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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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Expression level changes of NUP98 target genes during neural differentiation.Fold change in expression levels of neural progenitor cell-NUP98 binding genes from embryonic stem cells (ESC) to neural progenitor cells (NeuPC) and to neurons (Neuron) on a log2-scale. Different groups of developmentally regulated NUP98 binding genes were labeled in red, green, aqua or grey. Error bars were computed as standard deviation from triplicates.
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pgen-1003308-g006: Expression level changes of NUP98 target genes during neural differentiation.Fold change in expression levels of neural progenitor cell-NUP98 binding genes from embryonic stem cells (ESC) to neural progenitor cells (NeuPC) and to neurons (Neuron) on a log2-scale. Different groups of developmentally regulated NUP98 binding genes were labeled in red, green, aqua or grey. Error bars were computed as standard deviation from triplicates.

Mentions: To obtain further insights into the role of NUP98 during differentiation we monitored the mRNA levels of 24 NUP98 target genes that were in the neural development gene ontology category through differentiation from ESCs to NeuPCs, and subsequently to postmitotic neurons in which Nup98 does not seem to bind the genome (Figure 6). We found that all 24 genes were upregulated when ESCs were differentiated to NeuPCs, consistent with the genome-wide correlation analysis and supporting a role of NUP98 in the induction of transcription (Figure 3D). When NeuPCs were further differentiated to neurons, the majority of genes (20 genes) showed continued transcriptional induction. Among those 20 genes, we focused on 6 genes that exhibited the most dramatic increase in expression in neurons. We observed that these genes could be largely divided into two groups (Figure 6). Group I genes (GRIK1, NRG1, and MAP2; colored in red) showed modest transcriptional induction in NeuPCs compared to ESCs. However, this cohort of genes underwent a robust increase in expression during the transition from NeuPCs to neurons. Group II genes (GPM6B, SOX5, and ERBB4; colored in green) underwent a dramatic activation in the initial commitment of ESCs to NeuPCs and only slight upregulation during subsequent neuronal differentiation. This suggests that NUP98 associates with both genes starting to be developmentally induced (Group I genes) and genes that are at a later stage of induction (Group II genes) in NeuPCs.


Dynamic association of NUP98 with the human genome.

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

Expression level changes of NUP98 target genes during neural differentiation.Fold change in expression levels of neural progenitor cell-NUP98 binding genes from embryonic stem cells (ESC) to neural progenitor cells (NeuPC) and to neurons (Neuron) on a log2-scale. Different groups of developmentally regulated NUP98 binding genes were labeled in red, green, aqua or grey. Error bars were computed as standard deviation from triplicates.
© Copyright Policy
Related In: Results  -  Collection

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

pgen-1003308-g006: Expression level changes of NUP98 target genes during neural differentiation.Fold change in expression levels of neural progenitor cell-NUP98 binding genes from embryonic stem cells (ESC) to neural progenitor cells (NeuPC) and to neurons (Neuron) on a log2-scale. Different groups of developmentally regulated NUP98 binding genes were labeled in red, green, aqua or grey. Error bars were computed as standard deviation from triplicates.
Mentions: To obtain further insights into the role of NUP98 during differentiation we monitored the mRNA levels of 24 NUP98 target genes that were in the neural development gene ontology category through differentiation from ESCs to NeuPCs, and subsequently to postmitotic neurons in which Nup98 does not seem to bind the genome (Figure 6). We found that all 24 genes were upregulated when ESCs were differentiated to NeuPCs, consistent with the genome-wide correlation analysis and supporting a role of NUP98 in the induction of transcription (Figure 3D). When NeuPCs were further differentiated to neurons, the majority of genes (20 genes) showed continued transcriptional induction. Among those 20 genes, we focused on 6 genes that exhibited the most dramatic increase in expression in neurons. We observed that these genes could be largely divided into two groups (Figure 6). Group I genes (GRIK1, NRG1, and MAP2; colored in red) showed modest transcriptional induction in NeuPCs compared to ESCs. However, this cohort of genes underwent a robust increase in expression during the transition from NeuPCs to neurons. Group II genes (GPM6B, SOX5, and ERBB4; colored in green) underwent a dramatic activation in the initial commitment of ESCs to NeuPCs and only slight upregulation during subsequent neuronal differentiation. This suggests that NUP98 associates with both genes starting to be developmentally induced (Group I genes) and genes that are at a later stage of induction (Group II genes) in NeuPCs.

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