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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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Transcription factor motif and gene ontology analysis of NUP98 binding regions.(A) GA-boxes is an over-represented transcription factor motif in Drosophila from published NUP98 Dam-ID and ChIP-chip datasets [8], [17] and in human ESCs and NeuPCs. Z-score represents the distance from the population mean in units of the population standard deviation. (B) Biological processes enriched in NUP98 binding genes in ESCs and NeuPCs by gene ontology analysis.
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pgen-1003308-g002: Transcription factor motif and gene ontology analysis of NUP98 binding regions.(A) GA-boxes is an over-represented transcription factor motif in Drosophila from published NUP98 Dam-ID and ChIP-chip datasets [8], [17] and in human ESCs and NeuPCs. Z-score represents the distance from the population mean in units of the population standard deviation. (B) Biological processes enriched in NUP98 binding genes in ESCs and NeuPCs by gene ontology analysis.

Mentions: In order to identify potential DNA sequence motifs and/or potential NUP98-interacting transcription factors that direct NUP98-DNA binding, we analyzed the transcription factor motifs overrepresented in NUP98-binding sequences found in ESCs and NeuPCs. We found that GA-boxes were an evolutionarily conserved NUP98-associated motif. This motif was not only overrepresented in human NUP98-binding genomic regions, but also in published Drosophila NUP98 binding sequences (Figure 2A, Figure S5A and S5B) [8], [17]. In Drosophila, GA-boxes are recognized by GAGA factor, which is a transcriptional activator that is crucial for the proper expression of several homeotic genes [33]. This suggests that the interaction between NUP98 and GA-box motifs, potentially related to the regulation of developmental genes, is evolutionary conserved and further validates our ChIP-Seq results.


Dynamic association of NUP98 with the human genome.

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

Transcription factor motif and gene ontology analysis of NUP98 binding regions.(A) GA-boxes is an over-represented transcription factor motif in Drosophila from published NUP98 Dam-ID and ChIP-chip datasets [8], [17] and in human ESCs and NeuPCs. Z-score represents the distance from the population mean in units of the population standard deviation. (B) Biological processes enriched in NUP98 binding genes in ESCs and NeuPCs by gene ontology analysis.
© Copyright Policy
Related In: Results  -  Collection

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

pgen-1003308-g002: Transcription factor motif and gene ontology analysis of NUP98 binding regions.(A) GA-boxes is an over-represented transcription factor motif in Drosophila from published NUP98 Dam-ID and ChIP-chip datasets [8], [17] and in human ESCs and NeuPCs. Z-score represents the distance from the population mean in units of the population standard deviation. (B) Biological processes enriched in NUP98 binding genes in ESCs and NeuPCs by gene ontology analysis.
Mentions: In order to identify potential DNA sequence motifs and/or potential NUP98-interacting transcription factors that direct NUP98-DNA binding, we analyzed the transcription factor motifs overrepresented in NUP98-binding sequences found in ESCs and NeuPCs. We found that GA-boxes were an evolutionarily conserved NUP98-associated motif. This motif was not only overrepresented in human NUP98-binding genomic regions, but also in published Drosophila NUP98 binding sequences (Figure 2A, Figure S5A and S5B) [8], [17]. In Drosophila, GA-boxes are recognized by GAGA factor, which is a transcriptional activator that is crucial for the proper expression of several homeotic genes [33]. This suggests that the interaction between NUP98 and GA-box motifs, potentially related to the regulation of developmental genes, is evolutionary conserved and further validates our ChIP-Seq results.

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