ,congenital, hereditary, and neonatal diseases and abnormalities ,Huntingtin ,Immunoprecipitation ,Mutant ,Nerve Tissue Proteins ,Biology ,immunoprecipitation ,03 medical and health sciences ,Cellular and Molecular Neuroscience ,Mice ,0302 clinical medicine ,proteomics ,Huntington's disease ,Tandem Mass Spectrometry ,mental disorders ,Huntingtin Protein ,medicine ,Animals ,Wild type ,Brain ,Translation (biology) ,medicine.disease ,Cell biology ,nervous system diseases ,Vesicular transport protein ,030104 developmental biology ,Huntington Disease ,Synaptotagmin I ,cerebral cortex ,protein interaction mapping ,Mutant Proteins ,Neurology (clinical) ,cross-linking reagents ,030217 neurology & neurosurgery ,Huntington’s disease ,Chromatography, Liquid - Abstract
Background: Huntington’s disease is a neurodegenerative disorder caused by a CAG expansion in the huntingtin gene, resulting in a polyglutamine expansion in the ubiquitously expressed mutant huntingtin protein. Objective: Here we set out to identify proteins interacting with the full-length wild-type and mutant huntingtin protein in the mice cortex brain region to understand affected biological processes in Huntington’s disease pathology. Methods: Full-length huntingtin with 20 and 140 polyQ repeats were formaldehyde-crosslinked and isolated via their N-terminal Flag-tag from 2-month-old mice brain cortex. Interacting proteins were identified and quantified by label-free liquid chromatography-mass spectrometry (LC-MS/MS). Results: We identified 30 interactors specific for wild-type huntingtin, 14 interactors specific for mutant huntingtin and 14 shared interactors that interacted with both wild-type and mutant huntingtin, including known interactors such as F8a1/Hap40. Syt1, Ykt6, and Snap47, involved in vesicle transport and exocytosis, were among the proteins that interacted specifically with wild-type huntingtin. Various other proteins involved in energy metabolism and mitochondria were also found to associate predominantly with wild-type huntingtin, whereas mutant huntingtin interacted with proteins involved in translation including Mapk3, Eif3h and Eef1a2. Conclusion: Here we identified both shared and specific interactors of wild-type and mutant huntingtin, which are involved in different biological processes including exocytosis, vesicle transport, translation and metabolism. These findings contribute to the understanding of the roles that wild-type and mutant huntingtin play in a variety of cellular processes both in healthy conditions and Huntington’s disease pathology.
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- 2021
13. CLEC16A interacts with retromer and TRIM27, and its loss impairs endosomal trafficking and neurodevelopment
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Daphne J, Smits, Jordy, Dekker, Rachel, Schot, Brahim, Tabarki, Amal, Alhashem, Jeroen A A, Demmers, Dick H W, Dekkers, Antonio, Romito, Peter J, van der Spek, Tjakko J, van Ham, Aida M, Bertoli-Avella, and Grazia M S, Mancini
- Abstract
CLEC16A is a membrane-associated C-type lectin protein that functions as a E3-ubiquitin ligase. CLEC16A regulates autophagy and mitophagy, and reportedly localizes to late endosomes. GWAS studies have associated CLEC16A SNPs to various auto-immune and neurological disorders, including multiple sclerosis and Parkinson disease. Studies in mouse models imply a role for CLEC16A in neurodegeneration. We identified bi-allelic CLEC16A truncating variants in siblings from unrelated families presenting with a severe neurodevelopmental disorder including microcephaly, brain atrophy, corpus callosum dysgenesis, and growth retardation. To understand the function of CLEC16A in neurodevelopment we used in vitro models and zebrafish embryos. We observed CLEC16A localization to early endosomes in HEK293T cells. Mass spectrometry of human CLEC16A showed interaction with endosomal retromer complex subunits and the endosomal ubiquitin ligase TRIM27. Expression of the human variant leading to C-terminal truncated CLEC16A, abolishes both its endosomal localization and interaction with TRIM27, suggesting a loss-of-function effect. CLEC16A knockdown increased TRIM27 adhesion to early endosomes and abnormal accumulation of endosomal F-actin, a sign of disrupted vesicle sorting. Mutagenesis of clec16a by CRISPR-Cas9 in zebrafish embryos resulted in accumulated acidic/phagolysosome compartments, in neurons and microglia, and dysregulated mitophagy. The autophagocytic phenotype was rescued by wild-type human CLEC16A but not the C-terminal truncated CLEC16A. Our results demonstrate that CLEC16A closely interacts with retromer components and regulates endosomal fate by fine-tuning levels of TRIM27 and polymerized F-actin on the endosome surface. Dysregulation of CLEC16A-mediated endosomal sorting is associated with neurodegeneration, but it also causes accumulation of autophagosomes and unhealthy mitochondria during brain development.
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- 2022
14. Single-Cell Atlas of Patient-Derived Trophoblast Organoids in Ongoing Pregnancies
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Schäffers, Olivier J. M., primary, Dupont, Catherine, additional, Bindels, Eric M., additional, Van Opstal, Diane, additional, Dekkers, Dick H. W., additional, Demmers, Jeroen A. A., additional, Gribnau, Joost, additional, and van Rijn, Bas B., additional
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- 2022
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15. Characterization of the TBR1 interactome: variants associated with neurodevelopmental disorders disrupt novel protein interactions.
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Sollis, Elliot, Hoed, Joery den, Quevedo, Marti, Estruch, Sara B, Vino, Arianna, Dekkers, Dick H W, Demmers, Jeroen A A, Poot, Raymond, Deriziotis, Pelagia, and Fisher, Simon E
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- 2023
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16. Publisher Correction: Mediator complex interaction partners organize the transcriptional network that defines neural stem cells
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Marti Quevedo, Lize Meert, Mike R. Dekker, Dick H. W. Dekkers, Johannes H. Brandsma, Debbie L. C. van den Berg, Zeliha Ozgür, Wilfred F. J. van IJcken, Jeroen Demmers, Maarten Fornerod, and Raymond A. Poot
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Science - Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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- 2019
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17. C. elegans TFIIH subunit GTF-2H5/TTDA is a non-essential transcription factor indispensable for DNA repair
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Dick H. W. Dekkers, Carlota Davó-Martínez, Karen L. Thijssen, Hannes Lans, Wim Vermeulen, Mariangela Sabatella, Jeroen Demmers, Melanie van der Woude, Molecular Genetics, Erasmus MC other, and Biochemistry
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DNA Repair ,DNA repair ,DNA damage ,QH301-705.5 ,Protein subunit ,Trichothiodystrophy ,Medicine (miscellaneous) ,Biology ,General Biochemistry, Genetics and Molecular Biology ,Article ,Transcription (biology) ,medicine ,Animals ,Biology (General) ,Caenorhabditis elegans ,Caenorhabditis elegans Proteins ,Transcription factor ,DNA, Helminth ,medicine.disease ,Cell biology ,Nucleotide excision repair ,Transcription factor II H ,General Agricultural and Biological Sciences ,Transcription ,Transcription Factors - Abstract
The 10-subunit TFIIH complex is vital to transcription and nucleotide excision repair. Hereditary mutations in its smallest subunit, TTDA/GTF2H5, cause a photosensitive form of the rare developmental disorder trichothiodystrophy. Some trichothiodystrophy features are thought to be caused by subtle transcription or gene expression defects. TTDA/GTF2H5 knockout mice are not viable, making it difficult to investigate TTDA/GTF2H5 in vivo function. Here we show that deficiency of C. elegans TTDA ortholog GTF-2H5 is, however, compatible with life, in contrast to depletion of other TFIIH subunits. GTF-2H5 promotes TFIIH stability in multiple tissues and is indispensable for nucleotide excision repair, in which it facilitates recruitment of TFIIH to DNA damage. Strikingly, when transcription is challenged, gtf-2H5 embryos die due to the intrinsic TFIIH fragility in absence of GTF-2H5. These results support the idea that TTDA/GTF2H5 mutations cause transcription impairment underlying trichothiodystrophy and establish C. elegans as model for studying pathogenesis of this disease., Hereditary mutations in TTDA/GTF2H5 cause a photosensitive form of the rare developmental disorder trichothiodystrophy, however the development of models has been hampered by mutations being lethal. Thijssen et al. show that deficiency of C. elegans TTDA ortholog GTF-2H5 is, compatible with life, in contrast to depletion of other TFIIH subunits and thus propose that this model could be used for studying the pathogenesis of trichothiodystrophy.
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- 2021
18. Caldendrin and myosin V regulate synaptic spine apparatus localization via ER stabilization in dendritic spines
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Anja Konietzny, Jasper Grendel, Alan Kadek, Michael Bucher, Yuhao Han, Nathalie Hertrich, Dick H W Dekkers, Jeroen A A Demmers, Kay Grünewald, Charlotte Uetrecht, Marina Mikhaylova, and Biochemistry
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musculoskeletal diseases ,Dendritic Spines ,Myosin Type V ,macromolecular substances ,myosin ,Endoplasmic Reticulum ,Hippocampus ,General Biochemistry, Genetics and Molecular Biology ,Mass Spectrometry ,03 medical and health sciences ,0302 clinical medicine ,Calmodulin ,synaps ,ddc:570 ,spine apparatus ,Animals ,Humans ,Protein Interaction Domains and Motifs ,Rats, Wistar ,Molecular Biology ,030304 developmental biology ,Mice, Knockout ,0303 health sciences ,General Immunology and Microbiology ,General Neuroscience ,Calcium-Binding Proteins ,Endoplasmic Reticulum, Smooth ,musculoskeletal system ,caldendrin ,Actins ,endoplasmic reticulum ,540 Chemie und zugeordnete Wissenschaften ,HEK293 Cells ,ddc:540 ,030217 neurology & neurosurgery - Abstract
The EMBO journal 41(4), e106523 (2022). doi:10.15252/embj.2020106523, Excitatory synapses of principal hippocampal neurons are frequently located on dendritic spines. The dynamic strengthening or weakening of individual inputs results in structural and molecular diversity of dendritic spines. Active spines with large calcium ion (Ca$^{2+}$) transients are frequently invaded by a single protrusion from the endoplasmic reticulum (ER), which is dynamically transported into spines via the actin-based motor myosin V. An increase in synaptic strength correlates with stable anchoring of the ER, followed by the formation of an organelle referred to as the spine apparatus. Here, we show that myosin V binds the Ca$^{2+}$ sensor caldendrin, a brain-specific homolog of the well-known myosin V interactor calmodulin. While calmodulin is an essential activator of myosin V motor function, we found that caldendrin acts as an inhibitor of processive myosin V movement. In mouse and rat hippocampal neurons, caldendrin regulates spine apparatus localization to a subset of dendritic spines through a myosin V-dependent pathway. We propose that caldendrin transforms myosin into a stationary F-actin tether that enables the localization of ER tubules and formation of the spine apparatus in dendritic spines., Published by Wiley, Hoboken, NJ [u.a.]
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- 2021
19. Caldendrin and myosin V regulate synaptic spine apparatus localization via ER stabilization in dendritic spines
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Konietzny, Anja, primary, Grendel, Jasper, additional, Kadek, Alan, additional, Bucher, Michael, additional, Han, Yuhao, additional, Hertrich, Nathalie, additional, Dekkers, Dick H W, additional, Demmers, Jeroen A A, additional, Grünewald, Kay, additional, Uetrecht, Charlotte, additional, and Mikhaylova, Marina, additional
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- 2021
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20. Author response: In vivo analysis reveals that ATP-hydrolysis couples remodeling to SWI/SNF release from chromatin
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C. Peter Verrijzer, Gillian E. Chalkley, Dick H. W. Dekkers, Tsung Wai Kan, Jan A. van der Knaap, B. C. Tilly, Yuri M. Moshkin, and Jeroen Demmers
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ATP hydrolysis ,Chemistry ,In vivo analysis ,SWI/SNF ,Chromatin ,Cell biology - Published
- 2021
21. Heterogeneous clinical phenotypes and cerebral malformations reflected by rotatin cellular dynamics
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Marianne L. T. van der Sterre, Rachel Schot, Peter J. van der Spek, Daphne Heijsman, Leontine van Unen, Gert-Jan Kremers, Martyna M. Grochowska, Grazia M.S. Mancini, Laura Vandervore, Roy Masius, Gerben J. Schaaf, Martina Wilke, Nadia Bahi-Buisson, Anna Grandone, Renske Oegema, Anna Jansen, Patrick Rump, Arie van Haeringen, Tugba Kalayci, Frans W. Verheijen, Katrien Stouffs, Peter Elfferich, Els A. J. Peeters, Esmee Kasteleijn, Anton J. van Essen, Umut Altunoglu, Alexander Gheldof, Dick H. W. Dekkers, Johan A. Slotman, Jeroen Demmers, Raymond A. Poot, WB Dobyns, Vandervore, L. V., Schot, R., Kasteleijn, E., Oegema, R., Stouffs, K., Gheldof, A., Grochowska, M. M., Van Der Sterre, M. L. T., Van Unen, L. M. A., Wilke, M., Elfferich, P., Van Der Spek, P. J., Heijsman, D., Grandone, A., Demmers, J. A. A., Dekkers, D. H. W., Slotman, J. A., Kremers, G. -J., Schaaf, G. J., Masius, R. G., Van Essen, A. J., Rump, P., Van Haeringen, A., Peeters, E., Altunoglu, U., Kalayci, T., Poot, R. A., Dobyns, W. B., Bahi-Buisson, N., Verheijen, F. W., Jansen, A. C., Mancini, G. M. S., Clinical Genetics, Pathology, Molecular Genetics, Cell biology, Clinical sciences, Faculty of Medicine and Pharmacy, Medical Genetics, Reproduction and Genetics, Faculty of Psychology and Educational Sciences, Public Health Sciences, Mental Health and Wellbeing research group, Neurogenetics, and Pediatrics
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0301 basic medicine ,Microcephaly ,MIGRATION ,MYH10 ,Clinical Neurology ,Lissencephaly ,PRIMARY CILIA ,Cell Cycle Proteins ,Biology ,medicine.disease_cause ,NONMUSCLE MYOSIN-II ,03 medical and health sciences ,0302 clinical medicine ,Ciliogenesis ,medicine ,Polymicrogyria ,Basal body ,Humans ,mitosis ,Mutation ,mitosi ,DEFECTS ,Original Articles ,medicine.disease ,POINT MUTATION ,Cell biology ,030104 developmental biology ,Phenotype ,Centrosome ,Neurology (clinical) ,centrosome amplification ,Carrier Proteins ,Multipolar spindles ,RTTN ,030217 neurology & neurosurgery - Abstract
See Uzquiano and Francis (doi:10.1093/brain/awz048) for a scientific commentary on this article. Mutations in RTTN, which encodes Rotatin, give rise to various brain malformations. Vandervore et al. reveal mitotic failure, aneuploidy, apoptosis and defective ciliogenesis in patient cells. Rotatin binds to myosin subunits in the leading edge of human neurons, which may explain the proliferation and migration defects observed., Recessive mutations in RTTN, encoding the protein rotatin, were originally identified as cause of polymicrogyria, a cortical malformation. With time, a wide variety of other brain malformations has been ascribed to RTTN mutations, including primary microcephaly. Rotatin is a centrosomal protein possibly involved in centriolar elongation and ciliogenesis. However, the function of rotatin in brain development is largely unknown and the molecular disease mechanism underlying cortical malformations has not yet been elucidated. We performed both clinical and cell biological studies, aimed at clarifying rotatin function and pathogenesis. Review of the 23 published and five unpublished clinical cases and genomic mutations, including the effect of novel deep intronic pathogenic mutations on RTTN transcripts, allowed us to extrapolate the core phenotype, consisting of intellectual disability, short stature, microcephaly, lissencephaly, periventricular heterotopia, polymicrogyria and other malformations. We show that the severity of the phenotype is related to residual function of the protein, not only the level of mRNA expression. Skin fibroblasts from eight affected individuals were studied by high resolution immunomicroscopy and flow cytometry, in parallel with in vitro expression of RTTN in HEK293T cells. We demonstrate that rotatin regulates different phases of the cell cycle and is mislocalized in affected individuals. Mutant cells showed consistent and severe mitotic failure with centrosome amplification and multipolar spindle formation, leading to aneuploidy and apoptosis, which could relate to depletion of neuronal progenitors often observed in microcephaly. We confirmed the role of rotatin in functional and structural maintenance of primary cilia and determined that the protein localized not only to the basal body, but also to the axoneme, proving the functional interconnectivity between ciliogenesis and cell cycle progression. Proteomics analysis of both native and exogenous rotatin uncovered that rotatin interacts with the neuronal (non-muscle) myosin heavy chain subunits, motors of nucleokinesis during neuronal migration, and in human induced pluripotent stem cell-derived bipolar mature neurons rotatin localizes at the centrosome in the leading edge. This illustrates the role of rotatin in neuronal migration. These different functions of rotatin explain why RTTN mutations can lead to heterogeneous cerebral malformations, both related to proliferation and migration defects.
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- 2019
22. In vivo Analysis Reveals that ATP-hydrolysis Couples Remodeling to SWI/SNF Release from Chromatin
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Yuri M. Moshkin, Jan A. van der Knaap, Jeroen Demmers, Gillian E. Chalkley, B. C. Tilly, C. Peter Verrijzer, Tsung Wai Kan, Dick H. W. Dekkers, and Biochemistry
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polytene chromosomes ,animal structures ,QH301-705.5 ,Science ,ATP-dependent chromatin remodeling ,Cell Cycle Proteins ,General Biochemistry, Genetics and Molecular Biology ,live-cell imaging ,Cell Line ,Ribonucleoprotein, U1 Small Nuclear ,Histones ,Adenosine Triphosphate ,brahma ,Prophase ,Biochemistry and Chemical Biology ,ATP hydrolysis ,Animals ,Drosophila Proteins ,Nucleosome ,Biology (General) ,Adenosine Triphosphatases ,Polytene chromosome ,D. melanogaster ,General Immunology and Microbiology ,biology ,Chemistry ,Hydrolysis ,General Neuroscience ,General Medicine ,Chromatin Assembly and Disassembly ,Chromosomes and Gene Expression ,SWI/SNF ,Nucleosomes ,Chromatin ,Cell biology ,Drosophila melanogaster ,Histone ,Nucleosome mobilization ,Trans-Activators ,biology.protein ,Medicine ,RNA polymerase II ,Research Article - Abstract
ATP-dependent chromatin remodelers control the accessibility of genomic DNA through nucleosome mobilization. However, the dynamics of genome exploration by remodelers, and the role of ATP hydrolysis in this process remain unclear. We used live-cell imaging ofDrosophilapolytene nuclei to monitor Brahma (BRM) remodeler interactions with its chromosomal targets. In parallel, we measured local chromatin condensation and its effect on BRM association. Surprisingly, only a small portion of BRM is bound to chromatin at any given time. BRM binds decondensed chromatin but is excluded from condensed chromatin, limiting its genomic search space. BRM-chromatin interactions are highly dynamic, whereas histone-exchange is limited and much slower. Intriguingly, loss of ATP hydrolysis enhanced chromatin retention and clustering of BRM, which was associated with reduced histone turnover. Thus, ATP hydrolysis couples nucleosome remodeling to remodeler release, driving a continuous transient probing of the genome.
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- 2021
23. The Rise of a Middle Class and the Changing Concept of Equity in Indonesia: An Interpretation
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Dick, H. W.
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- 1985
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24. Dipeptidyl peptidase 4 is a functional receptor for the emerging human coronavirus-EMC
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Raj, V. Stalin, Mou, Huihui, Smits, Saskia L., Dekkers, Dick H. W., Müller, Marcel A., Dijkman, Ronald, and Muth, Doreen
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Zoonoses -- Genetic aspects -- Patient outcomes -- Distribution ,Coronaviruses -- Genetic aspects -- Patient outcomes -- Distribution ,Company distribution practices ,Environmental issues ,Science and technology ,Zoology and wildlife conservation - Abstract
Human coronavirus-EMC (hCoV-EMC) is a new coronavirus that has killed around half of the few humans infected so far; this study now identifies DPP4 as the receptor that this virus uses to infect cells. Human receptor for emerging coronavirus The emerging pathogenic coronavirus hCoV-EMC, first identified in September 2012, has been fatal in about half of the few humans infected so far. Bart Haagmans and colleagues have now identified the receptor that this virus uses to infect cells. In contrast to the related virus SARS-CoV, which uses angiotensin converting enzyme 2, the functional receptor for hCoV-EMC is dipeptidyl peptidase 4 (DPP4, also known as CD26), an exopeptidase found on non-ciliated cells in the lower respiratory tract. This enzyme is highly conserved across different species, and hCoV-EMC can also use bat DPP4 as a functional receptor -- a possible clue as to the host range and epidemiological history of this new virus. The findings may also be important for the development of intervention strategies. Most human coronaviruses cause mild upper respiratory tract disease but may be associated with more severe pulmonary disease in immunocompromised individuals.sup.1. However, SARS coronavirus caused severe lower respiratory disease with nearly 10% mortality and evidence of systemic spread.sup.2. Recently, another coronavirus (human coronavirus-Erasmus Medical Center (hCoV-EMC)) was identified in patients with severe and sometimes lethal lower respiratory tract infection.sup.3,4. Viral genome analysis revealed close relatedness to coronaviruses found in bats.sup.5. Here we identify dipeptidyl peptidase 4 (DPP4; also known as CD26) as a functional receptor for hCoV-EMC. DPP4 specifically co-purified with the receptor-binding S1 domain of the hCoV-EMC spike protein from lysates of susceptible Huh-7 cells. Antibodies directed against DPP4 inhibited hCoV-EMC infection of primary human bronchial epithelial cells and Huh-7 cells. Expression of human and bat (Pipistrellus pipistrellus) DPP4 in non-susceptible COS-7 cells enabled infection by hCoV-EMC. The use of the evolutionarily conserved DPP4 protein from different species as a functional receptor provides clues about the host range potential of hCoV-EMC. In addition, it will contribute critically to our understanding of the pathogenesis and epidemiology of this emerging human coronavirus, and may facilitate the development of intervention strategies., Author(s): V. Stalin Raj [sup.1] , Huihui Mou [sup.2] , Saskia L. Smits [sup.1] [sup.3] , Dick H. W. Dekkers [sup.4] , Marcel A. Müller [sup.5] , Ronald Dijkman [sup.6] [...]
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- 2013
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25. Synaptic anchoring of the endoplasmic reticulum depends on myosin V and caldendrin activity
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Nathalie Hertrich, Jeroen Demmers, Anja Konietzny, Marina Mikhaylova, Jasper Grendel, and Dick H. W. Dekkers
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Spine apparatus ,Dendritic spine ,Calmodulin ,biology ,Chemistry ,Endoplasmic reticulum ,Organelle ,Myosin ,Biophysics ,Excitatory postsynaptic potential ,biology.protein ,Actin - Abstract
Excitatory synapses of principal hippocampal neurons are frequently located on dendritic spines. The dynamic strengthening or weakening of individual inputs results in a great structural and molecular diversity of dendritic spines. Active spines with large Ca2+ transients are frequently invaded by a single protrusion from the endoplasmic reticulum (ER), which is dynamically transported into and out of spines by the actin-based motor myosin V. An increase in synaptic strength often correlates with stable anchoring of the ER, followed by the formation of the spine apparatus organelle. Here we show that synaptic ER stabilization depends on the interplay of two Ca2+-binding proteins: calmodulin serves as a light chain of myosin V and activates the motor function, whereas caldendrin acts as an inhibitor which transforms myosin into a stationary F-actin tether. Together, they provide a Ca2+-sensing module for fine-tuning myosin V activity and thereby regulate the formation of the spine apparatus in a subset of active dendritic spines.
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- 2020
26. Histone H1 eviction by the histone chaperone SET reduces cell survival following DNA damage
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Jeroen Demmers, Jurgen A. Marteijn, Eran Meshorer, Serena T. Bruens, Pernette J. Verschure, Di Zhou, Raghu Ram Edupuganti, Imke K Mandemaker, Dick H. W. Dekkers, Synthetic Systems Biology (SILS, FNWI), Molecular Genetics, and Biochemistry
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0303 health sciences ,biology ,DNA repair ,DNA damage ,Cell Survival ,Cell Biology ,Genotoxic Stress ,Chromatin remodeling ,Chromatin ,Cell biology ,Histones ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Histone ,Histone H1 ,chemistry ,030220 oncology & carcinogenesis ,biology.protein ,Histone Chaperones ,DNA ,030304 developmental biology ,DNA Damage - Abstract
Many chromatin remodeling and modifying proteins are involved in the DNA damage response, where they stimulate repair or induce DNA damage signaling. Interestingly, we identified that downregulation of the histone H1 (H1)-interacting protein SET results in increased resistance to a wide variety of DNA damaging agents. We found that this increased resistance does not result from alleviation of an inhibitory effect of SET on DNA repair but, rather, is the consequence of a suppressed apoptotic response to DNA damage. Furthermore, we provide evidence that the histone chaperone SET is responsible for the eviction of H1 from chromatin. Knockdown of H1 in SET-depleted cells resulted in re-sensitization of cells to DNA damage, suggesting that the increased DNA damage resistance in SET-depleted cells is the result of enhanced retention of H1 on chromatin. Finally, clonogenic survival assays showed that SET and p53 act epistatically in the attenuation of DNA damage-induced cell death. Taken together, our data indicate a role for SET in the DNA damage response as a regulator of cell survival following genotoxic stress.This article has an associated First Person interview with the first author of the paper.
- Published
- 2020
27. On the localization of the cleavage site in human alpha-2-antiplasmin, involved in the generation of the non-plasminogen binding form
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Robert A. S. Ariëns, Shiraazkhan Abdul, Shirley Uitte de Willige, Frank W.G. Leebeek, Dingeman C. Rijken, Dick H. W. Dekkers, Hematology, and Biochemistry
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Proteases ,proteolysis ,Plasmin ,Proteolysis ,030204 cardiovascular system & hematology ,Cleavage (embryo) ,alpha‐2‐antiplasmin ,Epitope ,03 medical and health sciences ,0302 clinical medicine ,Tandem Mass Spectrometry ,Alpha 2-antiplasmin ,medicine ,Humans ,FIBRINOLYSIS ,Fibrinolysin ,mass spectrometry ,alpha-2-Antiplasmin ,western blot ,biology ,medicine.diagnostic_test ,Chemistry ,Plasminogen ,Hematology ,Original Articles ,epitope mapping ,Epitope mapping ,Biochemistry ,biology.protein ,Original Article ,Protein G ,medicine.drug ,Chromatography, Liquid - Abstract
Background: Alpha‐2‐antiplasmin (α2AP) is the main natural inhibitor of plasmin. The C‐terminus of α2AP is crucial for the initial interaction with plasmin(ogen) and the rapid inhibitory mechanism. Approximately 35% of circulating α2AP has lost its C‐terminus (non‐plasminogen binding α2AP/NPB‐α2AP) and thereby its rapid inhibitory capacity. The C‐terminal cleavage site of α2AP is still unknown. A commercially available monoclonal antibody against α2AP (TC 3AP) detects intact but not NPB‐α2AP, suggesting that the cleavage site is located N‐terminally from the epitope of TC 3AP. Objectives: To determine the epitope of TC 3AP and then to localize the C‐terminal cleavage site of α2AP. Methods: For epitope mapping of TC 3AP, commercially available plasma purified α2AP was enzymatically digested with Asp‐N, Glu‐C, or Lys‐N. The resulting peptides were immunoprecipitated using TC 3AP‐loaded Dynabeads® Protein G. Bound peptides were eluted and analyzed by liquid chromatography‐tandem mass spectometry (LC‐MS/MS). To localize the C‐terminal cleavage site precisely, α2AP (intact and NPB) was purified from plasma and analyzed by LC‐MS/MS after enzymatic digestion with Arg‐C. Results: We localized the epitope of TC 3AP between amino acid residues Asp428 and Gly439. LC‐MS/MS data from plasma purified α2AP showed that NPB‐α2AP results from cleavage at Gln421‐Asp422 as preferred site, but also after Leu417, Glu419, Gln420, or Asp422. Conclusions: The C‐terminal cleavage site of human α2AP is located N‐terminally from the TC 3AP epitope. Because C‐terminal cleavage of α2AP can occur after multiple residues, different proteases may be responsible for the generation of NPB‐α2AP.
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- 2019
28. Caldendrin and myosin V regulate synaptic spine apparatus localization via ER stabilization in dendritic spines.
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Konietzny, Anja, Grendel, Jasper, Kadek, Alan, Bucher, Michael, Han, Yuhao, Hertrich, Nathalie, Dekkers, Dick H W, Demmers, Jeroen A A, Grünewald, Kay, Uetrecht, Charlotte, and Mikhaylova, Marina
- Subjects
DENDRITIC spines ,MYOSIN ,ORGANELLE formation ,SPINE ,CALCIUM ions ,ENDOPLASMIC reticulum - Abstract
Excitatory synapses of principal hippocampal neurons are frequently located on dendritic spines. The dynamic strengthening or weakening of individual inputs results in structural and molecular diversity of dendritic spines. Active spines with large calcium ion (Ca2+) transients are frequently invaded by a single protrusion from the endoplasmic reticulum (ER), which is dynamically transported into spines via the actin‐based motor myosin V. An increase in synaptic strength correlates with stable anchoring of the ER, followed by the formation of an organelle referred to as the spine apparatus. Here, we show that myosin V binds the Ca2+ sensor caldendrin, a brain‐specific homolog of the well‐known myosin V interactor calmodulin. While calmodulin is an essential activator of myosin V motor function, we found that caldendrin acts as an inhibitor of processive myosin V movement. In mouse and rat hippocampal neurons, caldendrin regulates spine apparatus localization to a subset of dendritic spines through a myosin V‐dependent pathway. We propose that caldendrin transforms myosin into a stationary F‐actin tether that enables the localization of ER tubules and formation of the spine apparatus in dendritic spines. SYNOPSIS: Activity‐dependent formation of the spine apparatus organelle, a marker of large and stable spines, involves synaptic anchoring of an ER protrusion. Here, this process is shown to depend on caldendrin, a brain‐specific calmodulin homolog modulating myosin V function. Caldendrin binds myosin V in a calcium‐dependent manner via a region containing myosin's first calmodulin binding site, IQ1.Binding of calmodulin or caldendrin to IQ1‐containing region is mutually exclusive.While calmodulin promotes myosin V motility on actin filaments, caldendrin impairs processive movement, but does not affect myosin V ability to bind to F‐actin.In rodent hippocampal neurons, caldendrin increases dwell‐time of spine‐inserted ER tubules transported by myosin V, and facilitates the formation of the spine apparatus organelle. [ABSTRACT FROM AUTHOR]
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- 2022
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29. Identification of Chloride Intracellular Channel Protein 3 as a Novel Gene Affecting Human Bone Formation
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Marijke Schreuders-Koedam, Dick H. W. Dekkers, Cindy S. van der Leije, Johannes P.T.M. van Leeuwen, Jeroen van de Peppel, Andrea M Brum, Jeroen Demmers, Marco Eijken, Jeroen Verhoeven, Bram C. J. van der Eerden, and Mark Janssen
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0301 basic medicine ,Gene knockdown ,Chemistry ,Endocrinology, Diabetes and Metabolism ,Mesenchymal stem cell ,Osteoblast ,Anatomy ,Bone morphogenetic protein 2 ,Cell biology ,Bone morphogenetic protein 7 ,03 medical and health sciences ,Bone morphogenetic protein 6 ,030104 developmental biology ,0302 clinical medicine ,medicine.anatomical_structure ,Skeletal disorder ,030220 oncology & carcinogenesis ,medicine ,Orthopedics and Sports Medicine ,Bone marrow - Abstract
Osteoporosis is a common skeletal disorder characterized by low bone mass leading to increased bone fragility and fracture susceptibility. The bone building cells, osteoblasts, are derived from mesenchymal stromal cells (MSCs); however, with increasing age osteogenic differentiation is diminished and more adipocytes are seen in the bone marrow, suggesting a shift in MSC lineage commitment. Identification of specific factors that stimulate osteoblast differentiation from human MSCs may deliver therapeutic targets to treat osteoporosis. The aim of this study was to identify novel genes involved in osteoblast differentiation of human bone marrow-derived MSCs (hMSCs). We identified the gene chloride intracellular channel protein 3 (CLIC3) to be strongly upregulated during MSC-derived osteoblast differentiation. Lentiviral overexpression of CLIC3 in hMSCs caused a 60% increase of matrix mineralization. Conversely, knockdown of CLIC3 in hMSCs using two short-hairpin RNAs (shRNAs) against CLIC3 resulted in a 69% to 76% reduction in CLIC3 mRNA expression, 53% to 37% less alkaline phosphatase (ALP) activity, and 78% to 88% less matrix mineralization compared to scrambled control. Next, we used an in vivo human bone formation model in which hMSCs lentivirally transduced with the CLIC3 overexpression construct were loaded onto a scaffold (hydroxyapatite-tricalcium-phosphate), implanted under the skin of NOD-SCID mice, and analyzed for bone formation 8 weeks later. CLIC3 overexpression led to a 15-fold increase in bone formation (0.33% versus 5.05% bone area relative to scaffold). Using a Clic3-His-tagged pull-down assay and liquid chromatography-mass spectrometry (LS/MS)-based proteomics analysis in lysates of osteogenically differentiated hMSCs, we showed that CLIC3 interacts with NIMA-related kinase 9 (NEK9) and phosphatidylserine synthase 1 (PTDSS1) in vitro, and this finding was supported by immunofluorescent analysis. In addition, inhibition of NEK9 or PTDSS1 gene expression by shRNAs inhibited osteoblast differentiation and mineralization. In conclusion, we successfully identified CLIC3 to be a lineage-specific gene regulating osteoblast differentiation and bone formation through its interaction with NEK9 and PTDSS1. © The Authors. JBMR Plus is published by Wiley Periodicals, Inc. on behalf of the American Society for Bone and Mineral Research.
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- 2017
30. Nipbl Interacts with Zfp609 and the Integrator Complex to Regulate Cortical Neuron Migration
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François Guillemot, Dick H. W. Dekkers, Noelia Urbán, Roberta Azzarelli, Koji Oishi, Ben Martynoga, Jeroen Demmers, Debbie L. C. van den Berg, and Biochemistry
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0301 basic medicine ,Cornelia de Lange Syndrome ,Chromosomal Proteins, Non-Histone ,Integrator complex ,Neuroscience(all) ,Cell Cycle Proteins ,RNA polymerase II ,Article ,Promoter Regions ,Mice ,03 medical and health sciences ,Genetic ,Neural Stem Cells ,Cell Movement ,Transcription (biology) ,De Lange Syndrome ,medicine ,Zfp609 ,Animals ,Developmental ,Promoter Regions, Genetic ,10. No inequality ,Transcription factor ,Cerebral Cortex ,Neurons ,Genetics ,neuronal migration ,biology ,Cohesin ,General Neuroscience ,Gene Expression Regulation, Developmental ,Integrator ,NIPBL ,Promoter ,Non-Histone ,medicine.disease ,Cornelia de Lange syndrome ,Nipbl ,RNA pol2 pausing ,transcription ,RNA Polymerase II ,Trans-Activators ,Transcription Factors ,Chromosomal Proteins ,030104 developmental biology ,Gene Expression Regulation ,biology.protein ,Neuroscience - Abstract
Summary Mutations in NIPBL are the most frequent cause of Cornelia de Lange syndrome (CdLS), a developmental disorder encompassing several neurological defects, including intellectual disability and seizures. How NIPBL mutations affect brain development is not understood. Here we identify Nipbl as a functional interaction partner of the neural transcription factor Zfp609 in brain development. Depletion of Zfp609 or Nipbl from cortical neural progenitors in vivo is detrimental to neuronal migration. Zfp609 and Nipbl overlap at genomic binding sites independently of cohesin and regulate genes that control cortical neuron migration. We find that Zfp609 and Nipbl interact with the Integrator complex, which functions in RNA polymerase 2 pause release. Indeed, Zfp609 and Nipbl co-localize at gene promoters containing paused RNA polymerase 2, and Integrator similarly regulates neuronal migration. Our data provide a rationale and mechanistic insights for the role of Nipbl in the neurological defects associated with CdLS., Highlights • Nipbl interacts with the transcription factor Zfp609 and the Integrator complex • Nipbl, Zfp609, and Integrator are required for cortical neuron migration • Nipbl, Zfp609, and Integrator co-occupy genomic binding sites independently of cohesin • Nipbl, Zfp609, and Integrator directly regulate neuronal migration genes, NIPBL mutations cause Cornelia de Lange syndrome, but Nipbl function in brain development is not well understood. Van den Berg et al. show that Nipbl interacts with Zfp609 and the Integrator complex to transcriptionally regulate cortical neuron migration.
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- 2017
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31. Characterization of neuronal synaptopodin reveals a myosin V-dependent mechanism of synaptopodin clustering at the post-synaptic sites
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Thomas G. Oertner, Alexander Drakew, Matthias Kneussel, Wolfgang Wagner, Anja Konietzny, Michael Frotscher, Jeroen Demmers, Dick H. W. Dekkers, Judit Gonzalez-Gallego, Urban Maier, Alberto Perez-Alvarez, Julia G. Baer, John A. Hammer, and Marina Mikhaylova
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0303 health sciences ,Dendritic spine ,Chemistry ,Cell biology ,Spine apparatus ,Motor protein ,Synapse ,03 medical and health sciences ,0302 clinical medicine ,Microtubule ,Myosin ,Synaptopodin ,030217 neurology & neurosurgery ,Actin ,030304 developmental biology - Abstract
The spine apparatus (SA) is an endoplasmic reticulum-related organelle which is present in a subset of dendritic spines in cortical and pyramidal neurons. The synaptopodin protein localizes between the stacks of the spine apparatus and is essential for the formation of this unique organelle. Although several studies have demonstrated the significance of the SA and synaptopodin in calcium homeostasis and plasticity of dendritic spines, it is still unclear what factors contribute to its stability at the synapse and whether the SA is locally formed or it is actively delivered to the spines. In this study we show that synaptopodin clusters are stable at their locations. We found no evidence of active microtubule-based transport for synaptopodin. Instead new clusters were emerging in the spines, which we interpret as the SA being assembled on-site. Furthermore, using super-resolution microscopy we show a tight association of synaptopodin with actin filaments. We identify the actin-based motor proteins myosin V and VI as novel interaction partners of synaptopodin and demonstrate that myosin V is important for the formation and/or maintenance of the SA.
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- 2019
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32. Myosin V regulates synaptopodin clustering and localization in dendrites of hippocampal neurons
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Judit Gonzalez-Gallego, Alberto Perez-Alvarez, Jeroen Demmers, Dick H. W. Dekkers, John A. Hammer, Marina Mikhaylova, Wolfgang Wagner, Michael Frotscher, Anja Konietzny, Alexander Drakew, Thomas G. Oertner, Matthias Kneussel, Julia Bär, and Biochemistry
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Dendritic spine ,Myosin Type V ,Myosin ,Biology ,Hippocampal formation ,Hippocampus ,Dendritic spines ,Motor protein ,Mice ,F-actin ,03 medical and health sciences ,0302 clinical medicine ,Microtubule ,Animals ,Rats, Wistar ,Actin ,030304 developmental biology ,Spine apparatus ,0303 health sciences ,Microfilament Proteins ,Dendrites ,Cell Biology ,Rats ,Cell biology ,Female ,Synaptopodin ,030217 neurology & neurosurgery ,Research Article - Abstract
The spine apparatus (SA) is an endoplasmic reticulum-related organelle that is present in a subset of dendritic spines in cortical and pyramidal neurons, and plays an important role in Ca2+ homeostasis and dendritic spine plasticity. The protein synaptopodin is essential for the formation of the SA and is widely used as a maker for this organelle. However, it is still unclear which factors contribute to its localization at selected synapses, and how it triggers local SA formation. In this study, we characterized development, localization and mobility of synaptopodin clusters in hippocampal primary neurons, as well as the molecular dynamics within these clusters. Interestingly, synaptopodin at the shaft-associated clusters is less dynamic than at spinous clusters. We identify the actin-based motor proteins myosin V (herein referring to both the myosin Va and Vb forms) and VI as novel interaction partners of synaptopodin, and demonstrate that myosin V is important for the formation and/or maintenance of the SA. We found no evidence of active microtubule-based transport of synaptopodin. Instead, new clusters emerge inside spines, which we interpret as the SA being assembled on-site., Summary: The spine apparatus is assembled locally in dendrites. This process, which relies on the presence of synaptopodin and F-actin, is disrupted by interfering with myosin V activity.
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- 2019
33. HSF2BP Interacts with a Conserved Domain of BRCA2 and Is Required for Mouse Spermatogenesis
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Nicole van Vliet, Hanny Odijk, Roland Kanaar, Alex N. Zelensky, Willy M. Baarends, Koichi Sato, Dik C. van Gent, Claire Wyman, Esther Sleddens, Jeroen Demmers, Inger Brandsma, Sari E. van Rossum-Fikkert, Joyce H.G. Lebbink, Puck Knipscheer, Nathalie van den Tempel, Jeroen Essers, Dick H. W. Dekkers, Alex Maas, Marcel Reuter, Karel Bezstarosti, Molecular Genetics, Biochemistry, Neurosurgery, Radiotherapy, Developmental Biology, and Hubrecht Institute for Developmental Biology and Stem Cell Research
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0301 basic medicine ,DNA repair ,Protein domain ,Mutation, Missense ,Biology ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,chemistry.chemical_compound ,Mice ,0302 clinical medicine ,Meiosis ,Protein Domains ,Cell Line, Tumor ,Animals ,Humans ,skin and connective tissue diseases ,Spermatogenesis ,lcsh:QH301-705.5 ,Gene ,Heat-Shock Proteins ,BRCA2 Protein ,DNA-binding domain ,Cell biology ,030104 developmental biology ,lcsh:Biology (General) ,chemistry ,Armadillo repeats ,Homologous recombination ,Carrier Proteins ,030217 neurology & neurosurgery ,DNA - Abstract
Summary: The tumor suppressor BRCA2 is essential for homologous recombination (HR), replication fork stability, and DNA interstrand crosslink repair in vertebrates. We identify HSF2BP, a protein previously described as testis specific and not characterized functionally, as an interactor of BRCA2 in mouse embryonic stem cells, where the 2 proteins form a constitutive complex. HSF2BP is transcribed in all cultured human cancer cell lines tested and elevated in some tumor samples. Inactivation of the mouse Hsf2bp gene results in male infertility due to a severe HR defect during spermatogenesis. The BRCA2-HSF2BP interaction is highly evolutionarily conserved and maps to armadillo repeats in HSF2BP and a 68-amino acid region between the BRC repeats and the DNA binding domain of human BRCA2 (Gly2270-Thr2337) encoded by exons 12 and 13. This region of BRCA2 does not harbor known cancer-associated missense mutations and may be involved in the reproductive rather than the tumor-suppressing function of BRCA2. : BRCA2 is a key homologous recombination mediator in vertebrates. Brandsma et al. show that it directly interacts with a testis-expressed protein, HSF2BP, and that male mice deficient for HSF2BP are infertile due to a meiotic recombination defect. They also find that HSF2BP contributes to DNA repair in mouse embryonic stem cells. Keywords: HSF2BP, BRCA2, homologous recombination, meiosis, spermatogenesis
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- 2019
34. HSF2BP Interacts with a Conserved Domain of BRCA2 and Is Required for Mouse Spermatogenesis
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Brandsma, Inger, Sato, Koichi, van Rossum-Fikkert, Sari E, van Vliet, Nicole, Sleddens, Esther, Reuter, Marcel, Odijk, Hanny, van den Tempel, Nathalie, Dekkers, Dick H W, Bezstarosti, Karel, Demmers, Jeroen A A, Maas, Alex, Lebbink, Joyce, Wyman, Claire, Essers, Jeroen, van Gent, Dik C, Baarends, Willy M, Knipscheer, Puck, Kanaar, Roland, Zelensky, Alex N, Brandsma, Inger, Sato, Koichi, van Rossum-Fikkert, Sari E, van Vliet, Nicole, Sleddens, Esther, Reuter, Marcel, Odijk, Hanny, van den Tempel, Nathalie, Dekkers, Dick H W, Bezstarosti, Karel, Demmers, Jeroen A A, Maas, Alex, Lebbink, Joyce, Wyman, Claire, Essers, Jeroen, van Gent, Dik C, Baarends, Willy M, Knipscheer, Puck, Kanaar, Roland, and Zelensky, Alex N
- Abstract
The tumor suppressor BRCA2 is essential for homologous recombination (HR), replication fork stability, and DNA interstrand crosslink repair in vertebrates. We identify HSF2BP, a protein previously described as testis specific and not characterized functionally, as an interactor of BRCA2 in mouse embryonic stem cells, where the 2 proteins form a constitutive complex. HSF2BP is transcribed in all cultured human cancer cell lines tested and elevated in some tumor samples. Inactivation of the mouse Hsf2bp gene results in male infertility due to a severe HR defect during spermatogenesis. The BRCA2-HSF2BP interaction is highly evolutionarily conserved and maps to armadillo repeats in HSF2BP and a 68-amino acid region between the BRC repeats and the DNA binding domain of human BRCA2 (Gly2270-Thr2337) encoded by exons 12 and 13. This region of BRCA2 does not harbor known cancer-associated missense mutations and may be involved in the reproductive rather than the tumor-suppressing function of BRCA2.
- Published
- 2019
35. In vivo analysis reveals that ATP- hydrolysis couples remodeling to SWI/ SNF release from chromatin.
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Tilly, Ben C., Chalkley, Gillian E., van der Knaap, Jan A., Moshkin, Yuri M., Tsung Wai Kan, Dekkers, Dick H. W., Demmers, Jeroen A. A., and Verrijzer, C. Peter
- Published
- 2021
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36. Elevated Plasma Cardiac Troponin T Levels Caused by Skeletal Muscle Damage in Pompe Disease
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Michelle Michels, Gerben J. Schaaf, Ans T. van der Ploeg, Ron H.N. van Schaik, Esther Brusse, Tom J.M. van Gestel, Stijn L. M. in ‘t Groen, Jeroen Demmers, Lex B. Verdijk, Joon M. Pijnenburg, W.W.M. Pim Pijnappel, Dick H. W. Dekkers, Stephan C.A. Wens, Michelle E. Kruijshaar, Pieter A. van Doorn, RS: NUTRIM - HB/BW section A, RS: NUTRIM - R3 - Chronic inflammatory disease and wasting, Nutrition and Movement Sciences, Neurology, Cell biology, Pediatrics, Cardiology, Clinical Genetics, Biochemistry, and Clinical Chemistry
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Male ,INVOLVEMENT ,MULTICENTER ,CHILDREN ,030204 cardiovascular system & hematology ,RECOMMENDATIONS ,Electrocardiography ,0302 clinical medicine ,Troponin complex ,Troponin I ,Glycogen storage disease type II ,Medicine ,echocardiography ,Myocardial infarction ,Child ,Genetics (clinical) ,mass spectrometry ,troponin T ,Troponin T ,medicine.diagnostic_test ,biology ,Glycogen Storage Disease Type II ,Middle Aged ,medicine.anatomical_structure ,myocardial infarction ,Child, Preschool ,Cardiology ,Female ,Cardiology and Cardiovascular Medicine ,MESSENGER-RNA ,Adult ,EXPRESSION ,medicine.medical_specialty ,Adolescent ,Heart Ventricles ,99TH PERCENTILE ,03 medical and health sciences ,Internal medicine ,Genetics ,Humans ,Muscle, Skeletal ,HEALTHY ,CREATINE-KINASE-MB ,business.industry ,creatine kinase ,Infant ,Skeletal muscle ,ADULTS ,medicine.disease ,Gene Expression Regulation ,biology.protein ,Creatine kinase ,business ,030217 neurology & neurosurgery - Abstract
Background— Elevated plasma cardiac troponin T (cTnT) levels in patients with neuromuscular disorders may erroneously lead to the diagnosis of acute myocardial infarction or myocardial injury. Methods and Results— In 122 patients with Pompe disease, the relationship between cTnT, cardiac troponin I, creatine kinase (CK), CK-myocardial band levels, and skeletal muscle damage was assessed. ECG and echocardiography were used to evaluate possible cardiac disease. Patients were divided into classic infantile, childhood-onset, and adult-onset patients. cTnT levels were elevated in 82% of patients (median 27 ng/L, normal values P Conclusions— Elevated plasma cTnT levels in patients with Pompe disease are associated with skeletal muscle damage, rather than acute myocardial injury. Increased cTnT levels in Pompe disease and likely other neuromuscular disorders should be interpreted with caution to avoid unnecessary cardiac interventions.
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- 2016
37. HSF2BP Negatively Regulates Homologous Recombination in DNA Interstrand Crosslink Repair in Human Cells by Direct Interaction With BRCA2
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Claire Wyman, Nathalie van den Tempel, Puck Knipscheer, Koichi Sato, Alex N. Zelensky, Marcel Reuter, Inger Brandsma, Hanny Odijk, Dick H. W. Dekkers, Karel Bezstarosti, Roland Kanaar, Josephine C. Dorsman, Dik C. van Gent, Anneke B. Oostra, Sari E. van Rossum-Fikkert, Joyce H.G. Lebbink, Jeroen Demmers, and Nicole S. Verkaik
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Genome instability ,Cisplatin ,0303 health sciences ,Chemistry ,Poly ADP ribose polymerase ,RAD51 ,3. Good health ,Cell biology ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Cell culture ,030220 oncology & carcinogenesis ,medicine ,Ectopic expression ,Homologous recombination ,DNA ,030304 developmental biology ,medicine.drug - Abstract
SummaryThe tumor suppressor BRCA2 is essential for homologous recombination, replication fork stability and DNA interstrand crosslink (ICL) repair in vertebrates. We show that a functionally uncharacterized protein, HSF2BP, is involved in a novel, direct and highly evolutionarily conserved interaction with BRCA2. Although HSF2BP was previously described as testis-specific, we find it is expressed in mouse ES cells, in human cancer cell lines, and in tumor samples. Elevated levels of HSF2BP sensitize human cells to ICL-inducing agents (mitomycin C and cisplatin) and PARP inhibitors, resulting in a phenotype characteristic of cells from Fanconi anemia (FA) patients. We biochemically recapitulate the suppression of ICL repair and establish that excess HSF2BP specifically compromises homologous recombination by preventing BRCA2 and RAD51 loading at the ICL. As increased ectopic expression of HSF2BP occurs naturally, we suggest that it can be considered as a causative agent in FA and a source of cancer-promoting genomic instability.
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- 2018
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38. Mediator complex interaction partners organize the transcriptional network that defines neural stem cells
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Raymond A. Poot, Mike R. Dekker, Johannes H. Brandsma, Wilfred F. J. van IJcken, Debbie L. C. van den Berg, Dick H. W. Dekkers, Maarten Fornerod, Jeroen Demmers, Zeliha Ozgur, Lize Meert, Marti Quevedo, Cell biology, and Biochemistry
- Subjects
0301 basic medicine ,Jumonji Domain-Containing Histone Demethylases ,Protein-Arginine N-Methyltransferases ,Transcription, Genetic ,General Physics and Astronomy ,02 engineering and technology ,Biochemistry ,Histones ,Transcription Factor 4 ,Protein Interaction Mapping ,Gene Regulatory Networks ,Protein Interaction Maps ,lcsh:Science ,Promoter Regions, Genetic ,reproductive and urinary physiology ,Regulation of gene expression ,Multidisciplinary ,Mediator Complex ,Chemistry ,Gene Expression Regulation, Developmental ,TCF4 ,021001 nanoscience & nanotechnology ,Publisher Correction ,Chromatin ,Cell biology ,Enhancer Elements, Genetic ,biological phenomena, cell phenomena, and immunity ,0210 nano-technology ,Transcription ,Science ,Neurogenesis ,Chromatin structure ,General Biochemistry, Genetics and Molecular Biology ,Article ,Cell Line ,03 medical and health sciences ,Mediator ,Humans ,Enhancer ,Transcription factor ,Neural stem cells ,Promoter ,Oxidoreductases, N-Demethylating ,General Chemistry ,nervous system diseases ,Gene regulation ,030104 developmental biology ,nervous system ,lcsh:Q ,Transcription Factor Gene - 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., The Mediator complex regulates transcription by connecting enhancers to promoters. Here, the authors purify Mediator from neural stem cells (NSCs), identify 75 novel protein-protein interaction partners and characterize the Mediator-interacting network that regulates transcription and establishes NSC identity.
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- 2018
39. Proteomic analysis of FOXP proteins reveals interactions between cortical transcription factors associated with neurodevelopmental disorders
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Marti Quevedo, Raymond A. Poot, Simon E. Fisher, Sara Busquets Estruch, Pelagia Deriziotis, Elliot Sollis, Dick H. W. Dekkers, Arianna Vino, Jeroen Demmers, Sarah A. Graham, Cell biology, and Biochemistry
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0301 basic medicine ,Neuroinformatics ,Biology ,Interactome ,03 medical and health sciences ,Purkinje Cells ,0302 clinical medicine ,Gene expression ,Genetics ,Humans ,Transcription factor ,Molecular Biology ,Genetics (clinical) ,Regulation of gene expression ,YY1 ,FOXP2 ,Forkhead Transcription Factors ,FOXP1 ,SATB1 ,General Medicine ,Cell biology ,Repressor Proteins ,030104 developmental biology ,HEK293 Cells ,Gene Expression Regulation ,Neurodevelopmental Disorders ,030217 neurology & neurosurgery ,Transcription Factors - 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.
- Published
- 2018
40. Improvement of ubiquitylation site detection by Orbitrap mass spectrometry
- Author
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Ype Elgersma, Lennart van der Wal, Jeroen Demmers, Erikjan Rijkers, Karel Bezstarosti, Edwin Mientjes, Dick H. W. Dekkers, Karen A. Sap, Biochemistry, Neurosciences, Cell Biology and Histology, and AGEM - Amsterdam Gastroenterology Endocrinology Metabolism
- Subjects
0301 basic medicine ,Proteomics ,Biophysics ,Peptide ,Orbitrap ,Mass spectrometry ,Biochemistry ,Mass Spectrometry ,law.invention ,03 medical and health sciences ,0302 clinical medicine ,Ubiquitin ,Clinical Protocols ,In vivo ,law ,Stable isotope labeling by amino acids in cell culture ,Methods ,Humans ,chemistry.chemical_classification ,Chromatography ,Binding Sites ,biology ,Glycylglycine ,Ubiquitination ,A-site ,030104 developmental biology ,chemistry ,Cell culture ,030220 oncology & carcinogenesis ,biology.protein ,Protein Processing, Post-Translational ,HeLa Cells - Abstract
Ubiquitylation is an important posttranslational protein modification that is involved in many cellular events. Immunopurification of peptides containing a K-e-diglycine (diGly) remnant as a mark of ubiquitylation combined with mass spectrometric detection has resulted in an explosion of the number of identified ubiquitylation sites. Here, we present several significant improvements to this workflow, including fast, offline and crude high pH reverse-phase fractionation of tryptic peptides into only three fractions with simultaneous desalting prior to immunopurification and better control of the peptide fragmentation settings in the Orbitrap HCD cell. In addition, more efficient sample cleanup using a filter plug to retain the antibody beads results in a higher specificity for diGly peptides and less non-specific binding. These relatively simple modifications of the protocol result in the routine detection of over 23,000 diGly peptides from HeLa cells upon proteasome inhibition. The efficacy of this strategy is shown for lysates of both non-labeled and SILAC labeled cell lines. Furthermore, we demonstrate that this strategy is useful for the in-depth analysis of the endogenous, unstimulated ubiquitinome of in vivo samples such as mouse brain tissue. This study presents a valuable addition to the toolbox for ubiquitylation site analysis to uncover the deep ubiquitinome. Significance A K-e-diglycine (diGly) mark on peptides after tryptic digestion of proteins indicates a site of ubiquitylation, a posttranslational modification involved in a wide range of cellular processes. Here, we report several improvements to methods for the isolation and detection of diGly peptides from complex biological mixtures such as cell lysates and brain tissue. This adapted method is robust, reproducible and outperforms previously published methods in terms of number of modified peptide identifications from a single sample. In-depth analysis of the ubiquitinome using mass spectrometry will lead to a better understanding of the roles of protein ubiquitylation in cellular events.
- Published
- 2018
41. Heterogeneous clinical phenotypes and cerebral malformations reflected by rotatin cellular dynamics
- Author
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Vandervore, Laura V, primary, Schot, Rachel, additional, Kasteleijn, Esmee, additional, Oegema, Renske, additional, Stouffs, Katrien, additional, Gheldof, Alexander, additional, Grochowska, Martyna M, additional, van der Sterre, Marianne L T, additional, van Unen, Leontine M A, additional, Wilke, Martina, additional, Elfferich, Peter, additional, van der Spek, Peter J, additional, Heijsman, Daphne, additional, Grandone, Anna, additional, Demmers, Jeroen A A, additional, Dekkers, Dick H W, additional, Slotman, Johan A, additional, Kremers, Gert-Jan, additional, Schaaf, Gerben J, additional, Masius, Roy G, additional, van Essen, Anton J, additional, Rump, Patrick, additional, van Haeringen, Arie, additional, Peeters, Els, additional, Altunoglu, Umut, additional, Kalayci, Tugba, additional, Poot, Raymond A, additional, Dobyns, William B, additional, Bahi-Buisson, Nadia, additional, Verheijen, Frans W, additional, Jansen, Anna C, additional, and Mancini, Grazia M S, additional
- Published
- 2019
- Full Text
- View/download PDF
42. Myosin V regulates synaptopodin clustering and localization in dendrites of hippocampal neurons
- Author
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Konietzny, Anja, primary, González-Gallego, Judit, additional, Bär, Julia, additional, Perez-Alvarez, Alberto, additional, Drakew, Alexander, additional, Demmers, Jeroen A. A., additional, Dekkers, Dick H. W., additional, Hammer, John A., additional, Frotscher, Michael, additional, Oertner, Thomas G., additional, Wagner, Wolfgang, additional, Kneussel, Matthias, additional, and Mikhaylova, Marina, additional
- Published
- 2019
- Full Text
- View/download PDF
43. Proteomic analysis of FOXP proteins reveals interactions between cortical transcription factors associated with neurodevelopmental disorders
- Author
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Estruch, S.B., Graham, S.A., Quevedo, Marti, Vino, A., Dekkers, Dick H. W., Deriziotis, P., Sollis, Elliot, Poot, R.A., Fisher, Simon E., Estruch, S.B., Graham, S.A., Quevedo, Marti, Vino, A., Dekkers, Dick H. W., Deriziotis, P., Sollis, Elliot, Poot, R.A., and Fisher, Simon E.
- Abstract
Contains fulltext : 198204.pdf (Publisher’s version ) (Closed access)
- Published
- 2018
44. Semi-quantitative proteomics of mammalian cells upon short-term exposure to nonionizing electromagnetic fields
- Author
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Arnold Kuzniar, Jeroen Demmers, Henri Woelders, Charlie Laffeber, Joyce H.G. Lebbink, Karel Bezstarosti, Dick H. W. Dekkers, Berina Eppink, Roland Kanaar, A.P.M. Zwamborn, Molecular Genetics, Biochemistry, and Radiotherapy
- Subjects
Proteomics ,0301 basic medicine ,ED - Electronic Defence ,Proteome ,Proteomes ,lcsh:Medicine ,Bioinformatics ,Biochemistry ,Mass Spectrometry ,Analytical Chemistry ,Histones ,Mice ,Database and Informatics Methods ,Spectrum Analysis Techniques ,Stable isotope labeling by amino acids in cell culture ,lcsh:Science ,Liquid Chromatography ,TS - Technical Sciences ,Spectrometric Identification of Proteins ,Multidisciplinary ,Proteomic Databases ,Physics ,Stable Isotope Labeling by Amino Acids in Cell Culture ,Chromatographic Techniques ,Observation, Weapon & Protection Systems ,Cell biology ,Nucleic acids ,Chemistry ,Physical Sciences ,Wireless Technology ,Research Article ,Animal Breeding & Genomics ,animal structures ,Liquid Chromatography-Mass Spectrometry ,Defence Research ,DNA repair ,Defence, Safety and Security ,Biology ,Research and Analysis Methods ,Cell Line ,03 medical and health sciences ,Electromagnetic Fields ,Electromagnetism ,DNA-binding proteins ,Genetics ,Animals ,Humans ,Life Science ,Extremely low frequency ,Fokkerij & Genomica ,lcsh:R ,Biology and Life Sciences ,Proteins ,DNA ,Embryonic stem cell ,Non-ionizing radiation ,In vitro ,Biological Databases ,030104 developmental biology ,Cell culture ,Protein Biosynthesis ,WIAS ,lcsh:Q ,Transcriptome ,Peptides ,Cell Phone - Abstract
The potential effects of non-ionizing electromagnetic fields (EMFs), such as those emitted by power-lines (in extremely low frequency range), mobile cellular systems and wireless networking devices (in radio frequency range) on human health have been intensively researched and debated. However, how exposure to these EMFs may lead to biological changes underlying possible health effects is still unclear. To reveal EMF-induced molecular changes, unbiased experiments (without a priori focusing on specific biological processes) with sensitive readouts are required. We present the first proteome-wide semi-quantitative mass spectrometry analysis of human fibroblasts, osteosarcomas and mouse embryonic stem cells exposed to three types of non-ionizing EMFs (ELF 50 Hz, UMTS 2.1 GHz and WiFi 5.8 GHz). We performed controlled in vitro EMF exposures of metabolically labeled mammalian cells followed by reliable statistical analyses of differential protein- and pathway-level regulations using an array of established bioinformatics methods. Our results indicate that less than 1% of the quantitated human or mouse proteome responds to the EMFs by small changes in protein abundance. Further network-based analysis of the differentially regulated proteins did not detect significantly perturbed cellular processes or pathways in human and mouse cells in response to ELF, UMTS or WiFi exposure. In conclusion, our extensive bioinformatics analyses of semi-quantitative mass spectrometry data do not support the notion that the short-time exposures to non-ionizing EMFs have a consistent biologically significant bearing on mammalian cells in culture.
- Published
- 2017
45. Nucleotide Biosynthetic Enzyme GMP Synthase Is a TRIM21-Controlled Relay of p53 Stabilization
- Author
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B. A. Ashok Reddy, Jan A. van der Knaap, Adone Mohd-Sarip, Dick H. W. Dekkers, Jeroen Demmers, C. Peter Verrijzer, Alice G. M. Bot, Mieke Timmermans, John W.M. Martens, Biochemistry, and Medical Oncology
- Subjects
biology ,ATP synthase ,HEK 293 cells ,Guanosine ,Cell Biology ,Ubiquitin ligase ,chemistry.chemical_compound ,chemistry ,Biochemistry ,Ubiquitin ,Cytoplasm ,GMP synthase ,biology.protein ,Mdm2 ,Molecular Biology - Abstract
Nucleotide biosynthesis is fundamental to normal cell proliferation as well as to oncogenesis. Tumor suppressor p53, which prevents aberrant cell proliferation, is destabilized through ubiquitylation by MDM2. Ubiquitin-specific protease 7 (USP7) plays a dualistic role in p53 regulation and has been proposed to deubiquitylate either p53 or MDM2. Here, we show that guanosine 5'-monophosphate synthase (GMPS) is required for USP7-mediated stabilization of p53. Normally, most GMPS is sequestered in the cytoplasm, separated from nuclear USP7 and p53. In response to genotoxic stress or nucleotide deprivation, GMPS becomes nuclear and facilitates p53 stabilization by promoting its transfer from MDM2 to a GMPS-USP7 deubiquitylation complex. Intriguingly, cytoplasmic sequestration of GMPS requires ubiquitylation by TRIM21, a ubiquitin ligase associated with autoimmune disease. These results implicate a classic nucleotide biosynthetic enzyme and a ubiquitin ligase, better known for its role in autoimmune disease, in p53 control.
- Published
- 2014
46. Publisher Correction: Mediator complex interaction partners organize the transcriptional network that defines neural stem cells
- Author
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Johannes H. Brandsma, Raymond A. Poot, Lize Meert, Zeliha Ozgur, Debbie L. C. van den Berg, Dick H. W. Dekkers, Wilfred F. J. van IJcken, Marti Quevedo, Maarten Fornerod, Mike R. Dekker, and Jeroen Demmers
- Subjects
0301 basic medicine ,Multidisciplinary ,Computer science ,Published Erratum ,Science ,General Physics and Astronomy ,02 engineering and technology ,General Chemistry ,Link (geometry) ,021001 nanoscience & nanotechnology ,General Biochemistry, Genetics and Molecular Biology ,Neural stem cell ,03 medical and health sciences ,030104 developmental biology ,Mediator ,lcsh:Q ,0210 nano-technology ,lcsh:Science ,Neuroscience - Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
- Published
- 2019
47. Erratum to: Proteomic analysis of FOXP proteins reveals interactions between cortical transcription factors associated with neurodevelopmental disorders
- Author
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Estruch, Sara B, primary, Graham, Sarah A, additional, Quevedo, Martí, additional, Vino, Arianna, additional, Dekkers, Dick H W, additional, Deriziotis, Pelagia, additional, Sollis, Elliot, additional, Demmers, Jeroen, additional, Poot, Raymond A, additional, and Fisher, Simon E, additional
- Published
- 2018
- Full Text
- View/download PDF
48. Proteomic analysis of FOXP proteins reveals interactions between cortical transcription factors associated with neurodevelopmental disorders
- Author
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Estruch, Sara B, primary, Graham, Sarah A, additional, Quevedo, Martí, additional, Vino, Arianna, additional, Dekkers, Dick H W, additional, Deriziotis, Pelagia, additional, Sollis, Elliot, additional, Demmers, Jeroen, additional, Poot, Raymond A, additional, and Fisher, Simon E, additional
- Published
- 2018
- Full Text
- View/download PDF
49. Isolation of Functional Tubulin Dimers and of Tubulin- Associated Proteins from Mammalian Cells
- Author
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Kris Leslie, Dick H. W. Dekkers, Luca Signorile, Niels Galjart, Joyce H.G. Lebbink, Nuo Yu, Sophie Ottema, Sreya Basu, Jeroen Demmers, Ihor Smal, Cell biology, Molecular Genetics, Radiotherapy, Radiology & Nuclear Medicine, and Biochemistry
- Subjects
0301 basic medicine ,macromolecular substances ,Biology ,General Biochemistry, Genetics and Molecular Biology ,Mass Spectrometry ,Tubulin binding ,03 medical and health sciences ,Mice ,0302 clinical medicine ,Microtubule ,Tubulin ,Ciliogenesis ,Cell Line, Tumor ,Cell polarity ,Animals ,Humans ,Cytoskeleton ,Mitosis ,Genetics ,HEK 293 cells ,Epithelial Cells ,Cell biology ,030104 developmental biology ,HEK293 Cells ,biology.protein ,General Agricultural and Biological Sciences ,Microtubule-Associated Proteins ,030217 neurology & neurosurgery - Abstract
The microtubule (MT) cytoskeleton forms a dynamic filamentous network that is essential for many processes, including mitosis, cell polarity and shape, neurite outgrowth and migration, and ciliogenesis [1, 2]. MTs are built up of a/beta-tubulin heterodimers, and their dynamic behavior is in part regulated by tubulin-associated proteins (TAPs). Here we describe a novel system to study mammalian tubulins and TAPs. We co-expressed equimolar amounts of triple-tagged a-tubulin and beta-tubulin using a 2A ``self-cleaving'' peptide and isolated functional fluorescent tubulin dimers from transfected HEK293T cells with a rapid two-step approach. We also produced two mutant tubulins that cause brain malformations in tubulinopathy patients [3]. We then applied a paired mass-spectrometry-based method to identify tubulin-binding proteins in HEK293T cells and describe both novel and known TAPs. We find that CKAP5 and the CLASPs, which are MT plus-end-tracking proteins with TOG(L)-domains [4], bind tubulin efficiently, as does the Golgi-associated protein GCC185, which interacts with the CLASPs [5]. The N-terminal TOGL domain of CLASP1 contributes to tubulin binding and allows CLASP1 to function as an autonomous MT-growthpromoting factor. Interestingly, mutant tubulins bind less well to a number of TAPs, including CLASPs and GCC185, and incorporate less efficiently into cellular MTs. Moreover, expression of these mutants in cells impairs several MT-growth-related processes involving TAPs. Thus, stable tubulin-TAP interactions regulate MT nucleation and growth in cells. Combined, our results provide a resource for investigating tubulin interactions and functions and widen the spectrum of tubulin-related disease mechanisms.
- Published
- 2016
50. Remodelers Organize Cellular Chromatin by Counteracting Intrinsic Histone-DNA Sequence Preferences in a Class-Specific Manner
- Author
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B. A. Ashok Reddy, Andrew Travers, Dick H. W. Dekkers, Yuri M. Moshkin, Wilfred F. J. van IJcken, Zeliha Ozgur, Tsung Wai Kan, Gillian E. Chalkley, C. Peter Verrijzer, Jeroen Demmers, Biochemistry, and Cell biology
- Subjects
Nucleosome organization ,Histones ,chemistry.chemical_compound ,Transcription (biology) ,Nucleosome ,Animals ,Drosophila Proteins ,Molecular Biology ,Transcription factor ,Genetics ,Adenosine Triphosphatases ,Binding Sites ,Genome ,biology ,Cell Biology ,Articles ,DNA ,Chromatin Assembly and Disassembly ,Chromatin ,Cell biology ,Nucleosomes ,Histone ,Drosophila melanogaster ,chemistry ,Chromatosome ,biology.protein ,Mi-2 Nucleosome Remodeling and Deacetylase Complex ,Transcription Factors - Abstract
The nucleosome is the fundamental repeating unit of eukaryotic chromatin. Here, we assessed the interplay between DNA sequence and ATP-dependent chromatin-remodeling factors (remodelers) in the nucleosomal organization of a eukaryotic genome. We compared the genome-wide distribution of Drosophila NURD, (P)BAP, INO80, and ISWI, representing the four major remodeler families. Each remodeler has a unique set of genomic targets and generates distinct chromatin signatures. Remodeler loci have characteristic DNA sequence features, predicted to influence nucleosome formation. Strikingly, remodelers counteract DNA sequence-driven nucleosome distribution in two distinct ways. NURD, (P)BAP, and INO80 increase histone density at their target sequences, which intrinsically disfavor positioned nucleosome formation. In contrast, ISWI promotes open chromatin at sites that are propitious for precise nucleosome placement. Remodelers influence nucleosome organization genome-wide, reflecting their high genomic density and the propagation of nucleosome redistribution beyond remodeler binding sites. In transcriptionally silent early embryos, nucleosome organization correlates with intrinsic histone-DNA sequence preferences. Following differential expression of the genome, however, this relationship diminishes and eventually disappears. We conclude that the cellular nucleosome landscape is the result of the balance between DNA sequence-driven nucleosome placement and active nucleosome repositioning by remodelers and the transcription machinery.
- Published
- 2012
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