Nucleoporin downregulation modulates keratinocyte differentiation independent of nuclear pore numbers
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE209655 | GEO | 2023/10/06
REPOSITORIES: GEO
Similar Datasets
Project description:Nucleoporins (NUPs) comprise nuclear pore complexes, gateways for nucleocytoplasmic transport. As primary human keratinocytes switch from the progenitor state towards differentiation, most NUPs are strongly downregulated, with NUP93 being the most downregulated NUP in this process. To determine if this NUP downregulation is accompanied by a reduction in nuclear pore numbers, we leveraged Stochastic Optical Reconstruction Microscopy. No significant changes in nuclear pore numbers were detected using three independent NUP antibodies; however, NUP reduction in other subcellular compartments such as the cytoplasm was identified. To investigate how NUP reduction influences keratinocyte differentiation, we knocked down NUP93 in keratinocytes in the progenitor-state culture condition. NUP93 knockdown diminished keratinocytes' clonogenicity and epidermal regenerative capacity, without drastically affecting nuclear pore numbers or permeability. Using transcriptome profiling, we identified that NUP93 knockdown induces differentiation genes related to both mechanical and immune barrier functions, including the activation of known NF-κB target genes. Consistently, keratinocytes with NUP93 knockdown exhibited increased nuclear localization of the NF-κB p65/p50 transcription factors, and increased NF-κB reporter activity. Taken together, these findings highlight the gene regulatory roles contributed by differential NUP expression levels in keratinocyte differentiation, independent of nuclear pore numbers.
| S-EPMC10584948 | biostudies-literature
Project description:Nucleoporin downregulation modulates keratinocyte differentiation independent of nuclear pore numbers
| PRJNA862059 | ENA
Project description:The integrative computational analysis we developed has assigned NUP93 with important roles in progression of mammary cancer, which we confirmed in animals. Surprisingly, NUP93 emerges from these studies as a master driver of metastasis. This conclusion was supported by functional characterization of two groups of naturally occurring mutant alleles. Remarkably, mammary cells overexpressing NUP93 display over-activation of multiple growth factor pathways, including the WNT/beta-catenin pathway. This route has previously been associated with colorectal tumors, but recent network-based analysis linked it to breast cancer (Koval and Katanaev, 2018). We conclude that NUP93 integrates and enhances not only WNT but also additional growth factor signals. Thus, by seizing an essential step common to multiple signaling routes, NUP93 acquires robust oncogenic attributes. Beyond the identification of augmented nuclear transport as a new hallmark of cancer, our study exposes tumor vulnerabilities and offers not only a new target for intervention but also a pharmacological strategy tailored to the subset of NUP93 overexpressors.
2021-12-31 | GSE156103 | GEO
Project description:The organization of the genome in the three-dimensional space of the nucleus is coupled with cell type-specific gene expression. However, how nuclear architecture influences transcription that governs cell identity remains unknown. Here, we show that Nuclear Pore Complex (NPC) components Nup93 and Nup153 bind super-enhancers (SE), regulatory structures that drive the expression of key genes that specify cell identity. We found that nucleoporin-associated SEs localize preferentially to the nuclear periphery, and absence of Nup153 and Nup93 results in dramatic transcriptional changes of SE-associated genes. Our results reveal a crucial role of NPC components in the regulation of cell type specifying genes and highlight nuclear architecture as a regulatory layer of genome functions in cell fate.
2016-11-15 | GSE87831 | GEO
Project description:The central role of nucleoporins is to transport RNA and proteins. In addtion, nucleoporins are also involved in gene regulation. Furthermore, nucleoporins - Nup93, Nup153, Nup98 and Nup210, directly associate with developmental genes and regulate developmental processes by direct association with developmental genes. Here, we identified genome wide binding profile of Nup93 - a core component of the nuclear pore complex in colorectal cancer cell line DLD-1 by ChIP-seq. Our ChIP-seq analysis revealed significant association of Nup93 with developmental genes and known enhancer marks such as H3K4me1 and H3K27Ac . We found that Nup93 shares binding sites with CTCF - the well known chromatin organizer, suggesting a functional overlap between Nup93 and CTCF in the organization and regulation of developmental gene expression such as the the HOXA gene cluster.
2021-12-06 | GSE130656 | GEO
Project description:Interactions between the genome and the nuclear pore complex (NPC) have been implicated in multiple gene regulatory processes, but the underlying logic of these interactions remains poorly defined. Here, we report high-resolution chromatin binding maps of two core components of the NPC, Nup107 and Nup93, which reveal differential binding of these NPC subunits to active genes and Polycomb-covered silent regions, respectively. Comparison to Lamin-associated domains (LADs) revealed that NPC binding sites are often found within LADs, demonstrating a linear binding of the genome along the nuclear envelope. Significantly, we identified a functional role of Nup93 in silencing of Polycomb target genes and in spatial folding of Polycomb domains. Our findings lend to a model where nuclear pores bind different types of chromatin via interactions with specific core sub-complexes of the NPC, and the Nup93 sub-complex functions as a stabilizing scaffold for Polycomb domains.
2020-01-07 | GSE136115 | GEO
Project description:Interactions between the genome and the nuclear pore complex (NPC) have been implicated in multiple gene regulatory processes, but the underlying logic of these interactions remains poorly defined. Here, we report high-resolution chromatin binding maps of two core components of the NPC, Nup107 and Nup93, which reveal differential binding of these NPC subunits to active genes and Polycomb-covered silent regions, respectively. Comparison to Lamin-associated domains (LADs) revealed that NPC binding sites are often found within LADs, demonstrating a linear binding of the genome along the nuclear envelope. Significantly, we identified a functional role of Nup93 in silencing of Polycomb target genes and in spatial folding of Polycomb domains. Our findings lend to a model where nuclear pores bind different types of chromatin via interactions with specific core sub-complexes of the NPC, and the Nup93 sub-complex functions as a stabilizing scaffold for Polycomb domains.
2020-01-07 | GSE135610 | GEO
Project description:Disrupted skin barrier due to altered keratinocyte differentiation is common in pathologic conditions such as atopic dermatitis, ichthyosis and psoriasis. However, the molecular cascades governing keratinocyte terminal differentiation are still poorly understood. We have previously demostrated that a dominante mutation in ZNF750 leads to a clinical phenotype that reminiscent of psoriasis and seborrehic dermatitis. We defined ZNF750 as a nuclear effector that is atrongly activated in and essiential for keratinocyte terminal differentiation. ZNF750 knockdown in HaCaT keratinocytes markedly reduced the expression of epidermal late differentiation markers, including gene subsets of epidermal differentiation complex and skin barrier formation such as FLG, LOR, SPINK5, ALOX12B and DSG1, known to be mutated in various human skin diseases. Furthermore, ZNF750 over-expression in undifferentiated cells induced terminal differentiation genes. Thus, ZNF750 is a regulator of keratinocyte terminal differnetiation, and with its downstream targets can serve in future elucidation of therapeutics for common disease of skin barrier Gene expression analysis: To determine the differentaition signature for HaCaT keratinocytes, with ZNF750 gene silencing, total RNA was isolated in biologic triplicates from cells induced to differentiate for twelve days and hybridized to Affymerix Human Gene 1.0 ST arrays.
2012-09-24 | E-GEOD-38039 | biostudies-arrayexpress
Project description:We performed comprehensive proteome profiling (ECM and cell lysate) of human collagen VII deficient and control epidermal keratinocytes to generate global and detailed images of dysregulated epidermal molecular pathways linked to loss of collagen VII. These revealed downregulation of interaction partners of collagen VII, but also increased abundance of S100 pro-inflammatory proteins and enhanced activity of lysosomal proteases. Thus, loss of a single extracellular structural protein, collagen VII, induced persistent fibrosis enabling inflammatory and tissue destabilizing activities of keratinocytes.
2018-01-16 | PXD005873 | Pride
Project description:The nuclear pore complex (NPC) is one of the largest supramolecular structures in eukaryotic cells. Its octagonal ring-scaffold perforates the nuclear envelope and features a unique molecular machinery that regulates nucleocytoplasmic transport. NPCs are composed of ~30 different nucleoporins (Nups), averaged at 8, 16 or 32 copies per NPC. This estimate has not been confirmed for individual NPCs in living cells due to the inherent difficulty of counting proteins inside single supramolecular complexes. Here we used single-molecule SPEED microscopy to directly count the copy-number of twenty-four different Nups within individual NPCs of live yeast, and found agreement as well as significant deviation from previous estimates. As expected, we counted 8 copies of four peripheral Nups and 16 copies of fourteen scaffold Nups. Unexpectedly, we counted a maximum of 16 copies of Nsp1 and Nic96, rather than 32 as previously estimated; and found only 10-15 copies of six other Nups, rather than 8 or 16 copies as expected. This in situ molecular-counting technology can test structure-function models of NPCs and other supramolecular structures in cells.
| S-EPMC4894440 | biostudies-literature