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Dynamic association of NUP98 with the human genome.

Liang Y, Franks TM, Marchetto MC, Gage FH, Hetzer MW - PLoS Genet. (2013)

Bottom Line: Overexpression of a dominant negative fragment of NUP98 levels decreases expression levels of NUP98-bound genes.Alternatively, genes that are highly induced can interact with NUP98 in the nuclear interior, away from the nuclear pores.This work demonstrates for the first time that NUP98 dynamically associates with the human genome during differentiation, revealing a role of a nuclear pore protein in regulating developmental gene expression programs.

View Article: PubMed Central - PubMed

Affiliation: Salk Institute for Biological Studies, Molecular and Cell Biology Laboratory, La Jolla, California, USA.

ABSTRACT
Faithful execution of developmental gene expression programs occurs at multiple levels and involves many different components such as transcription factors, histone-modification enzymes, and mRNA processing proteins. Recent evidence suggests that nucleoporins, well known components that control nucleo-cytoplasmic trafficking, have wide-ranging functions in developmental gene regulation that potentially extend beyond their role in nuclear transport. Whether the unexpected role of nuclear pore proteins in transcription regulation, which initially has been described in fungi and flies, also applies to human cells is unknown. Here we show at a genome-wide level that the nuclear pore protein NUP98 associates with developmentally regulated genes active during human embryonic stem cell differentiation. Overexpression of a dominant negative fragment of NUP98 levels decreases expression levels of NUP98-bound genes. In addition, we identify two modes of developmental gene regulation by NUP98 that are differentiated by the spatial localization of NUP98 target genes. Genes in the initial stage of developmental induction can associate with NUP98 that is embedded in the nuclear pores at the nuclear periphery. Alternatively, genes that are highly induced can interact with NUP98 in the nuclear interior, away from the nuclear pores. This work demonstrates for the first time that NUP98 dynamically associates with the human genome during differentiation, revealing a role of a nuclear pore protein in regulating developmental gene expression programs.

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NUP98 binding correlates with developmental gene expression in neural progenitor cells.(A, B) Expression levels of NUP98 binding genes (-NUP98) and same number of randomly selected genes (-Random) in embryonic stem cells (ESC-) (A) and neural progenitor cells (NeuPC-) (B) were plotted. P value was obtained by Mann-Whitney U tests. Randomization was conducted for at least 10 times and similar results were obtained (data not shown). Gene expression values were obtained from [42], [43]. Top and bottom of the boxes in the plot are 25th and 75th percentile, centerline is the 50th, and whiskers extend to 1.5 interquartile range from the upper and lower quantile. (C) Positional correlation between expressed mRNA and NUP98-binding (blue) or three sets of same number- and size-matched, randomly selected regions (green, yellow, and black) in NeuPCs. mRNA expression data were from [43]. (D) Expression level change of neural progenitor cell-NUP98 targets during development, i.e. in ESCs, NeuPCs, and IMR90 cells (left). All NUP98 binding regions detected in neural progenitor cells that overlap with genes (promoters/exons/introns) were used. Expression level change of same number of randomly selected genes during development, i.e. in ESCs, NeuPCs, and IMR90 cells, were shown as negative control (right). Randomization was conducted for at least 10 times and similar results were obtained (data not shown). P values were obtained by Mann-Whitney U tests. Gene expression values were obtained from [42], [43]. Top and bottom of the boxes in the plot are 25th and 75th percentile, centerline is the 50th, and whiskers extend to 1.5 interquartile range from the upper and lower quantile.
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pgen-1003308-g003: NUP98 binding correlates with developmental gene expression in neural progenitor cells.(A, B) Expression levels of NUP98 binding genes (-NUP98) and same number of randomly selected genes (-Random) in embryonic stem cells (ESC-) (A) and neural progenitor cells (NeuPC-) (B) were plotted. P value was obtained by Mann-Whitney U tests. Randomization was conducted for at least 10 times and similar results were obtained (data not shown). Gene expression values were obtained from [42], [43]. Top and bottom of the boxes in the plot are 25th and 75th percentile, centerline is the 50th, and whiskers extend to 1.5 interquartile range from the upper and lower quantile. (C) Positional correlation between expressed mRNA and NUP98-binding (blue) or three sets of same number- and size-matched, randomly selected regions (green, yellow, and black) in NeuPCs. mRNA expression data were from [43]. (D) Expression level change of neural progenitor cell-NUP98 targets during development, i.e. in ESCs, NeuPCs, and IMR90 cells (left). All NUP98 binding regions detected in neural progenitor cells that overlap with genes (promoters/exons/introns) were used. Expression level change of same number of randomly selected genes during development, i.e. in ESCs, NeuPCs, and IMR90 cells, were shown as negative control (right). Randomization was conducted for at least 10 times and similar results were obtained (data not shown). P values were obtained by Mann-Whitney U tests. Gene expression values were obtained from [42], [43]. Top and bottom of the boxes in the plot are 25th and 75th percentile, centerline is the 50th, and whiskers extend to 1.5 interquartile range from the upper and lower quantile.

Mentions: The specific association between NUP98 and neurogenesis genes in NeuPCs raised the possibility of a positive correlation between NUP98 binding and the activation of these genes during neural differentiation. To test this possibility, we compared the expression levels of genes bound by NUP98 to those of the same number of randomly selected genes in ESCs and NeuPCs using published RNA-Seq datasets [42], [43] (Figure 3A, 3B). We found that genes bound by NUP98 had higher expression levels in NeuPCs compared to randomly selected gene sets, suggesting that NUP98-binding was associated with elevated gene expression levels. As an independent test, we correlated the genomic localization of NUP98-binding regions to that of expressed mRNA in NeuPCs (Figure 3C). We were able to detect a positive correlation between the location of NUP98 binding on the genome and the location of mRNA production, indicating the positive correlation between NUP98 binding and mRNA expression.


Dynamic association of NUP98 with the human genome.

Liang Y, Franks TM, Marchetto MC, Gage FH, Hetzer MW - PLoS Genet. (2013)

NUP98 binding correlates with developmental gene expression in neural progenitor cells.(A, B) Expression levels of NUP98 binding genes (-NUP98) and same number of randomly selected genes (-Random) in embryonic stem cells (ESC-) (A) and neural progenitor cells (NeuPC-) (B) were plotted. P value was obtained by Mann-Whitney U tests. Randomization was conducted for at least 10 times and similar results were obtained (data not shown). Gene expression values were obtained from [42], [43]. Top and bottom of the boxes in the plot are 25th and 75th percentile, centerline is the 50th, and whiskers extend to 1.5 interquartile range from the upper and lower quantile. (C) Positional correlation between expressed mRNA and NUP98-binding (blue) or three sets of same number- and size-matched, randomly selected regions (green, yellow, and black) in NeuPCs. mRNA expression data were from [43]. (D) Expression level change of neural progenitor cell-NUP98 targets during development, i.e. in ESCs, NeuPCs, and IMR90 cells (left). All NUP98 binding regions detected in neural progenitor cells that overlap with genes (promoters/exons/introns) were used. Expression level change of same number of randomly selected genes during development, i.e. in ESCs, NeuPCs, and IMR90 cells, were shown as negative control (right). Randomization was conducted for at least 10 times and similar results were obtained (data not shown). P values were obtained by Mann-Whitney U tests. Gene expression values were obtained from [42], [43]. Top and bottom of the boxes in the plot are 25th and 75th percentile, centerline is the 50th, and whiskers extend to 1.5 interquartile range from the upper and lower quantile.
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Related In: Results  -  Collection

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pgen-1003308-g003: NUP98 binding correlates with developmental gene expression in neural progenitor cells.(A, B) Expression levels of NUP98 binding genes (-NUP98) and same number of randomly selected genes (-Random) in embryonic stem cells (ESC-) (A) and neural progenitor cells (NeuPC-) (B) were plotted. P value was obtained by Mann-Whitney U tests. Randomization was conducted for at least 10 times and similar results were obtained (data not shown). Gene expression values were obtained from [42], [43]. Top and bottom of the boxes in the plot are 25th and 75th percentile, centerline is the 50th, and whiskers extend to 1.5 interquartile range from the upper and lower quantile. (C) Positional correlation between expressed mRNA and NUP98-binding (blue) or three sets of same number- and size-matched, randomly selected regions (green, yellow, and black) in NeuPCs. mRNA expression data were from [43]. (D) Expression level change of neural progenitor cell-NUP98 targets during development, i.e. in ESCs, NeuPCs, and IMR90 cells (left). All NUP98 binding regions detected in neural progenitor cells that overlap with genes (promoters/exons/introns) were used. Expression level change of same number of randomly selected genes during development, i.e. in ESCs, NeuPCs, and IMR90 cells, were shown as negative control (right). Randomization was conducted for at least 10 times and similar results were obtained (data not shown). P values were obtained by Mann-Whitney U tests. Gene expression values were obtained from [42], [43]. Top and bottom of the boxes in the plot are 25th and 75th percentile, centerline is the 50th, and whiskers extend to 1.5 interquartile range from the upper and lower quantile.
Mentions: The specific association between NUP98 and neurogenesis genes in NeuPCs raised the possibility of a positive correlation between NUP98 binding and the activation of these genes during neural differentiation. To test this possibility, we compared the expression levels of genes bound by NUP98 to those of the same number of randomly selected genes in ESCs and NeuPCs using published RNA-Seq datasets [42], [43] (Figure 3A, 3B). We found that genes bound by NUP98 had higher expression levels in NeuPCs compared to randomly selected gene sets, suggesting that NUP98-binding was associated with elevated gene expression levels. As an independent test, we correlated the genomic localization of NUP98-binding regions to that of expressed mRNA in NeuPCs (Figure 3C). We were able to detect a positive correlation between the location of NUP98 binding on the genome and the location of mRNA production, indicating the positive correlation between NUP98 binding and mRNA expression.

Bottom Line: Overexpression of a dominant negative fragment of NUP98 levels decreases expression levels of NUP98-bound genes.Alternatively, genes that are highly induced can interact with NUP98 in the nuclear interior, away from the nuclear pores.This work demonstrates for the first time that NUP98 dynamically associates with the human genome during differentiation, revealing a role of a nuclear pore protein in regulating developmental gene expression programs.

View Article: PubMed Central - PubMed

Affiliation: Salk Institute for Biological Studies, Molecular and Cell Biology Laboratory, La Jolla, California, USA.

ABSTRACT
Faithful execution of developmental gene expression programs occurs at multiple levels and involves many different components such as transcription factors, histone-modification enzymes, and mRNA processing proteins. Recent evidence suggests that nucleoporins, well known components that control nucleo-cytoplasmic trafficking, have wide-ranging functions in developmental gene regulation that potentially extend beyond their role in nuclear transport. Whether the unexpected role of nuclear pore proteins in transcription regulation, which initially has been described in fungi and flies, also applies to human cells is unknown. Here we show at a genome-wide level that the nuclear pore protein NUP98 associates with developmentally regulated genes active during human embryonic stem cell differentiation. Overexpression of a dominant negative fragment of NUP98 levels decreases expression levels of NUP98-bound genes. In addition, we identify two modes of developmental gene regulation by NUP98 that are differentiated by the spatial localization of NUP98 target genes. Genes in the initial stage of developmental induction can associate with NUP98 that is embedded in the nuclear pores at the nuclear periphery. Alternatively, genes that are highly induced can interact with NUP98 in the nuclear interior, away from the nuclear pores. This work demonstrates for the first time that NUP98 dynamically associates with the human genome during differentiation, revealing a role of a nuclear pore protein in regulating developmental gene expression programs.

Show MeSH
Related in: MedlinePlus