Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

VRN1-associated proteins in Arabidopsis thaliana plants during cold exposure

ABSTRACT: 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.

INSTRUMENT(S): Orbitrap Eclipse

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

TISSUE(S): Seedling

SUBMITTER: Gerhard Saalbach

LAB HEAD: Miguel Montez

PROVIDER: PXD060769 | Pride | 2025-05-07

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	240725_01_20240725204611.raw	Raw
	240725_01_results.msf	Msf
	240725_01_results.mzML	Mzml
	240725_01_results.mzid	Mzid
	240725_02.raw	Raw

Items per page:

1 - 5 of 13

Similar Datasets

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

VAL1 acts as an assembly platform co-ordinating co-transcriptional repression and chromatin 2 regulation at Arabidopsis FLC

Project description:• Polycomb (PcG) regulation is crucial for development across eukaryotes, but how PcG targets are specified is still incompletely understood. The slow timescale of cold-induced Polycomb Repressive Complex 2 silencing during vernalization at Arabidopsis thaliana FLOWERING LOCUS C (FLC) provides an excellent system to elucidate the sequence of events. Association of the DNA binding protein VAL1 to an FLC intronic RY motif within the PcG nucleation region is an important step. VAL1 is associated in vivo with APOPTOSIS AND SPLICING ASSOCIATED PROTEIN (ASAP) complex and Polycomb Repressive Complex 1 (PRC1). Here, we show that ASAP and PRC1 functions are necessary for co-transcriptional repression and chromatin regulation during FLC silencing. ASAP mutants affect FLC transcription in warm conditions, but the rate of FLC silencing in the cold is unaffected. PRC1-mediated H2Aub accumulation increases at the nucleation region upon exposure to cold, but unlike the PRC2-delivered H3K27me3 does not spread across the locus. H2Aub is thus involved in the transition to epigenetic silencing at FLC facilitating H3K27me3 accumulation, which in turn is necessary for long-term epigenetic memory. Overall, our work highlights the importance of the DNA sequence-specific binding protein VAL1 as an assembly platform coordinating the co-transcriptional repression and chromatin regulation necessary for the epigenetic silencing of FLC.

2022-10-13 | PXD036548 | Pride

A CPSF-like phosphatase module links transcription termination to chromatin silencing

Project description:Aiming to find the connection between RNA processing and chromatin remodelling, we found that a complex removing activating histone marks at FLC named FLD complex interacts with ARPF1, one of the homologs in Arabidopsis of the yeast Swd2. In this experiment, we used a FLAG-tagged version of the ARPF1 protein to find its protein partners.

2024-05-13 | PXD049114 | Pride

VAL1 acts as an assembly platform co-ordinating co-transcriptional repression and chromatin regulation at Arabidopsis FLC

Project description:Polycomb (PcG) silencing is crucial for development, but how targets are specified remains incompletely understood. The cold-induced Polycomb Repressive Complex 2 (PRC2) silencing of Arabidopsis thaliana FLOWERING LOCUS C (FLC) provides an excellent system to elucidate PcG regulation. Association of the DNA binding protein VAL1 to the PcG nucleationregion at FLC is an important step. VAL1 interacts with APOPTOSIS AND SPLICING ASSOCIATED PROTEIN (ASAP) complex and PRC1. Here, we show that ASAP and PRC1 are necessary for co-transcriptional repression and chromatin regulation during FLC silencing. ASAP mutants affect FLC transcription in warm conditions, but the rate of FLC silencing in the cold is unaffected. PRC1-mediated H2Aub accumulates at FLC nucleation region during cold, but unlike the PRC2-delivered H3K27me3 does not spread across the locus. H2Aub thus marks the transition to epigenetic silencing, while H3K27me3 is necessary for long-term epigenetic memory. Overall, our work highlights the importance of VAL1 as an assembly platform co-ordinating the co-transcriptional repression and chromatin regulation necessary for the epigenetic silencing of FLC.

2022-08-15 | PXD036057 |

Cold-induced silencing mediated by long antisense FLC transcripts

Project description:Hight throughput techniques have revealed huge complexity in antisense RNAs in many organisms. We have explored the complexity of this class of transcripts and functional links to Polycomb silencing thought analysis of non-coding RNAs of Arabidopsis FLC. FLC is repressed and epigenetically silenced by prolonged cold, enabling plants to undergo the floral transition. Single nucleotide resolution tiling array revealed long non-coding transcripts covering the entire FLC locus. The most abundant of these are capped and polyadenylated, initiate over a 100 nucleotide window just downstream of the sense polyA site, are differentially spliced and terminate either within the sense gene or its promoter. Their levels correlate with FLC sense transcripts in all mutants and conditions tested except cold treatment. The antisense transcripts were strongly but transiently cold-induced, much earlier than other vernalization markers, and this coincided with reduction in sense FLC transcription but not sense FLC mRNA levels. Addition of the FLC antisense 5'/sense 3' region to a GFP transgene was sufficient to confer cold-induced silencing of thet fusion; however this silencing was not epigenetically manteined. These processes were all independent of the function of the Polycomb proteins required for maintenance of FLC silencing. Our data suggest that FLC antisense transcripts induce transient FLC transcriptional silencing, possibly through promoter interference, with the epigenetic silencing requiring subsequent recruitment of Polycomb machinery. Total seedling RNA from different genotypes and different conditions: WT, FRIGIDA, 35s::FCA (giving overexpression of FCA), FRIGIDA + 2 weeks cold, FRIGIDA + 2 weeks cold + 7 days warm.

2009-12-31 | E-GEOD-16977 | biostudies-arrayexpress

Cold-induced silencing mediated by long antisense FLC transcripts

2009-12-31 | GSE16977 | GEO

Nucleosome positioning dynamics during the cold-induced silencing of the Arabidopsis FLC gene using targeted MNase-seq

Project description:Micrococcal nuclease (MNase) has been extensively used to map nucleosomes genome wide. Here, we used a targeted MNase-seq approach to map nucleosomes at high resolution at the FLC locus during the cold-induced silencing. This strategy uncovered that the +1 nucleosome at FLC is repositioned closer to the promoter in response to cold. The nucleosome repositioning alters the chromatin structure locally at the 5’ end of FLC and is linked to the silencing of the gene. Moreover, this is in part modulated by VRN1, a non-sequence-specific DNA binding protein that associates with FLC promoter and is required for its silencing.

2025-05-07 | GSE274066 | GEO

Transcription profiling of Arabidopsis plants of three different genotypes (FRI FLC, FRI flc and fri flc) induced to flowering by shifting from short day conditions to long day conditions

Project description:Plants of three different genotypes (FRI FLC, FRI flc and fri flc) were induced to flowering by shifting from short day conditions to long day conditions. FRI=FRIGIDA, FLC=FLOWERING LOCUS C.

2005-09-08 | E-TABM-19 | biostudies-arrayexpress

Antagonistic activities of co-transcriptional regulators within an early developmental window sets quantitative FLC expression

Project description:Quantitative variation in expression of the Arabidopsis floral repressor FLC influences whether plants overwinter before flowering or have a rapid cycling habit, enabling multiple generations a year. Genetic analysis has identified activators and repressors of FLC expression, but how they interact to set expression level is poorly understood. Here, we show that antagonistic functions of the FLC activator FRIGIDA (FRI), and the repressor FCA, at a specific stage of embryo development, determines FLC expression and flowering. FRI antagonizes an FCA-induced proximal polyadenylation to increase FLC expression and delay flowering. Sector analysis shows that FRI activity during the early heart stage of embryo development maximally delays flowering. Opposing functions of co-transcriptional regulators during an early embryonic developmental window thus set FLC expression levels and determine flowering time.

2021-03-19 | GSE166728 | GEO

Flower development FRI/FLC

Project description:Arabiposis plants with conbinations of different FRIGIDA (FRI) and FLOWERING LOCUS C (FLC) alleles grown in short days (9L:15D) for 30 days at 21°C, then shifted to long days (16L:8D). Genotypes: Columbia wild type (Col-0): fri FLC Columbia with introgressed FRI from Sf-2: FRI FLC Columbia with introgressed FRI and deleted FLC (flc-3): FRI flc Columbia with deleted FLC (flc-3): fri flc Time points: 0, 2, and 4 days after shift to long days Keywords = flowering Keywords: time-course

2003-08-06 | GSE577 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data