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Article ; Online: GFI1B and LSD1 repress myeloid traits during megakaryocyte differentiation.

Venhuizen, Jeron / van Bergen, Maaike G J M / Bergevoet, Saskia M / Gilissen, Daan / Spruijt, Cornelia G / Wingens, Laura / van den Akker, Emile / Vermeulen, Michiel / Jansen, Joop H / Martens, Joost H A / van der Reijden, Bert A

Communications biology

2024 Volume 7, Issue 1, Page(s) 374

Abstract: The transcription factor Growth Factor Independence 1B (GFI1B) recruits Lysine Specific Demethylase 1 A (LSD1/KDM1A) to stimulate gene programs relevant for megakaryocyte and platelet biology. Inherited pathogenic GFI1B variants result in ... ...

Abstract	The transcription factor Growth Factor Independence 1B (GFI1B) recruits Lysine Specific Demethylase 1 A (LSD1/KDM1A) to stimulate gene programs relevant for megakaryocyte and platelet biology. Inherited pathogenic GFI1B variants result in thrombocytopenia and bleeding propensities with varying intensity. Whether these affect similar gene programs is unknow. Here we studied transcriptomic effects of four patient-derived GFI1B variants (GFI1B
MeSH term(s)	Humans ; Megakaryocytes/metabolism ; Cell Differentiation/genetics ; Hematopoiesis/genetics ; Histone Demethylases/genetics ; Histone Demethylases/metabolism ; Gene Expression Regulation ; Proto-Oncogene Proteins/genetics ; Proto-Oncogene Proteins/metabolism ; Repressor Proteins/metabolism
Chemical Substances	Histone Demethylases (EC 1.14.11.-) ; GFI1B protein, human ; Proto-Oncogene Proteins ; Repressor Proteins ; KDM1A protein, human (EC 1.5.-)
Language	English
Publishing date	2024-03-28
Publishing country	England
Document type	Journal Article
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-024-06090-z
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Article: Cross‐linking mass spectrometry reveals the structural topology of peripheral NuRD subunits relative to the core complex

Spruijt, Cornelia G / Gräwe, Cathrin / Kleinendorst, Simone C / Baltissen, Marijke P. A / Vermeulen, Michiel

FEBS journal. 2021 May, v. 288, no. 10

2021

Abstract: The multi‐subunit nucleosome remodeling and deacetylase (NuRD) complex consists of seven subunits, each of which comprises two or three paralogs in vertebrates. These paralogs define mutually exclusive and functionally distinct complexes. In addition, ... ...

Abstract	The multi‐subunit nucleosome remodeling and deacetylase (NuRD) complex consists of seven subunits, each of which comprises two or three paralogs in vertebrates. These paralogs define mutually exclusive and functionally distinct complexes. In addition, several proteins in the complex are multimeric, which complicates structural studies. Attempts to purify sufficient amounts of endogenous complex or recombinantly reconstitute the complex for structural studies have proven quite challenging. Until now, only substructures of individual domains or proteins and low‐resolution densities of (partial) complexes have been reported. In this study, we comprehensively investigated the relative orientation of different subunits within the NuRD complex using multiple cross‐link IP mass spectrometry (xIP‐MS) experiments. Our results confirm that the core of the complex is formed by MTA, RBBP, and HDAC proteins. Assembly of a copy of MBD and GATAD2 onto this core enables binding of the peripheral CHD and CDK2AP proteins. Furthermore, our experiments reveal that not only CDK2AP1 but also CDK2AP2 interacts with the NuRD complex. This interaction requires the C terminus of CHD proteins. Our data provide a more detailed understanding of the topology of the peripheral NuRD subunits relative to the core complex. DATABASE: Proteomics data are available in the PRIDE database under the accession numbers PXD017244 and PXD017378.
Keywords	crosslinking ; databases ; mass spectrometry ; nucleosomes ; proteomics ; topology
Language	English
Dates of publication	2021-05
Size	p. 3231-3245.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	NAL-AP-2-clean ; JOURNAL ARTICLE
ZDB-ID	2173655-8
ISSN	1742-4658 ; 1742-464X
ISSN (online)	1742-4658
ISSN	1742-464X
DOI	10.1111/febs.15650
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Article ; Online: Arbovirus-vector protein interactomics identifies Loquacious as a co-factor for dengue virus replication in Aedes mosquitoes.

Besson, Benoit / Lezcano, Oscar M / Overheul, Gijs J / Janssen, Kirsten / Spruijt, Cornelia G / Vermeulen, Michiel / Qu, Jieqiong / van Rij, Ronald P

PLoS pathogens

2022 Volume 18, Issue 9, Page(s) e1010329

Abstract: Efficient virus replication in Aedes vector mosquitoes is essential for the transmission of arboviral diseases such as dengue virus (DENV) in human populations. Like in vertebrates, virus-host protein-protein interactions are essential for viral ... ...

Abstract	Efficient virus replication in Aedes vector mosquitoes is essential for the transmission of arboviral diseases such as dengue virus (DENV) in human populations. Like in vertebrates, virus-host protein-protein interactions are essential for viral replication and immune evasion in the mosquito vector. Here, 79 mosquito host proteins interacting with DENV non-structural proteins NS1 and NS5 were identified by label-free mass spectrometry, followed by a functional screening. We confirmed interactions with host factors previously observed in mammals, such as the oligosaccharyltransferase complex, and we identified protein-protein interactions that seem to be specific for mosquitoes. Among the interactors, the double-stranded RNA (dsRNA) binding protein Loquacious (Loqs), an RNA interference (RNAi) cofactor, was found to be essential for efficient replication of DENV and Zika virus (ZIKV) in mosquito cells. Loqs did not affect viral RNA stability or translation of a DENV replicon and its proviral activity was independent of its RNAi regulatory activity. Interestingly, Loqs colocalized with DENV dsRNA replication intermediates in infected cells and directly interacted with high affinity with DENV RNA in the 3' untranslated region in vitro (KD = 48-62 nM). Our study provides an interactome for DENV NS1 and NS5 and identifies Loqs as a key proviral host factor in mosquitoes. We propose that DENV hijacks a factor of the RNAi mechanism for replication of its own RNA.
MeSH term(s)	3' Untranslated Regions ; Aedes ; Animals ; Arboviruses/genetics ; Dengue ; Dengue Virus/genetics ; Humans ; Mammals ; Mosquito Vectors ; RNA, Double-Stranded/metabolism ; Virus Replication/genetics ; Zika Virus/genetics ; Zika Virus Infection
Chemical Substances	3' Untranslated Regions ; RNA, Double-Stranded
Language	English
Publishing date	2022-09-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2205412-1
ISSN	1553-7374 ; 1553-7374
ISSN (online)	1553-7374
ISSN	1553-7374
DOI	10.1371/journal.ppat.1010329
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Article ; Online: DNA methylation: old dog, new tricks?

Spruijt, Cornelia G / Vermeulen, Michiel

Nature structural & molecular biology

2014 Volume 21, Issue 11, Page(s) 949–954

Abstract: DNA methylation is an epigenetic modification that is generally associated with repression of transcription initiation at CpG-island promoters. Here we argue that, on the basis of recent high-throughput genomic and proteomic screenings, DNA methylation ... ...

Abstract	DNA methylation is an epigenetic modification that is generally associated with repression of transcription initiation at CpG-island promoters. Here we argue that, on the basis of recent high-throughput genomic and proteomic screenings, DNA methylation can also have different outcomes, including activation of transcription. This is evidenced by the fact that transcription factors can interact with methylated DNA sequences. Furthermore, in certain cellular contexts, genes containing methylated promoters are highly transcribed. Interestingly, this uncoupling between methylated DNA and repression of transcription seems to be particularly evident in germ cells and pluripotent cells. Thus, contrary to previous assumptions, DNA methylation is not exclusively associated with repression of transcription initiation.
MeSH term(s)	Animals ; CpG Islands ; DNA Methylation ; Epigenesis, Genetic ; Genome ; Germ Cells/cytology ; Germ Cells/growth & development ; Germ Cells/metabolism ; Humans ; Pluripotent Stem Cells/cytology ; Pluripotent Stem Cells/metabolism ; Promoter Regions, Genetic ; Proteomics ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Transcription, Genetic
Chemical Substances	Transcription Factors
Language	English
Publishing date	2014-11-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2126708-X
ISSN	1545-9985 ; 1545-9993
ISSN (online)	1545-9985
ISSN	1545-9993
DOI	10.1038/nsmb.2910
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Article ; Online: Cross-linking mass spectrometry reveals the structural topology of peripheral NuRD subunits relative to the core complex.

Spruijt, Cornelia G / Gräwe, Cathrin / Kleinendorst, Simone C / Baltissen, Marijke P A / Vermeulen, Michiel

The FEBS journal

2020 Volume 288, Issue 10, Page(s) 3231–3245

Abstract: The multi-subunit nucleosome remodeling and deacetylase (NuRD) complex consists of seven subunits, each of which comprises two or three paralogs in vertebrates. These paralogs define mutually exclusive and functionally distinct complexes. In addition, ... ...

Abstract	The multi-subunit nucleosome remodeling and deacetylase (NuRD) complex consists of seven subunits, each of which comprises two or three paralogs in vertebrates. These paralogs define mutually exclusive and functionally distinct complexes. In addition, several proteins in the complex are multimeric, which complicates structural studies. Attempts to purify sufficient amounts of endogenous complex or recombinantly reconstitute the complex for structural studies have proven quite challenging. Until now, only substructures of individual domains or proteins and low-resolution densities of (partial) complexes have been reported. In this study, we comprehensively investigated the relative orientation of different subunits within the NuRD complex using multiple cross-link IP mass spectrometry (xIP-MS) experiments. Our results confirm that the core of the complex is formed by MTA, RBBP, and HDAC proteins. Assembly of a copy of MBD and GATAD2 onto this core enables binding of the peripheral CHD and CDK2AP proteins. Furthermore, our experiments reveal that not only CDK2AP1 but also CDK2AP2 interacts with the NuRD complex. This interaction requires the C terminus of CHD proteins. Our data provide a more detailed understanding of the topology of the peripheral NuRD subunits relative to the core complex. DATABASE: Proteomics data are available in the PRIDE database under the accession numbers PXD017244 and PXD017378.
MeSH term(s)	Amino Acid Sequence ; Binding Sites ; Cell Line, Tumor ; Cross-Linking Reagents/chemistry ; Cyclin-Dependent Kinases/chemistry ; Cyclin-Dependent Kinases/genetics ; Cyclin-Dependent Kinases/metabolism ; GATA Transcription Factors/chemistry ; GATA Transcription Factors/genetics ; GATA Transcription Factors/metabolism ; HeLa Cells ; Histone Deacetylases/chemistry ; Histone Deacetylases/genetics ; Histone Deacetylases/metabolism ; Humans ; Mass Spectrometry/methods ; Mi-2 Nucleosome Remodeling and Deacetylase Complex/chemistry ; Mi-2 Nucleosome Remodeling and Deacetylase Complex/genetics ; Mi-2 Nucleosome Remodeling and Deacetylase Complex/metabolism ; Models, Molecular ; Nucleosomes/genetics ; Nucleosomes/metabolism ; Nucleosomes/ultrastructure ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Interaction Domains and Motifs ; Protein Interaction Mapping ; Protein Subunits/chemistry ; Protein Subunits/genetics ; Protein Subunits/metabolism ; Recombinant Proteins/chemistry ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid
Chemical Substances	Cross-Linking Reagents ; GATA Transcription Factors ; Nucleosomes ; Protein Subunits ; Recombinant Proteins ; Cyclin-Dependent Kinases (EC 2.7.11.22) ; Histone Deacetylases (EC 3.5.1.98) ; Mi-2 Nucleosome Remodeling and Deacetylase Complex (EC 3.5.1.98)
Language	English
Publishing date	2020-12-14
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2173655-8
ISSN	1742-4658 ; 1742-464X
ISSN (online)	1742-4658
ISSN	1742-464X
DOI	10.1111/febs.15650
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Article ; Online: Galectin-9 interacts with Vamp-3 to regulate cytokine secretion in dendritic cells.

Santalla Méndez, Rui / Rodgers Furones, Andrea / Classens, René / Fedorova, Kristina / Haverdil, Manon / Canela Capdevila, Marta / van Duffelen, Anne / Spruijt, Cornelia G / Vermeulen, Michiel / Ter Beest, Martin / van Spriel, Annemiek B / Querol Cano, Laia

Cellular and molecular life sciences : CMLS

2023 Volume 80, Issue 10, Page(s) 306

Abstract: Intracellular vesicle transport is essential for cellular homeostasis and is partially mediated by SNARE proteins. Endosomal trafficking to the plasma membrane ensures cytokine secretion in dendritic cells (DCs) and the initiation of immune responses. ... ...

Abstract	Intracellular vesicle transport is essential for cellular homeostasis and is partially mediated by SNARE proteins. Endosomal trafficking to the plasma membrane ensures cytokine secretion in dendritic cells (DCs) and the initiation of immune responses. Despite its critical importance, the specific molecular components that regulate DC cytokine secretion are poorly characterised. Galectin-9, a ß-galactoside-binding protein, has emerged as a novel cellular modulator although its exact intracellular roles in regulating (immune) cell homeostasis and vesicle transport are virtually unknown. We investigated galectin-9 function in primary human DCs and report that galectin-9 is essential for intracellular cytokine trafficking to the cell surface. Galectin-9-depleted DCs accumulate cytokine-containing vesicles in the Golgi complex that eventually undergo lysosomal degradation. We observed galectin-9 to molecularly interact with Vamp-3 using immunoprecipitation-mass-spectrometry and identified galectin-9 was required for rerouting Vamp-3-containing endosomes upon DC activation as the underlying mechanism. Overall, this study identifies galectin-9 as a necessary mechanistic component for intracellular trafficking. This may impact our general understanding of vesicle transport and sheds new light into the multiple roles galectins play in governing cell function.
Language	English
Publishing date	2023-09-27
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1358415-7
ISSN	1420-9071 ; 1420-682X
ISSN (online)	1420-9071
ISSN	1420-682X
DOI	10.1007/s00018-023-04954-x
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Article ; Online: Identifying nuclear protein-protein interactions using GFP affinity purification and SILAC-based quantitative mass spectrometry.

Baymaz, H Irem / Spruijt, Cornelia G / Vermeulen, Michiel

Methods in molecular biology (Clifton, N.J.)

2014 Volume 1188, Page(s) 207–226

Abstract: Many cellular proteins assemble into macromolecular protein complexes. Therefore, identifying protein-protein interactions (PPIs) is essential to gain insight into the function of proteins. Recently established quantitative mass spectrometry-based ... ...

Abstract	Many cellular proteins assemble into macromolecular protein complexes. Therefore, identifying protein-protein interactions (PPIs) is essential to gain insight into the function of proteins. Recently established quantitative mass spectrometry-based techniques have significantly improved the unbiased search for PPIs. In this chapter, we describe a single-step GFP affinity purification method combined with SILAC-based quantitative mass spectrometry that can be used to identify nuclear PPIs in mammalian cells.
MeSH term(s)	Amino Acids/chemistry ; Cell Line ; Cell Nucleus/metabolism ; Chromatography, Affinity ; Green Fluorescent Proteins/metabolism ; Isotope Labeling/methods ; Mass Spectrometry/methods ; Nuclear Proteins/chemistry ; Nuclear Proteins/genetics ; Nuclear Proteins/isolation & purification ; Nuclear Proteins/metabolism ; Peptides/isolation & purification ; Peptides/metabolism ; Protein Interaction Mapping/methods ; Proteolysis ; Transfection
Chemical Substances	Amino Acids ; Nuclear Proteins ; Peptides ; Green Fluorescent Proteins (147336-22-9)
Language	English
Publishing date	2014
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-1142-4_15
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Article ; Online: Identifying specific protein-DNA interactions using SILAC-based quantitative proteomics.

Spruijt, Cornelia G / Baymaz, H Irem / Vermeulen, Michiel

Methods in molecular biology (Clifton, N.J.)

2013 Volume 977, Page(s) 137–157

Abstract: A comprehensive identification of protein-DNA interactions that drive processes such as transcription and replication, both in prokaryotic and eukaryotic organisms, remains a major technical challenge. In this chapter, we present a SILAC-based DNA ... ...

Abstract	A comprehensive identification of protein-DNA interactions that drive processes such as transcription and replication, both in prokaryotic and eukaryotic organisms, remains a major technical challenge. In this chapter, we present a SILAC-based DNA affinity purification method that can be used to identify specific interactions between proteins and functional DNA elements in an unbiased manner.
MeSH term(s)	Animals ; Cell Fractionation ; Cell Nucleus/chemistry ; Chromatography, Affinity ; DNA/isolation & purification ; DNA-Binding Proteins/chemistry ; DNA-Binding Proteins/isolation & purification ; Humans ; Isotope Labeling ; Mass Spectrometry ; Protein Binding ; Proteomics ; Sequence Analysis, Protein
Chemical Substances	DNA-Binding Proteins ; DNA (9007-49-2)
Language	English
Publishing date	2013
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-62703-284-1_11
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Article ; Online: SALL4 controls cell fate in response to DNA base composition.

Pantier, Raphaël / Chhatbar, Kashyap / Quante, Timo / Skourti-Stathaki, Konstantina / Cholewa-Waclaw, Justyna / Alston, Grace / Alexander-Howden, Beatrice / Lee, Heng Yang / Cook, Atlanta G / Spruijt, Cornelia G / Vermeulen, Michiel / Selfridge, Jim / Bird, Adrian

Molecular cell

2021 Volume 81, Issue 4, Page(s) 845–858.e8

Abstract: Mammalian genomes contain long domains with distinct average compositions of A/T versus G/C base pairs. In a screen for proteins that might interpret base composition by binding to AT-rich motifs, we identified the stem cell factor SALL4, which contains ... ...

Abstract	Mammalian genomes contain long domains with distinct average compositions of A/T versus G/C base pairs. In a screen for proteins that might interpret base composition by binding to AT-rich motifs, we identified the stem cell factor SALL4, which contains multiple zinc fingers. Mutation of the domain responsible for AT binding drastically reduced SALL4 genome occupancy and prematurely upregulated genes in proportion to their AT content. Inactivation of this single AT-binding zinc-finger cluster mimicked defects seen in Sall4 null cells, including precocious differentiation of embryonic stem cells (ESCs) and embryonic lethality in mice. In contrast, deletion of two other zinc-finger clusters was phenotypically neutral. Our data indicate that loss of pluripotency is triggered by downregulation of SALL4, leading to de-repression of a set of AT-rich genes that promotes neuronal differentiation. We conclude that base composition is not merely a passive byproduct of genome evolution and constitutes a signal that aids control of cell fate.
MeSH term(s)	Animals ; Base Composition ; Cell Differentiation ; Cell Line ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; Down-Regulation ; Mice ; Mice, Mutant Strains ; Mouse Embryonic Stem Cells/cytology ; Mouse Embryonic Stem Cells/metabolism ; Mutation ; Neurons/cytology ; Neurons/metabolism ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Up-Regulation ; Zinc Fingers
Chemical Substances	DNA-Binding Proteins ; Sall4 protein, mouse ; Transcription Factors
Language	English
Publishing date	2021-01-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2020.11.046
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Article: SALL4 controls cell fate in response to DNA base composition

Molecular cell. 2021 Feb. 18, v. 81, no. 4

2021

Abstract	Mammalian genomes contain long domains with distinct average compositions of A/T versus G/C base pairs. In a screen for proteins that might interpret base composition by binding to AT-rich motifs, we identified the stem cell factor SALL4, which contains multiple zinc fingers. Mutation of the domain responsible for AT binding drastically reduced SALL4 genome occupancy and prematurely upregulated genes in proportion to their AT content. Inactivation of this single AT-binding zinc-finger cluster mimicked defects seen in Sall4 null cells, including precocious differentiation of embryonic stem cells (ESCs) and embryonic lethality in mice. In contrast, deletion of two other zinc-finger clusters was phenotypically neutral. Our data indicate that loss of pluripotency is triggered by downregulation of SALL4, leading to de-repression of a set of AT-rich genes that promotes neuronal differentiation. We conclude that base composition is not merely a passive byproduct of genome evolution and constitutes a signal that aids control of cell fate.
Keywords	byproducts ; embryonic mortality ; evolution ; mutation ; neurons ; nucleobases ; stem cell factor ; zinc
Language	English
Dates of publication	2021-0218
Size	p. 845-858.e8.
Publishing place	Elsevier Inc.
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2020.11.046
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