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: Identification of interactors of Arabidopsis VIN3 wildtype and VIN3 chimeric mutant protein in vernalized seedlings

ABSTRACT: The Arabidopsis VEL proteins VIN3 and VRN5 are accessory proteins of the Polycomb Repressive Complex 2 (PRC2). Their function is most well-understood in the epigenetic PRC2-mediated silencing of the floral repressor gene Flowering Locus C (FLC) during prolonged cold (vernalization). To identify protein interactors of VIN3 and VIN3 chimeric mutant protein carrying VRN5VEL instead of VIN3VEL, we used stable Arabidopsis transgenic lines expressing VIN3-GFP WT and VIN3-GFP VRN5VEL under endogenous promoters to perform native co-immunoprecipitation assays in seedlings vernalized for six weeks at 5 °C. Non-transgenic Col-FRI was used as a negative control.

INSTRUMENT(S):

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

TISSUE(S): Seedling

SUBMITTER: Gerhard Saalbach

LAB HEAD: Caroline Dean

PROVIDER: PXD064199 | Pride | 2025-08-28

REPOSITORIES: Pride

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			Action	DRS
	250318_01.mzML	Mzml
	250318_01.mzid	Mzid
	250318_01.raw	Raw
	250318_02.raw	Raw
	250318_03.raw	Raw

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Publications

VEL-dependent polymerization maintains the chromatin association of Polycomb proteins for the switch to epigenetic silencing.

Schulten Anna A Jang Geng-Jen GJ Payne-Dwyer Alex A Fiedler Marc M Nielsen Mathias L ML Mateo-Bonmatí Eduardo E Bienz Mariann M Leake Mark C MC Dean Caroline C

Molecular cell 20250825 17

Multivalent protein-chromatin interactions facilitated by higher-order protein assemblies are emerging as a crucial theme in eukaryotic gene regulation. However, understanding the underlying mechanisms in their functional context remains challenging. Arabidopsis VEL proteins assemble biomolecular condensates by head-to-tail polymerization. Here, we dissect the role of VEL polymerization domains in conferring the epigenetic switch to Polycomb repressive complex 2 (PRC2) silencing at Arabidopsis F ...[more]

PMID: 40858112

Similar Datasets

Identification of interactors of Arabidopsis VIN3 and VRN5 proteins in vernalized seedlings

Project description:The Arabidopsis VEL proteins VIN3 and VRN5 are accessory proteins of the Polycomb Repressive Complex 2 (PRC2). Their function is most well-understood in the epigenetic PRC2-mediated silencing of the floral repressor gene Flowering Locus C (FLC) during prolonged cold (vernalization). To identify protein interactors of VIN3 and VRN5, also dependent on their C-terminal VEL domains, we used stable Arabidopsis transgenic lines expressing VIN3-GFP WT, VIN3-GFP deltaVEL, VRN5-SYFP2 WT and VRN5-SYFP2 deltaVEL under endogenous promoters to perform native co-immunoprecipitation assays in seedlings vernalized for six weeks at 5 °C. Non-transgenic Col-FRI was used as a negative control.

2025-08-28 | PXD048844 | Pride

VRN1-associated proteins in Arabidopsis thaliana plants during cold exposure

Project description:The epigenetic silencing of the Arabidopsis floral repressor gene FLOWERING LOCUS C (FLC) is induced by a prolonged period of cold and promotes the developmental transition to flowering post-cold. FLC silencing requires the function of VRN1, a non-sequence-specific DNA binding protein. Here, we used Arabidopsis seedlings subjected to cold, carrying a FLAG-tagged VRN1 under its endogenous promoter in the vrn1FRI mutant background. We performed FLAG immunoprecipitation followed by mass spectrometry (IP-MS) on crosslinked tissue. The proteomics analysis revealed several proteins that support the role of VRN1 as a chromatin regulator. The identified proteins associated with VRN1 in vivo also support its contribution to gene silencing.

2025-05-07 | PXD060769 | Pride

VRN1-associated proteins in Arabidopsis thaliana

Project description:The epigenetic silencing of the Arabidopsis floral repressor gene FLOWERING LOCUS C (FLC) is induced by a prolonged period of cold and promotes the developmental transition to flowering post-cold. FLC silencing requires the function of VRN1, a non-sequence-specific DNA binding protein. Here, we used Arabidopsis seedlings growing at ambient temperature carrying a FLAG-tagged VRN1 under its endogenous promoter in the vrn1FRI mutant background. We performed FLAG immunoprecipitation followed by mass spectrometry (IP-MS) on crosslinked tissue. The proteomics analysis revealed several proteins that support the role of VRN1 as a chromatin regulator. The identified proteins associated with VRN1 in vivo also support its contribution to gene silencing.

2025-05-07 | PXD054597 | Pride

The proximity interactome of the peach-potato aphid (Myzus persicae) cathepsin B in Arabidopsis thaliana

Project description:The peach-potato aphid, Myzus persicae, is a globally pervasive crop pest, primarily reproducing clonally, allowing single females to rapidly generate exact copies of themselves. Moreover, its extreme polyphagy enables it to colonize over 400 plant species. Studies on the genetic underpinnings of M. persicae colonization have highlighted the differential expression and transcriptional regulation of a family of cysteine proteases, Cathepsin B (CathB), in response to various plant species. Among all M. persicae CathB proteins, CathB6 is most highly expressed in aphids on A. thaliana and most abundantly detected in M. persicae oral secretions. To investigate the potential plant target of CathB6 in A. thaliana, we conducted TurboID-based proximity labelling and MS (PL-MS).

2024-11-18 | PXD057789 | Pride

Co-immuno precipitation of the aphid saliva protein Mp10 and the plant de-ubiquitinating enzyme AMSH2

Project description:This dataset corresponds to experiments described in the manuscript “The conserved aphid saliva chemosensory protein effector Mp10 targets plant AMSH deubiquitinases at cellular membranes to suppress pattern-triggered immunity”, and includes mass spectrometry analysis of Co-immuno-precipitation experiments of membrane-enriched fractions of Nicotiana benthamiana leaves transiently co-expression the aphid saliva effector protein Mp10 and it’s interacting plant target AMSH2.

2024-11-06 | PXD057543 | Pride

Co-immuno precipitation of the aphid saliva protein Mp10 and the plant de-ubiquitinating enzyme AMSH2

2024-11-06 | PXD055941 | Pride

The PRC2-associated factor C17orf96 is a novel CpG island regulator in mouse ES cells

Project description:CpG islands (CGIs) are key DNA regulatory elements in the vertebrate genome and are often found at gene promoters. In mammalian embryonic stem (ES) cells, CGIs are decorated by either the active or repressive histone marks, H3K4me3 and H3K27me3, respectively, or by both modifications (‘bivalent domains’), but their precise regulation is incompletely understood. Remarkably, we find that the polycomb repressive complex 2 (PRC2)-associated protein C17orf96 (a.k.a. esPRC2p48 and E130012A19Rik) is present at most CGIs in mouse ES cells. At PRC2-rich CGIs, loss of C17orf96 results in an increased chromatin binding of Suz12 and elevated H3K27me3 levels concomitant with gene repression. In contrast, at PRC2-poor CGIs, located at actively transcribed genes, C17orf96 colocalizes with RNA polymerase II and its depletion leads to a focusing of H3K4me3 in the core of CGIs. Our findings thus identify C17orf96 as a novel context-dependent CGI regulator. ChIP-seq of C17orf96, H3K4me3 and H3K27me3 in mouse ES cells (E14).

2015-04-29 | E-GEOD-63491 | biostudies-arrayexpress

Analysis of the methylation state of K510, K514 and K515 of human EZH2 within recombinant PRC2

Project description:Using mass-spectrometry, we are seeking to determine the extent of methylation of EZH2 K510, K514 and K515 in the above mentioned recombinant PRC2 variants, answering the question whether recombinant mutant PRC2 is automethylated to the same or similar extent as the wt PRC2 complex.

2024-09-11 | PXD051876 | Pride

Plasmid manipulation of bacterial behaviour through translational regulatory crosstalk

Project description:pQBR103 is a naturally occurring plasmid known to alter the behaviour of its host, Pseudomonas fluorescens. This plasmid encodes a predicted translational regulator, rsmQ which is a homologue of known global regulators within Pseudomonas. Within this study we compared Pseudomonas fluorescens SBW25 plasmid free cells with cells carrying either WT pQBR103 or pQBR103 lacking rsmQ. Using comparative quantitative proteomics and RNAseq we showed that the loss of rsmQ leads to widespread proteomic changes in the absence of changes in mRNA abundance, suggesting RsmQ is a translational regulator of its host chromosome.

2023-01-13 | PXD033640 | Pride

o Differential temporal release and lipoprotein loading in B. thetaiotaomicron bacterial extracellular vesicles

Project description:o Bacterial extracellular vesicles (BEVs) contribute to stress responses, quorum sensing, biofilm formation, and interspecies and interkingdom communication. However, the factors that regulate their release and heterogeneity are not well understood. We set out to investigate these factors in the common gut commensal Bacteroides thetaiotaomicron by studying BEV release throughout their growth cycle. Utilising a range of methods, we demonstrate that vesicles released at different stages of growth have significantly different composition, with early vesicles enriched in specifically released outer membrane vesicles (OMVs) containing a larger proportion of lipoproteins, while late phase BEVs primarily contain lytic vesicles with enrichment of cytoplasmic proteins. Furthermore, we demonstrate that lipoproteins containing a negatively charged signal peptide are preferentially incorporated in OMVs. We use this observation to predict all Bacteroides thetaiotaomicron OMV enriched lipoproteins and analyse their function. Overall, our findings highlight the need to understand media composition and BEV release dynamics prior to functional characterisation and define the theoretical functional capacity of Bacteroides thetaiotaomicron OMVs.

2024-01-22 | PXD043651 | Pride

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