Browse
Submit Data
Databases
API
Help

Dataset Information

322 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of potential human PML interacting proteins in Nicotiana benthamiana

ABSTRACT: In spite of the crucial tasks fulfilled by the subnuclear structures known as PML nuclear bodies (PML-NBs) in mammalian cells, the presence of PML-NBs in plant cells could not be shown yet. Interestingly, the key organizer of PML-NBs, human promyelocytic leukemia protein (PML), is not targeted to structures resembling PML-NBs when expressed heterologously in plants, but localizes to interchromosomal areas associated with the nucleolus. In order to identify plant proteins interacting with human PML, a GFP-fusion protein was ectopically expressed in Nicotiana benthamiana using Agrobacterium tumefaciens mediated transformation. The bait protein as well as potential interactors were immunoprecipitated by use of magnetic GFP-Trap beads (Chromotek). Precipitated proteins were analyzed by Nano-LC-MS/MS.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Nicotiana Benthamiana

TISSUE(S): Plant Cell, Leaf

DISEASE(S): Disease Free

SUBMITTER: Christian Lamm

LAB HEAD: Uwe Sonnewald

PROVIDER: PXD004254 | Pride | 2016-10-10

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	1_Empty_Vector_Control_1_1.mzxml	Mzxml
	1_Empty_Vector_Control_1_1.raw	Raw
	2_Empty_Vector_Control_2_1.mzxml	Mzxml
	2_Empty_Vector_Control_2_1.raw	Raw
	3_Empty_Vector_Control_3_1.mzxml	Mzxml

Items per page:

1 - 5 of 19

Similar Datasets

Identifying chromatin associations with promyelocytic leukemia nuclear bodies using immunoTRAP

Project description:Studies using fluorescence in situ hybridization (FISH) have attempted to determine whether specific gene loci associate with promyelocytic leukemia nuclear bodies (PML NBs). Two drawbacks accompany this approach; the lack of spatial resolution inherent with the technique, and the a priori basis for selecting which genes to probe. To overcome these limitations, we developed a technique, which we call immunoTRAP, which purifies the DNA contacting PML NBs at molecular dimensions. When we combined the immunoTRAP technique with immunoFISH and microarray analysis, not only did we verify a TP53-PML NB association, but were able also to identify novel locus associations such as PML, ABCA7, and TFF1. In addition, we observed that these associations are cell type specific, and induction of significantly higher levels of PML gene expression, as well as other physiological changes brought about by interferon treatment, can lead to a physical association of the PML gene with PML NBs in normal human fibroblasts. Thus, immunoTRAP is a technique capable of identifying the chromatin associations around nuclear subcompartments and is amenable for further downstream applications such as microarray analysis or deep sequencing. Identification of binding (Cy5) to PML vs. to non-specific binding in Jurkat cells (n=5)

2013-03-28 | E-GEOD-40554 | biostudies-arrayexpress

Recruitment of TRIM33 to cell-context specific PML nuclear bodies regulates Nodal signaling in mESCs

Project description:TRIM33 is a chromatin reader required for mesendoderm differentiation upon activation of Nodal signaling. But, its role in mESCs is still elusive. Here, we found that TRIM33 co-localizes with promyelocytic leukemia nuclear bodies (PML NBs) specifically in mESCs to mediate Nodal signaling-directed transcription of Lefty1/2. We showed that TRIM33 puncta formation in mESCs depends on PML and specific assembly of PML NBs. Moreover, TRIM33 and PML co-regulate Lefty1/2 expression in mESCs. In addition, both PML and mESCs-specific PML NBs are required for TRIM33 recruitment at Lefty1/2 loci. Remarkably, PML NBs directly associate with the Lefty1/2 loci in mESCs. Finally, a TurboID proximity labeling experiment confirmed that TRIM33 is highly enriched in the mESCs-specific PML NBs. Thus, our study provides the mechanistic insight about TRIM33 condensate in regulating Nodal signaling-directed transcription in mESCs, it also reveals that PML NBs recruit distinct sets of client proteins in cell context dependent manner.

2022-12-08 | GSE199738 | GEO

PML nuclear bodies form a regulatory hub via liquid-liquid phase separation for TRIM33 control of Lefty1/2 genes in mouse embryonic stem cells [RNA-seq]

Project description:TRIM33 is a chromatin reader required for nodal signaling during mesendoderm differentiation, although differences in its function between mouse embryonic stem cells (mESCs) and differentiated mesendoderm cells are unknown. Here, we found that TRIM33 co-condenses with PML nuclear bodies (NBs) via liquid-liquid phase separation specifically in mESCs to mediate nodal signaling-directed transcription of Lefty1/2. Our findings show that TRIM33 puncta formation depends on the presence of PML NBs. TurboID proximity labeling further revealed that PML NBs recruit distinct sets of client proteins in NaAsO2-treated, untreated mESCs, and differentiated cells. TRIM33 and PML co-regulate Lefty1/2 expression, while PML NBs directly associate with the Lefty1/2 loci and regulate a gene cluster that includes Lefty1/2 loci specifically in mESCs. Moreover, TRIM33 association with chromatin depends on PML NBs. Thus, PML NBs serve as a hub for transcriptional regulation of Lefty1/2 by TRIM33 and other pluripotency factors in mESCs.

2022-12-08 | GSE199737 | GEO

PML nuclear bodies form a regulatory hub via liquid-liquid phase separation for TRIM33 control of Lefty1/2 genes in mouse embryonic stem cells [CHIP-seq]

2022-12-08 | GSE199736 | GEO

Interplay between PML NBs and HIRA for H3.3 deposition on transcriptionally active interferon-stimulated genes

Project description:Promyelocytic Leukemia Nuclear Bodies (PML NBs) are nuclear membrane-less organelles physically associated with chromatin underscoring their crucial role in genome function. The H3.3 histone chaperone complex HIRA accumulates in PML NBs upon senescence, viral infection or IFN-I treatment in primary cells. Yet, the molecular mechanisms of this partitioning and its function in regulating histone dynamics have remained elusive. Here, by using specific siRNAs and protein Affimers, we identify intermolecular SUMO-SIM interactions as an essential mechanism for HIRA recruitment in PML NBs. In addition, we demonstrate that HIRA localization in the nuclear bodies is intimately linked to the presence of a soluble pool of H3.3-H4 dimers inside PML NBs, that is not found in cancer cells. Transcription inhibition prevents HIRA accumulation in PML NBs underscoring the importance of transcriptional activity to drive HIRA through PML NBs. Finally, in the context of inflammatory responses, HIRA and PML are necessary for the prolonged H3.3 deposition at the transcriptional end sites of interferon-stimulated genes (ISGs), well beyond the peak of transcription. We thus propose that HIRA partitioning in PML NBs is essential to regulate H3.3 deposition on transcriptionally active regions.

2023-05-30 | GSE186937 | GEO

Interplay between PML NBs and HIRA for H3.3 deposition on transcriptionally active interferon-stimulated genes

2023-05-25 | GSE233298 | GEO

PML2‐mediated thread‐like nuclear bodies mark late senescence in Hutchinson–Gilford progeria syndrome [ChIP-seq]

Project description:Regular nuclear structure is critical for genome maintenance and proper gene expression, disorder of which has a causal role in aging. Accumulation of Progerin in Hutchinson-Gilford progeria syndrome (HGPS) disrupts the integrity of nuclear lamina and causes nuclear structure abnormalities, leading to premature aging. However, the nuclear structure/function relationships in HGPS cells have not been well addressed, and roles of nuclear sub-compartments for HGPS pathogenesis are rarely reported. Here, evidence reveals that classical dot-like PML nuclear bodies (PML NBs) are reorganized into thread-like morphology in HGPS cells, and these irregular NBs are strongly associated with cell senescence. We demonstrate that farnesylated Progerin interacts with PML isoform 2 specifically, which accounts for the formation of thread-like PML NBs. Moreover, our findings uncover that irregular PML NBs perturb NBs-associated DNA repair and gene transcription, thereby promoting HGPS cell senescence. Thus, our work helps to clarify the roles of nuclear structure and sub-compartments such as PML NBs in cell aging, and evidence presented in this study strongly support that thread-like PML NBs could be a novel biomarker of human cell senescence.

2019-09-10 | GSE137084 | GEO

PML2‐mediated thread‐like nuclear bodies mark late senescence in Hutchinson–Gilford progeria syndrome [RNA-seq]

2019-09-10 | GSE137083 | GEO

Chromatin immunoprecipitation of Bacillus subtilis to identify Noc protein binding sites

Project description:Coordination of chromosome segregation and cytokinesis is crucial for efficient cell proliferation. In Bacillus subtilis the nucleoid occlusion protein Noc protects chromosomes by associating with the chromosome and preventing cell division in its vicinity. Using protein localization, ChAP-on-Chip and bioinformatics, we have identified a consensus Noc-binding DNA sequence (NBS), and show that Noc is targeted to about 70 discrete regions scattered around the chromosome, though absent from a large region around the replication terminus. Purified Noc bound specifically to an NBS in vitro. NBSs inserted near the replication terminus bound Noc-YFP and caused a delay in cell division. An autonomous plasmid carrying an NBS recruited Noc-YFP and conferred a severe Noc-dependent inhibition of cell division. This shows that Noc is a potent inhibitor of division but that its activity is strictly localized by interaction with NBS sites in vivo. We propose that Noc not only serves as a spatial regulator of cell division to protect the nucleoid, but also a timing device with an important role in the co-ordination of chromosome segregation and cell division.

2009-07-01 | E-MEXP-2133 | biostudies-arrayexpress

Unbiased in vivo exploration of nuclear bodies-enhanced sumoylation reveals that PML orchestrates embryonic stem cell fate

Project description:Membrane-less organelles are condensates formed by phase separation whose functions often remain enigmatic. Upon oxidative stress, PML scaffolds Nuclear Bodies (NBs) to regulate senescence or metabolic adaptation, but their role in pluripotency remains elusive. Here we establish that PML is required for basal SUMO2/3 conjugation in mESCs and oxidative stress-driven sumoylation in mESCs or in vivo. PML NBs create an oxidationprotective environment for UBC9-driven SUMO2/3 conjugation of PML partners, often followed by their poly-ubiquitination and degradation. Differential in vivo proteomics identified several members of the KAP1 complex as PML NB-dependent SUMO2-targets. The latter drives functional activation of this key epigenetic repressor. Accordingly, Pml-/- mESCs reexpress transposable elements and display features of totipotent-like cells, a process further enforced by PML-controlled SUMO2-conjugation of DPPA2. Finally, PML is required for adaptive stress responses in mESCs. Collectively, PML orchestrates mESC fate through SUMO2-conjugation of key transcriptional or epigenetic regulators, raising new mechanistic hypotheses about PML roles in normal or cancer stem cells.

2022-09-14 | PXD028865 | Pride

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