InteractiveFly: GeneBrief

Nucleoporin 98-96kD: Biological Overview | References

Gene name - Nucleoporin 98-96kD

Synonyms -

Cytological map position - 95B1-95B5

Function - Transcriptional regulator

Keywords - nuclear pore complex - innate immunity - viral-induced primary response gene - lymph gland hematopoietic development

Symbol - Nup98-96

FlyBase ID: FBgn0039120

Genetic map position - chr3R:19,599,947-19,607,343

Classification - Nup96: Nuclear protein 96

Cellular location - nuclear

NCBI links: EntrezGene
Nup98-96 orthologs: Biolitmine
Recent literature

Panda, D., Gold, B., Tartell, M. A., Rausch, K., Casas-Tinto, S. and Cherry, S. (2015) The transcription factor FoxK participates with Nup98 to regulate antiviral gene expression MB 6 [Epub ahead of print]. PubMed ID: 25852164
Nup98 regulates the expression of antiviral genes that restrict RNA virus infections in Drosophila by promoting RNA polymerase occupancy at the promoters of these antiviral genes. It was reasoned that additional transcription factors facilitate the Nup98-dependent expression of antiviral genes. In a genome-wide RNA interference (RNAi) screen, a forkhead transcription factor, FoxK, was identified as active against Sindbis virus (SINV) in Drosophila. FoxK is active against the panel of viruses that are restricted by Nup98, including vesicular stomatitis virus (VSV). FoxK was shown to coordinately regulate the Nup98-dependent expression of antiviral genes. Depletion of FoxK significantly reduces Nup98-dependent induction of antiviral genes and reduces the expression of a forkhead response element-containing luciferase reporter. Together, these data show that FoxK-mediated activation of gene expression is Nup98 dependent. The mammalian ortholog FOXK1 was also found to antiviral against two disparate RNA viruses, SINV and VSV, in human cells. FOXK1 was found to attenuate virus-inducible interferon-stimulated response element (ISRE) reporter expression. Overall, these results demonstrate a novel role for FOXK1 in regulating the expression of antiviral genes, from insects to humans.

Pascual-Garcia, P., Little, S. C. and Capelson, M. (2022). Nup98-dependent transcriptional memory is established independently of transcription. Elife 11. PubMed ID: 35289742
Cellular ability to mount an enhanced transcriptional response upon repeated exposure to external cues is termed transcriptional memory, which can be maintained epigenetically through cell divisions and can depend on a nuclear pore component Nup98. The majority of mechanistic knowledge on transcriptional memory has been derived from bulk molecular assays. To gain additional perspective on the mechanism and contribution of Nup98 to memory, single-molecule RNA FISH (smFISH) was used to examine the dynamics of transcription in Drosophila cells upon repeated exposure to the steroid hormone ecdysone. smFISH was combined with mathematical modeling and it was found that upon hormone exposure, cells rapidly activate a low-level transcriptional response, but simultaneously begin a slow transition into a specialized memory state characterized by a high rate of expression. Strikingly, the modeling predicted that this transition between non-memory and memory states is independent of the transcription stemming from initial activation. This prediction was confirmed experimentally by showing that inhibiting transcription during initial ecdysone exposure did not interfere with memory establishment. Together, these findings reveal that Nup98's role in transcriptional memory is to stabilize the forward rate of conversion from low to high expressing state, and that induced genes engage in two separate behaviors - transcription itself and the establishment of epigenetically propagated transcriptional memory.
Pulianmackal, A. J., Kanakousaki, K., Flegel, K., Grushko, O. G., Gourley, E., Rozich, E. and Buttitta, L. A. (2022). Misregulation of Nucleoporins 98 and 96 leads to defects in protein synthesis that promote hallmarks of tumorigenesis. Dis Model Mech 15(3). PubMed ID: 35107131
Nucleoporin 98KD (Nup98) is a promiscuous translocation partner in hematological malignancies. Most disease models of Nup98 translocations involve ectopic expression of the fusion protein under study, leaving the endogenous Nup98 loci unperturbed. Overlooked in these approaches is the loss of one copy of normal Nup98 in addition to the loss of Nup96 - a second Nucleoporin encoded within the same mRNA and reading frame as Nup98 - in translocations. Nup98 and Nup96 are also mutated in a number of other cancers, suggesting that their disruption is not limited to blood cancers. This study found that reducing Nup98-96 function in Drosophila melanogaster (in which the Nup98-96 shared mRNA and reading frame is conserved) de-regulates the cell cycle. Evidence was found of overproliferation in tissues with reduced Nup98-96, counteracted by elevated apoptosis and aberrant signaling associated with chronic wounding. Reducing Nup98-96 function led to defects in protein synthesis that triggered JNK signaling and contributed to hallmarks of tumorigenesis when apoptosis was inhibited. It is suggested that partial loss of Nup98-96 function in translocations could de-regulate protein synthesis, leading to signaling that cooperates with other mutations to promote tumorigenesis.


In response to infection, the innate immune system rapidly activates an elaborate and tightly orchestrated gene expression program to induce critical antimicrobial genes. While many key players in this program have been identified in disparate biological systems, it is clear that there are additional uncharacterized mechanisms at play. Previous studies revealed that a rapidly-induced antiviral gene expression program is active against disparate human arthropod-borne viruses in Drosophila. Moreover, one-half of this program is regulated at the level of transcriptional pausing. This study found that Nup98, a virus-induced gene, was antiviral against a panel of viruses both in cells and adult flies since its depletion significantly enhanced viral infection. Mechanistically, it was found that Nup98 promotes antiviral gene expression in Drosophila at the level of transcription. Expression profiling revealed that the virus-induced activation of 36 genes was abrogated upon loss of Nup98; and this study found that a subset of these Nup98-dependent genes were antiviral. These Nup98-dependent virus-induced genes are Cdk9-dependent and translation-independent suggesting that these are rapidly induced primary response genes. Biochemically, it was demonstrated that Nup98 is directly bound to the promoters of virus-induced genes, and that it promotes occupancy of the initiating form of RNA polymerase II at these promoters, which are rapidly induced on viral infection to restrict human arboviruses in insects (Panda, 2014).

Innate immunity is an evolutionarily conserved mode of defense against invading pathogens. A major facet of innate immunity involves the recognition of pathogen-associated molecular patterns by pattern recognition receptors to initiate signaling pathways to induce antimicrobial gene expression. This system is robust and is the sole mode of protection against invading pathogens in insects and plants. The gene expression programs activated on pathogen detection are tightly orchestrated to regulate downstream immune responses. The best-characterized example is the lipopolysaccharide (LPS)-dependent gene expression program. This response is divided into two stages; within minutes, a rapid primary response independent of new protein synthesis is initiated, which instructs the downstream translation-dependent secondary response. Many primary response genes have active chromatin marks and features of transcriptional pausing, including high occupancy of the initiating form of RNA polymerase II (RNAPII), S5 phosphorylated (S5P), along with negative elongation factor complex (NELF) and DRB Sensitivity- Inducing Factor complex (DSIF), which prevent transcriptional elongation. Paused RNAPII can be activated by the positive transcription elongation factor b (P-TEFb) in a stimulus-dependent manner, which phosphorylates NELF, DSIF, and RNAPII to release the pause and promote transcriptional elongation and thus the production of mature mRNAs. Indeed, a large number of LPS-induced primary response genes are controlled at the level of pausing including the classical gene TNF-α. Furthermore, this is conserved in Drosophila as the LPS-inducible homolog of TNF-α (Eiger) is also regulated by pausing. Furthermore, depletion of the pausing factor NELF reduced RNAPII occupancy on the promoters of LPS-stimulated genes in Drosophila (Panda, 2014).

Although many signaling pathways that regulate antibacterial and antifungal gene expression programs have been well characterized in insects, a understanding of antiviral gene expression programs is less clear. It was recently found that viral infection can lead to a rapid antiviral gene expression program, and that one-half of these virus-inducible genes are regulated at the level of transcriptional pausing (Xu, 2012). That study also found that NELF is required for RNAPII occupancy at these pausing-regulated genes. These data suggest a conserved role for this mode of gene regulation in the control of antiviral gene expression; however, whether there are specific factors required to promote high RNAPII occupancy at these promoters or to promote the future activation at particular loci remains unclear (Panda, 2014).

Nucleoporins (Nups), first identified for their role in nuclear-cytoplasmic transport, have recently been found to have roles outside of the nuclear pore. Initially, a subset of Nups was found to be mobile, able to move off and on the pore. The intranuclear accumulation of one such Nup, Nup98, is linked to ongoing nuclear transcription and chemical inhibition of RNA polymerase II was shown to abrogate its intranuclear mobility. Moreover, Nup98 was subsequently found to directly control gene expression of a subset of developmentally regulated genes. Nup98 is recruited to these loci during developmental transcriptional activation, and this association is required for the expression of such genes, particularly for the rapid induction of hormoneactivated developmental gene targets. It was recently shown that Nup98 is similarly involved in the transcriptional regulation of IFN-γ-induced gene expression, suggesting that the transcriptional roles of Nups may be involved in immunity (Panda, 2014).

Based on these findings, and given the fact that many developmental and immune genes are regulated by transcriptional pausing, it is hypothesized that Nup98 also may regulate virus-induced antiviral genes. Nup98 was found to play a broadly antiviral role in insects; cells or adult flies depleted of Nup98 are more susceptible to infection against a panel of disparate RNA viruses. This includes human arboviruses from diverse families of viruses: Sindbis virus (SINV), an alphavirus; vesicular stomatitis virus (VSV), a rhabdovirus; and West Nile virus (Kunjin strain), a flavivirus. Interestingly, this study found that in the experimental system that was used, transient depletion of Nup98 did not affect general nuclear pore function; nuclear import of NFκB and nuclear export of mRNAs and proteins were intact. This led us to the discovery of a role for Nup98 in promoting antiviral gene expression in Drosophila. Through transcriptional profiling, it was found that 36 genes were virus-induced and Nup98-dependent. Importantly, a subset of Nup98-dependent virus-induced genes were antiviral themselves, suggesting that Nup98 directly regulates expression of these antiviral genes. Moreover, single-molecule RNA fluorescent in situ hybridization (FISH) revealed reduced levels of virus-induced mRNAs, but not their localization, again supporting a role in the direct regulation of gene expression at the level of transcription. These Nup98- dependent virus-induced genes are translation-independent and regulated by the pausing-release factor P-TEFb. Mechanistically, Nup98 was found to binds to the promoter of these antiviral genes and positively regulates the levels of active RNAPII at these loci at the basal state. Taken together, the data suggest that Nup98 binds to these loci and facilitates the engagement of RNAPII; subsequent virus challenge signals P-TEFb to activate transcription at these loci, inducing antiviral gene expression. These findings demonstrate a previously unidentified requirement for Nup98 in antiviral defense via direct transcriptional initiation of antiviral genes and its coordination with transcriptional pausing to restrict viral infection (Panda, 2014).

The classically described role for Nups is within the nuclear pore complex, with specific functions in the transport of macromolecules in and out of the nucleus; however, recent studies have found both on-pore and off-pore roles for a subset of Nups. Using two independent assays, this study found no defect in nuclear export or import on depletion of Nup98 or several other nuclear pore proteins. This finding is consistent with two recent studies that found no role for Nup98 in nuclear transport when Nup98 was compromised (Light, 2013; Sabri, 2007). In addition, using single-molecule RNA FISH, this study detected no defect in nuclear export of B52 or CG9008 mRNA on depletion of Nup98. Nup98 may regulate the transport of additional antiviral genes, but nevertheless the results suggest that a subset of antiviral genes is regulated by Nup98 at the transcriptional level. Altogether, this suggests an off-pore transport-independent role for Nup98 in antiviral defense (Panda, 2014).

Viral infection leads to the rapid induction of an antiviral transcriptional response. In metazoans, RNAPII recruitment and activation are known to regulate signal-dependent gene transcription; however, the factors involved in recruiting and stabilizing RNAPII at the promoter in a context and gene-specific manner in response to diverse stimuli, including viral infection, are unclear. This study has demonstrated that Nup98 depletion reduces the level of RNAPII S5 phosphorylated (S5P) at the promoters of virally induced genes and, consequently, the level of transcripts. This suggests that Nup98 either promotes recruitment of RNAPII or maintains the initiating form of RNAPII at the promoters to facilitate transcription. Along with identifying this Nup98-dependent pathway in antiviral defense, the findings also shed light on the mechanistic involvement of Nups in transcription. Although several studies have identified a functional role for Nups in transcriptional activation, the detailed mechanism behind this role has not been fully deciphered. The current results suggest a specific step in the transcriptional process, RNAPII S5 activity at the target gene promoter, which is regulated by Nup98. It was recently shown that transcriptional pausing regulates one-half of the virus-induced genes in Drosophila, which is significantly enriched compared with the genome as a whole (Xu, 2012; Panda, 2014 and references therein).

Transcriptionally paused genes have high occupancy of RNAPII S5P, are primary response genes, and are dependent on P-TEFb for their induction. This study found that the seven virus-induced Nup98-dependent genes that were validated are primary response genes; there are high levels of RNAPII S5P at the promoters basally, and they are dependent on P-TEFb for their induction. This suggests that Nup98 maintains active RNAPII at these genes, keeping them poised for future activation by PTEFb. In the absence of Nup98, along with the loss of RNAPII S5P, these antiviral genes are no longer efficiently induced, resulting in elevated levels of viral infection. This model is consistent with the recent results demonstrating recruitment of Nup98 to the promoter of developmentally regulated genes independent of transcription elongation, because Nup98 recruitment is insensitive to flavopiridol treatment, and that many developmental genes are known to be regulated at the level of pausing. Consistent with the hypothesis that Nup98 is a specific transcription activator, it also has been demonstrated that Nup98 interacts with histone-modifying enzymes CBP/p300 and histone deacetylases (Kasper, 1999; Bai, 2006) (Panda, 2014).

Given that Nup98 regulates gene expression of developmental genes in mammals and Drosophila and this study observed regulation of antiviral genes in Drosophila, it is suggested that Nup98 may have functions in regulating cell intrinsic antiviral gene expression in mammalian systems. Indeed, it has long been recognized that Nup98 is involved in antiviral defense (Enninga, 2002, Satterly, 2007; Chen, 2010; von Kobbe, 2000). Nup98 depletion reduces the nuclear export of specific immune regulated genes, including IFN-stimulated genes (Satterly, 2007). Furthermore, viral infection was enhanced in Nup98-deficient MEFs (Satterly, 2007). These antiviral phenotypes were ascribed to transport defects; however, it has not been explored whether Nup98 also directly regulates the induction of antiviral primary response genes. Interestingly, a recent study found that Nup98 impacts the regulation of IFN-γ-responsive genes (Light, 2013). In this study, Nup98 was required to set the reactivation state of IFN-γ-responsive genes without affecting the initial activation (Light, 2013). Mechanistically, the study found that Nup98 binds the promoter of IFN-γ-responsive genes and is required for the maintenance of histone H3K4 dimethylation during transcriptional memory (Light, 2013). Whether Nup98 affects the transcriptional memory of immune-regulated genes in Drosophila remains to be seen (Panda, 2014).

The signal-dependent antiviral response is tightly regulated to induce the appropriate immune response. The current results shed light on how virus-specific gene regulation is controlled. This role for Nup98 in the regulation of a subset of antiviral genes unravels one additional layer in this complex control of innate immune gene expression programs. Given the finding that Nup98 is induced, it is possible that the newly synthesized Nup98 regulates a robust secondary response or alters the memory of these loci, as has been observed for IFN-γ-responsive genes. Future work examining the role of Nup98 in other immune contexts in insects and in viral infection in mammals will lead to better understanding of the transcriptional regulation of immune system and may help develop better therapeutic interventions against viral diseases (Panda, 2014).

Metazoan nuclear pores provide a scaffold for poised genes and mediate induced enhancer-promoter contacts

Nuclear pore complex components (Nups) have been implicated in transcriptional regulation, yet what regulatory steps are controlled by metazoan Nups remains unclear. This study identified the presence of multiple Nups at promoters, enhancers, and insulators in the Drosophila genome. In line with this binding, a functional role for Nup98 was uncovered in mediating enhancer-promoter looping at ecdysone-inducible genes. These genes were found to be stably associated with nuclear pores before and after activation. Although changing levels of Nup98 disrupted enhancer-promoter contacts, it did not affect ongoing transcription but instead compromised subsequent transcriptional activation or transcriptional memory. In support of the enhancer-looping role, Nup98 was found to gain and retain physical interactions with architectural proteins upon stimulation with ecdysone. Together, these data identify Nups as a class of architectural proteins for enhancers and supports a model in which animal genomes use the nuclear pore as an organizing scaffold for inducible poised genes (Pascual-Garcia, 2017).

Together, the results identify a specific transcriptional function for Nup98 in enhancer looping and reveal Nups as a class of architectural proteins that in addition to cohesins, CTCF, and Mediator components can promote enhancer-promoter interactions. Interestingly, the NPC has been recently shown to associate with the Mediator complex and to depend on a specific Mediator subunit, Med31, for binding the GAL1 gene in yeast. The current genome-wide analysis and identification of physical interactions with architectural proteins further suggest that Nups may contribute to other topological contacts, such as those of insulators. This notion is further supported by previous links of Nups to insulators in both yeast and fly cells (Pascual-Garcia, 2017).

Somewhat surprisingly, this study found that similarly to depletion of Nup98, Nup98 overexpression appears to disrupt the enhancer-promoter contact and transcriptional memory. This is likely due to the involvement of Nup98 in self-interactions, which can lead to aberrant oligomerization and mis-localized chromatin binding of Nup98 that prevent its participation in productive contacts. The biophysical properties of the intrinsically disordered FG domains of Nup98 involve the ability to polymerize and phase-separate. Given recent implications of intrinsically disordered and phase-separating proteins in transcriptional regulation and nuclear structure, it will be particularly interesting to determine whether these properties of the FG domains underlie the identified functions of Nup98 in enhancer-promoter looping or in epigenetic memory of transcription (Pascual-Garcia, 2017).

The implications of these findings are potentially far reaching in the context of developmental gene regulation. Establishment and maintenance of appropriate enhancer-promoter contacts may be a general mechanism by which Nups contribute to regulation of gene expression during cell differentiation. Mutations in multiple Nups lead to defects in differentiation of specific cell lineages in the fly, zebrafish, and mouse models. The identified roles of the NPC in genome architecture may represent one of the mechanisms by which Nups contribute to tissue-specific processes. In addition to ecdysone-inducible genes, chromatin binding analysis identified Hox genes as a recurrent target of NPC binding, previous work has identified a physical association between Nup98 and an epigenetic regulator of Hox gene activity, Trithorax (Trx). Trx and its mammalian homologs are HMTs responsible for methylation of H3 lysine K4, which is in line with the previously demonstrated dependence of promoter-associated H3K4 di-methylation levels on Nup98 in yeast and human cells. It remains to be determined how enhancer-promoter looping is integrated with H3K4 di-methylation in transcriptional memory, but an intriguing possibility is the potential role of Nup98-stabilized enhancer-promoter contacts in Trx-mediated epigenetic regulation during development (Pascual-Garcia, 2017).

The results also provide an example of uncoupling activation-induced enhancer-promoter contacts from transcriptional activation. A common model for how enhancers function proposes that enhancers loop over to contact their target promoters to drive transcriptional activation, implying a direct cause to effect relationship from looping to transcription. But the current data suggest that this relationship is not always this linear and can involve stabilization of enhancer-promoter loops that are not required for ongoing transcription. The increased enhancer-promoter interaction described in this study appears to function as part of a memory system through a period of repression (Pascual-Garcia, 2017).

Furthermore, genome-wide analysis of Nup binding revealed that nuclear pores target both active and silenced loci in similar proportions. PcG-bound regions, marked by the H3K27Me3 mark, appear to be common targets of the stable NPCs, which is supported by a previous report of Nup153 playing a role in PcG-mediated gene silencing. On the basis of the rest of the current findings, it is proposed that a specific subset of genes associates with NPCs independently of expression, for the purposes of stabilizing possible or future activation-induced long-range contacts. Although the transcriptional memory function of Nup98 is not limited to NPC targets and has been shown to apply to intranuclear genes, it is possible that NPC binding may be particularly beneficial for genes with complex regulatory landscapes, such as ecdysone-inducible or Hox genes, where pre-scaffolding and epigenetic maintenance of enhancer-promoter architecture is most critical (Pascual-Garcia, 2017).

Pvr expression regulators in equilibrium signal control and maintenance of Drosophila blood progenitors

Blood progenitors within the lymph gland, a larval organ that supports hematopoiesis in Drosophila melanogaster, are maintained by integrating signals emanating from niche-like cells and those from differentiating blood cells. The signal from differentiating cells has been termed the 'equilibrium signal' in order to distinguish it from the 'niche signal'. Earlier work showed that Equilibrium signaling utilizes Pvr (the Drosophila PDGF/VEGF receptor), STAT92E, and Adenosine deaminase-related growth factor A (ADGF-A). Little is known about how this signal initiates during hematopoietic development. To identify new genes involved in lymph gland blood progenitor maintenance, particularly those involved in equilibrium signaling, a genetic screen was performed that identified bip1 (bric a brac interacting protein 1; a THAP domain containing a C2CH-type zinc finger motif that is known to bind DNA) and Nucleoporin 98 (Nup98) as additional regulators of the equilibrium signal. The products of these genes along with the Bip1-interacting protein RpS8 (Ribosomal protein S8) are required for the proper expression of Pvr (Mondal, 2014).

The screen described in this study identified Nup98 as a potential equilibrium signaling component because its knockdown in differentiating cells specifically causes a loss of progenitors cells. Although Nup98 is widely known as a general component of the nuclear pore complex, recent work has demonstrated that Nup98 and other nuclear pore components such as Sec13 and Nup88, can regulate gene expression through the binding of target promoters. Moreover, chromatin immunoprecipitation experiments identified bip1, RpS8, and the equilibrium signaling genes Pvr and STAT (STAT92E) as in vivo Nup98 regulatory targets (Capelson, 2010). Consistent with a function in regulation of equilibrium signaling genes, Nup98 knockdown specifically in differentiating cells of lymph glands causes a strong reduction in Pvr expression. By contrast, RNAi knockdown of the nucleoporin Sec13 in differentiating cells has no effect on the maintenance of progenitor cells or Pvr expression underscoring the specific role of Nup98 in Pvr expression control. Furthermore, the close genetic relationship between Nup98 and Pvr is illustrated by the fact that single-copy loss of these genes in combination causes extensive loss of progenitor cells to differentiation. Interestingly, overexpression of bip1 in Nup98 RNAi lymph glands is sufficient to restore Pvr protein expression and to suppress the loss of progenitors to differentiation (Mondal, 2014).

Knockdown of bip1, Nup98, or RpS8 in differentiating cells each causes a strong reduction in Pvr expression in the lymph gland. The interpretation of this common phenotype is that each gene works in the equilibrium signaling pathway to control Pvr expression, although an alternative hypothesis is that the loss of Pvr expression is a common feature of highly differentiated lymph glands and is not specifically related to the function of these genes. To test this, Pvr expression was examined in collier (col) mutant lymph glands, which lack niche signaling and are strongly differentiated by late larval stages, and was found to be normal, compare with Pvr expression in wild-type cortical zone differentiating cells. Thus, Pvr requires bip1, RpS8, and Nup98 for proper developmental expression in the lymph gland (Mondal, 2014).

Several genetic screens, including overexpression and enhancer/suppressor screens of mutant or tumor phenotypes, have been conducted in the fly hematopoietic system; however, the screen described in this study represents the first loss-of-function screen targeting normal developmental mechanisms throughout the lymph gland. This was accomplished with the development and use of the pan-lymph gland expression tool HHLT-gal4 to drive UAS-mediated RNAi, which identified 20 different candidate genes that cause a loss of progenitor cells when knocked down within the lymph gland. From subsequent analyses using lymph gland zone-restricted Gal4 driver lines, a model is proposed in which Bip1, RpS8, and Nup98 are required in differentiating blood cells upstream of Pvr to control its expression and function in the equilibrium signaling pathway that maintains blood progenitors within the lymph gland. Future analyses will be required to identify additional components of this important signaling pathway and to provide more information about how equilibrium signaling interacts with other pathways in the control of blood cell progenitor maintenance, cell fate specification, and proliferation (Mondal, 2014).

The Pvr receptor, with its numerous developmental roles, is arguably one of the most important members of the Drosophila RTK family, yet most of what is known about Pvr stems from analyses of how it works in the context of intracellular signaling. Little is known about how Pvr gene or protein expression is regulated. Importantly, the work described in this study sheds new light upon this issue by demonstrating a role for bip1, RpS8, and Nup98 in the regulation of Pvr expression. The data and that of others suggest that this regulation of Pvr is likely taking place at the gene level, although other mechanisms are also possible. Ribosomes are required for protein translation, however specific ribosomal components or subunits may selectively stabilize transcripts and/or mediate preferential translation, while nucleoporins control both nuclear entry of regulatory proteins and the exit of mRNAs to the cytoplasm, and specific subcomponents are known to exhibit differential functions in this regard. Thus, RpS8 and Nup98 may selectively affect Pvr expression post-transcriptionally through transcript stabilization, transport, and translation. Although the specific mechanisms of molecular control of Pvr expression by bip1, RpS8, and Nup98 remain to be determined, their function is clearly critical in mediating proper equilibrium signaling and, therefore, proper blood progenitor maintenance within the lymph gland. The finding that bip1 regulates Pvr expression in the context of hematopoietic equilibrium signaling represents the first functional association for bip1 in Drosophila. The predicted Bip1 protein exhibits only one recognizable structural sequence, namely a THAP domain that contains a putative DNA-binding zinc finger motif. The results suggest that Bip1 behaves as a positive regulator of Pvr transcription, but whether this occurs directly through Bip1 interaction with the Pvr locus will require further investigation (Mondal, 2014).

Understanding how progenitor cell maintenance and homeostasis is controlled over developmental time is crucial for understanding normal cellular and tissue dynamics, especially in the context of ageing or disease. The identification of Bip1 and Nup98 as regulators of hematopoietic progenitors in Drosophila may be indicative of important conserved functions of related proteins within the vertebrate blood lineages similar to what has been shown previously for GATA, FOG, and RUNX factors. THAP-domain proteins are conserved across species and have been reported to have a variety of important functions in mammalian systems, including maintenance of murine embryonic stem cell pluripotency. What role, if any, THAP-domain proteins have in vertebrate blood progenitor maintenance (or hematopoiesis in general) remains to be established. Likewise, Nup98 has not been implicated in any normal hematopoietic role despite being a well-studied protein in other contexts (Mondal, 2014).

With regard to the diseased state, mutations in the human THAP1 gene have been associated with dystonia, a neuromuscular disorder that causes repetitive, involuntary muscular contraction, and THAP1/Par4 protein complexes have been shown to promote apoptosis in leukemic blood cells in various experimental contexts in vitro. Chromosomal translocations that generate Nup98 fusion proteins have been implicated in numerous human myelodysplastic syndromes and leukemias, further underscoring the need to explore Nup98 function in the hematopoietic system. Therefore, the study of bip1 and Nup98 in Drosophila, a powerful molecular genetic system, will likely be of benefit to understand the function of related vertebrate genes in normal and disease contexts (Mondal, 2014).

Chromatin-bound nuclear pore components regulate gene expression in higher eukaryotes

Nuclear pore complexes have recently been shown to play roles in gene activation; however their potential involvement in metazoan transcription remains unclear. This study shows that the nucleoporins Sec13, Nup98, and Nup88, as well as a group of FG-repeat nucleoporins, bind to the Drosophila genome at functionally distinct loci that often do not represent nuclear envelope contact sites. Whereas Nup88 localizes to silent loci, Sec13, Nup98, and a subset of FG-repeat nucleoporins bind to developmentally regulated genes undergoing transcription induction. Strikingly, RNAi-mediated knockdown of intranuclear Sec13 and Nup98 specifically inhibits transcription of their target genes and prevents efficient reactivation of transcription after heat shock, suggesting an essential role of NPC components in regulating complex gene expression programs of multicellular organisms (Capelson, 2010).

Functions of Nup98 orthologs in other species

A genetic screen in Drosophila uncovers the multifaceted properties of the NUP98-HOXA9 oncogene

Acute myeloid leukemia (AML) underlies the uncontrolled accumulation of immature myeloid blasts. Several cytogenetic abnormalities have been associated with AML. Among these is the NUP98-HOXA9 (NA9) translocation that fuses the Phe-Gly repeats of nucleoporin NUP98 (see Drosophila Nup98-96) to the homeodomain of the transcription factor HOXA9 (see Drosophila Abd-B) (, 2021). The mechanisms enabling NA9-induced leukemia are poorly understood. A genetic screen in Drosophila was conducted for modifiers of NA9. The screen uncovered 29 complementation groups, including genes with mammalian homologs known to impinge on NA9 activity. Markedly, the modifiers encompassed a diversity of functional categories, suggesting that NA9 perturbs multiple intracellular events. Unexpectedly, this study discovered that NA9 promotes cell fate transdetermination and that this phenomenon is greatly influenced by NA9 modifiers involved in epigenetic regulation. Together, this work reveals a network of genes functionally connected to NA9 that not only provides insights into its mechanism of action, but also represents potential therapeutic targets (Gavory, 2021).

Human Nup98 regulates the localization and activity of DExH/D-box helicase DHX9

Beyond their role at nuclear pore complexes, some nucleoporins function in the nucleoplasm. One such nucleoporin, Nup98 (see Drosophila Nup98-96), binds chromatin and regulates gene expression. To gain insight into how Nup98 contributes to this process, this study focused on identifying novel binding partners and understanding the significance of these interactions. The DExH/D-box helicase DHX9 (see Drosophila mle) as an intranuclear Nup98 binding partner (see Nup98 protein-protein interaction network). Various results, including in vitro assays, show that the FG/GLFG region of Nup98 binds to N- and C-terminal regions of DHX9 in an RNA facilitated manner. Importantly, binding of Nup98 stimulates the ATPase activity of DHX9, and a transcriptional reporter assay suggests Nup98 supports DHX9-stimulated transcription. Consistent with these observations, it was found that Nup98 and DHX9 bind interdependently to similar gene loci and their transcripts. Based on these data, the study proposes that Nup98 functions as a co-factor that regulates DHX9 and, potentially, other RNA helicases (Capitanio, 2017).

A conserved role for human Nup98 in altering chromatin structure and promoting epigenetic transcriptional memory

The interaction of nuclear pore proteins (Nups) with active genes can promote their transcription. In yeast, some inducible genes interact with the nuclear pore complex both when active and for several generations after being repressed, a phenomenon called epigenetic transcriptional memory. This interaction promotes future reactivation and requires Nup100, a homologue of human Nup98. A similar phenomenon occurs in human cells; for at least four generations after treatment with interferon gamma (IFN-gamma), many IFN-gamma-inducible genes are induced more rapidly and more strongly than in cells that have not previously been exposed to IFN-gamma. In both yeast and human cells, the recently expressed promoters of genes with memory exhibit persistent dimethylation of histone H3 lysine 4 (H3K4me2) and physically interact with Nups and a poised form of RNA polymerase II. However, in human cells, unlike yeast, these interactions occur in the nucleoplasm. In human cells transiently depleted of Nup98 or yeast cells lacking Nup100, transcriptional memory is lost; RNA polymerase II does not remain associated with promoters, H3K4me2 is lost, and the rate of transcriptional reactivation is reduced. These results suggest that Nup100/Nup98 binding to recently expressed promoters plays a conserved role in promoting epigenetic transcriptional memory (Light, 2013).


Search PubMed for articles about Drosophila Nup98

Bai, X. T., Gu, B. W., Yin, T., Niu, C., Xi, X. D., Zhang, J., Chen, Z. and Chen, S. J. (2006). Trans-repressive effect of NUP98-PMX1 on PMX1-regulated c-FOS gene through recruitment of histone deacetylase 1 by FG repeats. Cancer Res 66: 4584-4590. PubMed ID: 16651408

Capelson, M., Liang, Y., Schulte, R., Mair, W., Wagner, U. and Hetzer, M. W. (2010). Chromatin-bound nuclear pore components regulate gene expression in higher eukaryotes. Cell 140: 372-383. PubMed ID: 20144761

Capitanio, J.S., Montpetit, B. and Wozniak, R.W. (2017). Human Nup98 regulates the localization and activity of DExH/D-box helicase DHX9. Elife [Epub ahead of print]. PubMed ID: 28221134

Chen, J., Huang, S. and Chen, Z. (2010). Human cellular protein nucleoporin hNup98 interacts with influenza A virus NS2/nuclear export protein and overexpression of its GLFG repeat domain can inhibit virus propagation. J Gen Virol 91: 2474-2484. PubMed ID: 20554795

Enninga, J., Levy, D. E., Blobel, G. and Fontoura, B. M. (2002). Role of nucleoporin induction in releasing an mRNA nuclear export block. Science 295: 1523-1525. PubMed ID: 11809937

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Biological Overview

date revised: 12 September 2022

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