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A role for the nucleoporin Nup170p in chromatin structure and gene silencing [Agilent microarrays]

ABSTRACT: Embedded in the nuclear envelope, nuclear pore complexes (NPCs) not only regulate nuclear transport, but also interface with both transcriptionally active euchromatin and largely silenced heterochromatin, as well as the boundaries between these regions. It is unclear what functional role NPCs play in establishing or maintaining these distinct chromatin domains. Here we report that the yeast NPC protein Nup170p interacts with specific regions of the genome containing ribosomal protein and subtelomeric genes. At these locations, Nup170p functions to establish normal nucleosome positioning and as a repressor of transcription. We show that the function of Nup170p in subtelomeric gene silencing is linked to its association with the RSC chromatin-remodeling complex and the silencing factor Sir4p, and that the binding of Nup170p and Sir4p to subtelomeric chromatin is cooperative and necessary for the association of telomeres with the nuclear envelope. Our results establish the NPC as an active participant in the formation of peripheral heterochromatin.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE36793 | GEO | 2013/02/28

SECONDARY ACCESSION(S): PRJNA157375

REPOSITORIES: GEO

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A role for the nucleoporin Nup170p in chromatin structure and gene silencing

2013-02-28 | E-GEOD-36795 | biostudies-arrayexpress

A role for the nucleoporin Nup170p in chromatin structure and gene silencing [Agilent ChIP-chip]

Project description:Embedded in the nuclear envelope, nuclear pore complexes (NPCs) not only regulate nuclear transport, but also interface with both transcriptionally active euchromatin and largely silenced heterochromatin, as well as the boundaries between these regions. It is unclear what functional role NPCs play in establishing or maintaining these distinct chromatin domains. Here we report that the yeast NPC protein Nup170p interacts with specific regions of the genome containing ribosomal protein and subtelomeric genes. At these locations, Nup170p functions to establish normal nucleosome positioning and as a repressor of transcription. We show that the function of Nup170p in subtelomeric gene silencing is linked to its association with the RSC chromatin-remodeling complex and the silencing factor Sir4p, and that the binding of Nup170p and Sir4p to subtelomeric chromatin is cooperative and necessary for the association of telomeres with the nuclear envelope. Our results establish the NPC as an active participant in the formation of peripheral heterochromatin. The genome-wide localization profiles of Nup170p and Nup157p were determined by chromatin immunoprecipitation and DNA microarray analysis using agilent whole genome Saccharomyces cerevisiae arrays. In addition, the localization profile of Nup170p was determined in sir4∆ and yku70∆ strains.

2013-02-28 | E-GEOD-36794 | biostudies-arrayexpress

A role for the nucleoporin Nup170p in chromatin structure and gene silencing

2013-02-28 | GSE36795 | GEO

A role for the nucleoporin Nup170p in chromatin structure and gene silencing [Agilent ChIP-chip]

2013-02-28 | GSE36794 | GEO

A role for the nucleoporin Nup170p in chromatin structure and gene silencing [Agilent microarrays]

Project description:Embedded in the nuclear envelope, nuclear pore complexes (NPCs) not only regulate nuclear transport, but also interface with both transcriptionally active euchromatin and largely silenced heterochromatin, as well as the boundaries between these regions. It is unclear what functional role NPCs play in establishing or maintaining these distinct chromatin domains. Here we report that the yeast NPC protein Nup170p interacts with specific regions of the genome containing ribosomal protein and subtelomeric genes. At these locations, Nup170p functions to establish normal nucleosome positioning and as a repressor of transcription. We show that the function of Nup170p in subtelomeric gene silencing is linked to its association with the RSC chromatin-remodeling complex and the silencing factor Sir4p, and that the binding of Nup170p and Sir4p to subtelomeric chromatin is cooperative and necessary for the association of telomeres with the nuclear envelope. Our results establish the NPC as an active participant in the formation of peripheral heterochromatin. Two-color microarrays were performed using Agilent whole-genome Saccharomyces cerevisiae arrays (Agilent) to determine gene expression profiles in the nucleoporin mutant strains nup157M-bM-^HM-^F, nup170M-bM-^HM-^F, and nup188M-bM-^HM-^F. Similar analyses were performed on PMET3-HA3-STH1 cells depleted of Sth1p for either 2 hrs (sth1-deplete 2hrs) or depleted of Sth1p for 8 hrs followed by reinduction of Sth1p for an additional 4 hrs (sth1-reinduction 4hr), as well as WT cells grown in the presence or absence of methionine. All experiments were performed with duplicate experimental and duplicate technical replicates of each condition as previously described (Wan et al., 2009).

2013-02-28 | E-GEOD-36793 | biostudies-arrayexpress

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

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

2013-02-28 | GSE36792 | 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

Nuclear pore complexes mediate subtelomeric gene silencing by regulating PCNA levels on chro atin

Project description:The nuclear pore complex (NPC) physically interacts with chromatin and regulates gene expression. The Saccharomyces cerevisiae inner ring nucleoporin Nup170 has been implicated in chromatin organization and the maintenance of gene silencing in subtelomeric regions. To gain insight into how Nup170 regulates this process, we used protein-protein interactions, genetic interactions, and transcriptome correlation analyses to identify the Ctf18-RFC complex, an alternative proliferating cell nuclear antigen (PCNA) loader, as a facilitator of the gene regulatory functions of Nup170. The Ctf18-RFC complex is recruited to a subpopulation of NPCs that lack the nuclear basket proteins Mlp1 and Mlp2. In the absence of Nup170, PCNA levels on DNA are reduced, resulting in the loss of silencing of subtelomeric genes. Increasing PCNA levels on DNA by removing Elg1, which is required for PCNA unloading, rescues subtelomeric silencing defects in nup170Δ. The NPC therefore mediates subtelomeric gene silencing by regulating PCNA levels on DNA.

2023-06-13 | PXD041496 | Pride

Selective autophagy degrades nuclear pore complexes

Project description:Nuclear pore complexes (NPCs) are giant cylindrical structures embedded into the nuclear envelope and mediate nucleocytoplasmic exchange. NPC longevity has been linked to aging but since they appear to rarely turn over, the underlying mechanisms remain understudied. Here, we show that upon nitrogen starvation and genetic interference with NPC architecture, Nups are rapidly degraded in budding yeast. We demonstrate that NPC turnover involves 25 vacuolar proteases and the core autophagic machinery. Autophagic degradation is mediated by the cytoplasmically exposed Nup159 that serves as intrinsic cargo receptor and directly binds to the autophagic marker protein Atg8. The inducible manner of this mechanism might explain why NPCs are long-lived under specific conditions

2019-11-13 | PXD011571 | Pride

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