Limits...
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.

Show MeSH

Related in: MedlinePlus

NUP98 loses association with active chromatin domains in post-differentiation IMR90 cells.Histone modification levels of NUP98 binding genes (-NUP98) and same number of randomly selected genes (-Random) in embryonic stem cells (ESC-) (A) and lung fibroblasts (IMR90-) (B) were plotted. P values were obtained by Mann-Whitney U tests. Randomization was conducted for at least 10 times and similar results were obtained (data not shown). Histone modification levels were calculated from [42], GSM605321, and GSM605309. 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.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3585015&req=5

pgen-1003308-g004: NUP98 loses association with active chromatin domains in post-differentiation IMR90 cells.Histone modification levels of NUP98 binding genes (-NUP98) and same number of randomly selected genes (-Random) in embryonic stem cells (ESC-) (A) and lung fibroblasts (IMR90-) (B) were plotted. P values were obtained by Mann-Whitney U tests. Randomization was conducted for at least 10 times and similar results were obtained (data not shown). Histone modification levels were calculated from [42], GSM605321, and GSM605309. 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: In contrast to the direct correlation between NUP98 binding and gene activation in NeuPCs, the scenario in ESCs appears more complicated. To gain additional insight into the type of chromatin environment that NUP98 interacts with, we compared NUP98 binding to the levels of different histone modifications by comparing our ChIP-Seq datasets to published ChIP-Seq datasets of histone modifications in ESCs [42]. Specifically, we examined H3K79me2 and H3K36me3 that are linked to active transcription, as well as H3K27me3 and H3K9me3 that are linked to repressed chromatin domains [44]. We compared histone modification levels for NUP98-binding regions and randomly selected regions as negative controls. We found that, in ESCs, NUP98 binding showed positive correlation with both active and silent histone marks. In contrast, NUP98 binding in IMR90 cells, which does not target promoter regions, was exclusively linked to high H3K9me3 levels (Figure 4). This observation is consistent with the idea that NUP98 is preferentially, if not exclusively, involved in developmental gene regulation in pluri-/multi-potent cells whereas in differentiated cells either associates with repressive chromatin (e.g. IMR90 cells) or lacks chromatin association altogether (e.g. neurons).


Dynamic association of NUP98 with the human genome.

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

NUP98 loses association with active chromatin domains in post-differentiation IMR90 cells.Histone modification levels of NUP98 binding genes (-NUP98) and same number of randomly selected genes (-Random) in embryonic stem cells (ESC-) (A) and lung fibroblasts (IMR90-) (B) were plotted. P values were obtained by Mann-Whitney U tests. Randomization was conducted for at least 10 times and similar results were obtained (data not shown). Histone modification levels were calculated from [42], GSM605321, and GSM605309. 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.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3585015&req=5

pgen-1003308-g004: NUP98 loses association with active chromatin domains in post-differentiation IMR90 cells.Histone modification levels of NUP98 binding genes (-NUP98) and same number of randomly selected genes (-Random) in embryonic stem cells (ESC-) (A) and lung fibroblasts (IMR90-) (B) were plotted. P values were obtained by Mann-Whitney U tests. Randomization was conducted for at least 10 times and similar results were obtained (data not shown). Histone modification levels were calculated from [42], GSM605321, and GSM605309. 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: In contrast to the direct correlation between NUP98 binding and gene activation in NeuPCs, the scenario in ESCs appears more complicated. To gain additional insight into the type of chromatin environment that NUP98 interacts with, we compared NUP98 binding to the levels of different histone modifications by comparing our ChIP-Seq datasets to published ChIP-Seq datasets of histone modifications in ESCs [42]. Specifically, we examined H3K79me2 and H3K36me3 that are linked to active transcription, as well as H3K27me3 and H3K9me3 that are linked to repressed chromatin domains [44]. We compared histone modification levels for NUP98-binding regions and randomly selected regions as negative controls. We found that, in ESCs, NUP98 binding showed positive correlation with both active and silent histone marks. In contrast, NUP98 binding in IMR90 cells, which does not target promoter regions, was exclusively linked to high H3K9me3 levels (Figure 4). This observation is consistent with the idea that NUP98 is preferentially, if not exclusively, involved in developmental gene regulation in pluri-/multi-potent cells whereas in differentiated cells either associates with repressive chromatin (e.g. IMR90 cells) or lacks chromatin association altogether (e.g. neurons).

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