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The mobile nucleoporin Nup2p and chromatin-bound Prp20p function in endogenous NPC-mediated transcriptional control.

Dilworth DJ, Tackett AJ, Rogers RS, Yi EC, Christmas RH, Smith JJ, Siegel AF, Chait BT, Wozniak RW, Aitchison JD - J. Cell Biol. (2005)

Bottom Line: Nuclear pore complexes (NPCs) govern macromolecular transport between the nucleus and cytoplasm and serve as key positional markers within the nucleus.Among these, Nup2p is unique as it transiently associates with NPCs and, when artificially tethered to DNA, can prevent the spread of transcriptional activation or repression between flanking genes, a function termed boundary activity.These data combined with functional assays of boundary activity and epigenetic variegation suggest that Nup2p and the Ran guanylyl-nucleotide exchange factor, Prp20p, interact at specific chromatin regions and enable the NPC to play an active role in chromatin organization by facilitating the transition of chromatin between activity states.

View Article: PubMed Central - PubMed

Affiliation: Institute for Systems Biology, Seattle, WA 98103, USA.

ABSTRACT
Nuclear pore complexes (NPCs) govern macromolecular transport between the nucleus and cytoplasm and serve as key positional markers within the nucleus. Several protein components of yeast NPCs have been implicated in the epigenetic control of gene expression. Among these, Nup2p is unique as it transiently associates with NPCs and, when artificially tethered to DNA, can prevent the spread of transcriptional activation or repression between flanking genes, a function termed boundary activity. To understand this function of Nup2p, we investigated the interactions of Nup2p with other proteins and with DNA using immunopurifications coupled with mass spectrometry and microarray analyses. These data combined with functional assays of boundary activity and epigenetic variegation suggest that Nup2p and the Ran guanylyl-nucleotide exchange factor, Prp20p, interact at specific chromatin regions and enable the NPC to play an active role in chromatin organization by facilitating the transition of chromatin between activity states.

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Genes exhibiting aberrant expression in cells lacking Nup2p map to distinct chromosome regions. For the top 5% of significant Δnup2 induced or repressed ORFs, the distance from each ORF to the nearest telomere was determined. These distances were grouped into 10-kb bins and plotted as a function of telomeric distance. These plots reveal an enrichment of Δnup2-induced ORFs at subtelomeric regions, as 25% of induced ORFs reside within 20 kb of a chromosome end. Only 1% of significantly repressed ORFs were within this distance. The shaded histograms indicate the distribution of telomeric distances for all ORFs plotted at 1/8 scale on the y-axis. Statistical comparison of the Δnup2-induced and repressed distributions to the profile for all ORFs using a two-sample Kolmogorov-Smirnov test confirms that the induced profile is unique (P = 0.0000386), but the repressed profile is not (P = 0.287).
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fig3: Genes exhibiting aberrant expression in cells lacking Nup2p map to distinct chromosome regions. For the top 5% of significant Δnup2 induced or repressed ORFs, the distance from each ORF to the nearest telomere was determined. These distances were grouped into 10-kb bins and plotted as a function of telomeric distance. These plots reveal an enrichment of Δnup2-induced ORFs at subtelomeric regions, as 25% of induced ORFs reside within 20 kb of a chromosome end. Only 1% of significantly repressed ORFs were within this distance. The shaded histograms indicate the distribution of telomeric distances for all ORFs plotted at 1/8 scale on the y-axis. Statistical comparison of the Δnup2-induced and repressed distributions to the profile for all ORFs using a two-sample Kolmogorov-Smirnov test confirms that the induced profile is unique (P = 0.0000386), but the repressed profile is not (P = 0.287).

Mentions: The physical connections between Nup2p, Prp20p, chromatin-modifying proteins, and atypically modified nucleosomes suggest that Nup2p can act as an endogenous boundary factor. Therefore, we predicted that boundaries in Δnup2 cells would not be stably maintained and these cells would exhibit unique transcriptional profiles relative to their wild-type counterparts. To test this hypothesis, we determined the global steady-state mRNA levels in logarithmically growing wild-type and nup2 cells using DNA microarrays (representing 6,271 yeast ORFs) (Ideker et al., 2001; Smith et al., 2002) and analyzed the chromosomal locations of the top 5% (313) most significantly induced (123) or repressed (190) ORFs in Δnup2 cells. These experiments revealed a striking bias of Δnup2-induced ORFs to subtelomeric regions, whereas repressed ORFs tended toward intrachromosomal sites (Fig. 3). This pattern suggests a steady-state alleviation of telomeric repression in cells lacking Nup2p, supporting a role for Nup2p in maintaining chromosomal boundaries in these regions. We note this phenotype might also arise if Nup2p, like Nup60p, plays a direct role in maintaining the Mlp peripheral silencing apparatus; however, these possibilities are not mutually exclusive and, unlike NUP60, deletion of NUP2 does not alter the localization of Mlp1p nor Mlp2p (unpublished data).


The mobile nucleoporin Nup2p and chromatin-bound Prp20p function in endogenous NPC-mediated transcriptional control.

Dilworth DJ, Tackett AJ, Rogers RS, Yi EC, Christmas RH, Smith JJ, Siegel AF, Chait BT, Wozniak RW, Aitchison JD - J. Cell Biol. (2005)

Genes exhibiting aberrant expression in cells lacking Nup2p map to distinct chromosome regions. For the top 5% of significant Δnup2 induced or repressed ORFs, the distance from each ORF to the nearest telomere was determined. These distances were grouped into 10-kb bins and plotted as a function of telomeric distance. These plots reveal an enrichment of Δnup2-induced ORFs at subtelomeric regions, as 25% of induced ORFs reside within 20 kb of a chromosome end. Only 1% of significantly repressed ORFs were within this distance. The shaded histograms indicate the distribution of telomeric distances for all ORFs plotted at 1/8 scale on the y-axis. Statistical comparison of the Δnup2-induced and repressed distributions to the profile for all ORFs using a two-sample Kolmogorov-Smirnov test confirms that the induced profile is unique (P = 0.0000386), but the repressed profile is not (P = 0.287).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2171315&req=5

fig3: Genes exhibiting aberrant expression in cells lacking Nup2p map to distinct chromosome regions. For the top 5% of significant Δnup2 induced or repressed ORFs, the distance from each ORF to the nearest telomere was determined. These distances were grouped into 10-kb bins and plotted as a function of telomeric distance. These plots reveal an enrichment of Δnup2-induced ORFs at subtelomeric regions, as 25% of induced ORFs reside within 20 kb of a chromosome end. Only 1% of significantly repressed ORFs were within this distance. The shaded histograms indicate the distribution of telomeric distances for all ORFs plotted at 1/8 scale on the y-axis. Statistical comparison of the Δnup2-induced and repressed distributions to the profile for all ORFs using a two-sample Kolmogorov-Smirnov test confirms that the induced profile is unique (P = 0.0000386), but the repressed profile is not (P = 0.287).
Mentions: The physical connections between Nup2p, Prp20p, chromatin-modifying proteins, and atypically modified nucleosomes suggest that Nup2p can act as an endogenous boundary factor. Therefore, we predicted that boundaries in Δnup2 cells would not be stably maintained and these cells would exhibit unique transcriptional profiles relative to their wild-type counterparts. To test this hypothesis, we determined the global steady-state mRNA levels in logarithmically growing wild-type and nup2 cells using DNA microarrays (representing 6,271 yeast ORFs) (Ideker et al., 2001; Smith et al., 2002) and analyzed the chromosomal locations of the top 5% (313) most significantly induced (123) or repressed (190) ORFs in Δnup2 cells. These experiments revealed a striking bias of Δnup2-induced ORFs to subtelomeric regions, whereas repressed ORFs tended toward intrachromosomal sites (Fig. 3). This pattern suggests a steady-state alleviation of telomeric repression in cells lacking Nup2p, supporting a role for Nup2p in maintaining chromosomal boundaries in these regions. We note this phenotype might also arise if Nup2p, like Nup60p, plays a direct role in maintaining the Mlp peripheral silencing apparatus; however, these possibilities are not mutually exclusive and, unlike NUP60, deletion of NUP2 does not alter the localization of Mlp1p nor Mlp2p (unpublished data).

Bottom Line: Nuclear pore complexes (NPCs) govern macromolecular transport between the nucleus and cytoplasm and serve as key positional markers within the nucleus.Among these, Nup2p is unique as it transiently associates with NPCs and, when artificially tethered to DNA, can prevent the spread of transcriptional activation or repression between flanking genes, a function termed boundary activity.These data combined with functional assays of boundary activity and epigenetic variegation suggest that Nup2p and the Ran guanylyl-nucleotide exchange factor, Prp20p, interact at specific chromatin regions and enable the NPC to play an active role in chromatin organization by facilitating the transition of chromatin between activity states.

View Article: PubMed Central - PubMed

Affiliation: Institute for Systems Biology, Seattle, WA 98103, USA.

ABSTRACT
Nuclear pore complexes (NPCs) govern macromolecular transport between the nucleus and cytoplasm and serve as key positional markers within the nucleus. Several protein components of yeast NPCs have been implicated in the epigenetic control of gene expression. Among these, Nup2p is unique as it transiently associates with NPCs and, when artificially tethered to DNA, can prevent the spread of transcriptional activation or repression between flanking genes, a function termed boundary activity. To understand this function of Nup2p, we investigated the interactions of Nup2p with other proteins and with DNA using immunopurifications coupled with mass spectrometry and microarray analyses. These data combined with functional assays of boundary activity and epigenetic variegation suggest that Nup2p and the Ran guanylyl-nucleotide exchange factor, Prp20p, interact at specific chromatin regions and enable the NPC to play an active role in chromatin organization by facilitating the transition of chromatin between activity states.

Show MeSH
Related in: MedlinePlus