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VAPB interacts with phosphorylated ELYS at decondensing chromosomes during mitosis - phosphorylation analysis

ABSTRACT: ELYS is a nucleoporin that localizes to the nuclear side of the nuclear envelope in interphase cells. In mitosis, it serves as an assembly platform that interacts with chromatin and then with nucleoporin subcomplexes to initiate the formation of novel nuclear pore complexes. Here we describe the interaction of ELYS with the membrane protein VAPB. In mitosis, ELYS becomes phosphorylated at many sites, including a predicted FFAT (two phenylalanines in an acidic tract) motif, which is shown to mediate interaction with the MSP (major sperm protein)-domain of VAPB. Phosphorylation-dependent binding of VAPB to ELYS is demonstrated by peptide binding assays and co-immunoprecipitation experiments. In anaphase, the two proteins co-localize to the non-core region of the newly forming nuclear envelope. Depletion of VAPB resulted in prolonged mitosis and slow progression from meta- to anaphase and also to chromosome segregation defects. Together, our results suggest an active role of VAPB in recruiting membrane fragments to chromatin and in the biogenesis of a novel nuclear envelope during mitosis.

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Olexandr Dybkov

LAB HEAD: Henning Urlaub

PROVIDER: PXD048054 | Pride | 2024-04-17

REPOSITORIES: Pride

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			Action	DRS
	C_James_280823_300823_Expl2_asyn_TiO2_1a_1.raw	Raw
	C_James_280823_300823_Expl2_asyn_TiO2_1a_2.raw	Raw
	C_James_280823_300823_Expl2_asyn_TiO2_1a_3.raw	Raw
	C_James_280823_300823_Expl2_mit_TiO2_2a_1.raw	Raw
	C_James_280823_300823_Expl2_mit_TiO2_2a_2.raw	Raw

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VAPB interacts with phosphorylated ELYS at decondensing chromosomes during mitosis (AP-MS Data)

Project description:ELYS is a nucleoporin that localizes to the nuclear side of the nuclear pore complex (NPC) in interphase cells. In mitosis, it serves as an assembly platform that interacts with chromatin and then with nucleoporin subcomplexes to initiate post-mitotic NPC assembly. Here we identified and characterized ELYS as a major binding partner of the membrane protein VAPB during mitosis. In mitosis, ELYS becomes phosphorylated at many sites, including a predicted FFAT (two phenylalanines in an acidic tract) motif, which is shown to mediate interaction with the MSP (major sperm protein)-domain of VAPB. Phosphorylation-dependent binding of VAPB to ELYS is demonstrated by peptide binding assays and co-immunoprecipitation experiments. In anaphase, the two proteins co-localize to the non-core region of the newly forming nuclear envelope. Depletion of VAPB resulted in prolonged mitosis and slow progression from meta- to anaphase and also to chromosome segregation defects. Together, our results suggest a role of ELYS-VAPB-complexes in recruiting membrane fragments to chromatin.

2024-04-12 | PXD047720 | Pride

Nucleoporin Elys attaches peripheral chromatin to the nuclear pores in interphase nuclei

Project description:Transport of macromolecules through the nuclear envelope (NE) is mediated by nuclear pore complexes (NPCs) consisting of nucleoporins (Nups). Elys/Mel-28 is the Nup that binds and connects the decondensing chromatin with the reassembled NPCs at the end of mitosis. Whether Elys links chromatin with the NE during interphase is unknown. Using DamID-seq, we identified Elys binding sites in Drosophila late embryos and divided them into those associated with nucleoplasmic or with NPC-linked Elys. These Elys binding sites are located within active or inactive chromatin, respectively. Strikingly, Elys knockdown in S2 cells results in peripheral chromatin displacement from the NE, in decondensation of NE-attached chromatin, and in derepression of genes within. It also leads to slightly more compact active chromatin regions. Our findings indicate that NPC-linked Elys, together with the nuclear lamina, anchors peripheral chromatin to the NE, whereas nucleoplasmic Elys decompacts active chromatin.

2024-06-28 | GSE218886 | GEO

Nucleoporin Elys attaches peripheral chromatin to the nuclear pores in interphase nuclei

Project description:Transport of macromolecules through the nuclear envelope (NE) is mediated by nuclear pore complexes (NPCs) consisting of nucleoporins (Nups). Elys/Mel-28 is the Nup that binds and connects the decondensing chromatin with the reassembled NPCs at the end of mitosis. Whether Elys links chromatin with the NE during interphase is unknown. Using DamID-seq, we identified Elys binding sites in Drosophila late embryos and divided them into those associated with nucleoplasmic or NPC-linked Elys. These Elys binding sites are located within active or inactive chromatin, respectively. Strikingly, Elys knockdown in S2 cells results in peripheral chromatin displacement from the NE, in decondensation of NE-attached chromatin, and in derepression of genes within. It also leads to slightly more compact active chromatin regions. Our findings indicate that NPC-linked Elys, together with the nuclear lamina, anchors peripheral chromatin to the NE, whereas nucleoplasmic Elys decompacts active chromatin.

2024-07-01 | GSE219152 | GEO

Nucleoporin Elys attaches peripheral chromatin to the nuclear pores in interphase nuclei

Project description:Nucleoporin Elys attaches peripheral chromatin to the nuclear pores in interphase nuclei

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Nucleoporin Elys attaches peripheral chromatin to the nuclear pores in interphase nuclei

Project description:Nucleoporin Elys attaches peripheral chromatin to the nuclear pores in interphase nuclei

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Nucleoporins facilitate ORC loading onto chromatin

Project description:The origin recognition complex (ORC) binds throughout the genome to initiate DNA replication. In metazoans, it is still unclear how ORC is targeted to specific loci to facilitate helicase loading and replication initiation. Here, we performed immunoprecipitations coupled with mass spectrometry for ORC2 in Drosophila embryos. Surprisingly, we found that ORC2 associates with several subunits of the Nup107-160 subcomplex of the nuclear pore. Bioinformatic analysis revealed that, relative to all modENCODE factors, nucleoporins are among the most enriched factors at ORC2 binding sites. Critically, depletion of the nucleoporin Elys, a member of the Nup107-160 complex, results in decrease ORC2 loading onto chromatin. Depleting Elys also sensitized cells to replication fork stalling, which could reflect a defect in establishing dormant replication origins. Our work reveals a new connection between ORC, replication initiation and nucleoporins, highlighting a previously unrecognized function of nucleoporins in metazoan replication initiation.

2022-10-19 | GSE199896 | GEO

The nucleoporin Nup50 activates the Ran guanyl-nucleotide exchange factor RCC1 to promote NPC assembly at the end of mitosis

Project description:During mitotic exit, thousands of nuclear pore complexes (NPCs) assemble concomitant with the nuclear envelope to build a transport-competent nucleus. Here, we show that Nup50 plays a crucial role in NPC assembly independent of its well-established function in nuclear transport. RNAi-mediated downregulation in cells or immunodepletion of Nup50 protein in Xenopus egg extracts interferes with NPC assembly. We define a conserved central region of 46 residues in Nup50 that is crucial for Nup153 and MEL28/ELYS binding, and for NPC interaction. Surprisingly, neither NPC interaction nor binding of Nup50 to importin /, the GTPase Ran, or chromatin is crucial for its function in the assembly process. Instead, an N-terminal fragment of Nup50 can stimulate the Ran GTPase guanyl-nucleotide exchange factor RCC1 and NPC assembly, indicating that Nup50 acts via the Ran system in NPC reformation at the end of mitosis. In support of this conclusion, Nup50 mutants defective in RCC1 binding and stimulation cannot replace the wild-type protein in in vitro NPC assembly assays, while excess RCC1 can compensate the loss of Nup50.

2021-11-03 | PXD028701 | Pride

Identification of PP2A-B55 targets in Drosophila uncovers regulation of Emerin during nuclear envelope reassembly

Project description:Entry into mitosis is triggered by mitotic kinases that phosphorylate multiple proteins to induce profound cellular changes including nuclear envelope breakdown, chromosome condensation and spindle assembly. Conversely, mitotic exit requires protein dephosphorylation as cells return to their interphase organization. Protein Phosphatase 2A in complex with its B55/Tws regulatory subunit (PP2A-B55) is known to play a crucial role in this transition. However, the precise events and substrates that it regulates are incompletely understood. We used proteomic approaches in Drosophila to identify proteins that interact with PP2A-B55 and are dephosphorylated in a PP2A-B55 dependent manner. Among several candidates, we identified Otefin (also known as Emerin) as a target of PP2A-B55 in the process of nuclear envelope reformation after mitosis. Emerin is a protein of the inner nuclear membrane that interacts with the DNA-binding protein Barrier-to-Autointegration Factor (BAF) via a LEM domain. Our results indicate that phosphorylation of Emerin at Ser50 and Ser54 near its LEM domain negatively regulates its association with BAF, Lamin and additional Emerin. Using live imaging, we show that dephosphorylation of Emerin at the identified sites determines the timing of nuclear envelope reformation. Genetic rescue experiments indicate that this regulation is required in vivo during embryonic development. Phosphoregulation of the Emerin-BAF complex formation by PP2A-B55 appears as a key event of mitotic exit that is likely to be conserved across species.

2023-08-10 | PXD041032 | Pride

The nucleoporin Nup170p is required for subtelomeric chromatin structure and gene silencing. [MNase-Seq]

Project description:Transcriptionally silent heterochromatin preferentially localizes at the nuclear periphery, but, despite this, certain budding yeast genes relocate to the nuclear periphery following gene activation, implicating the nuclear envelope in both transcriptional activation and silencing. It is unclear how these distinct chromatin domains are established, maintained and distinguished from one another at the nuclear envelope. Here we report that nuclear pore complexes (NPCs) facilitate the transition between chromatin states by providing a platform to which chromatin-remodeling and chromatin-modifying complexes bind. In particular, we show that the RSC chromatin-remodeling complex associates with NPCs and that the nucleoporin Nup170p nucleates heterochromatin formation at telomeres through recruitment of Sir4p. Deletion of NUP170 altered subtelomeric chromatin structure, reduced SIR complex binding at telomeres, impaired telomeric silencing and abated telomere tethering. These results support a model in which telomeric heterochromatin formation occurs through telomere-NPC interactions that both promote Sir4p binding at telomeres and permit chromatin-remodeling complexes to mediate the transition between chromatin states. Examination of genome-wide nucleosome positions in WT and nup170∆ cells via next-generation sequencing of mononucleosomal DNA.

2013-02-28 | E-GEOD-36792 | biostudies-arrayexpress

Nucleoporins facilitate ORC loading onto chromatin

Project description:The origin recognition complex (ORC) binds throughout the genome to initiate DNA replication. In metazoans, it is still unclear how ORC is targeted to specific loci to facilitate helicase loading and replication initiation. Here, we performed immunoprecipitations coupled with mass spectrometry for ORC2 in Drosophila embryos. Surprisingly, we found that ORC2 associates with multiple subunits of the Nup107-160 subcomplex of the nuclear pore. Bioinformatic analysis revealed that, relative to all modENCODE factors, nucleoporins are among the most enriched factors at ORC2 binding sites. Critically, depletion of the nucleoporin Elys, a member of the Nup107-160 complex, results in decreased ORC2 loading onto chromatin. Depleting Elys also sensitized cells to replication fork stalling, which could reflect a defect in establishing dormant replication origins. Our work reveals a new connection between ORC, replication initiation and nucleoporins, highlighting a previously unrecognized function of nucleoporins in metazoan replication initiation.

2022-10-19 | PXD033045 | Pride

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