Search

The contribution of lncRNAs to tumour progression and the regulatory mechanisms driving their expression are areas of intense investigation. Here, we characterize the binding of heterogeneous nuclear ribonucleoprotein E1 (hnRNP E1) to a nucleic acid structural element located in exon 12 of PNUTS (also known as PPP1R10) pre-RNA that regulates its alternative splicing. HnRNP E1 release from this structural element, following its silencing, nucleocytoplasmic translocation or in response to TGFβ, allows alternative splicing and generates a non-coding isoform of PNUTS. Functionally the lncRNA-PNUTS serves as a competitive sponge for miR-205 during epithelial-mesenchymal transition (EMT). In mesenchymal breast tumour cells and in breast tumour samples, the expression of lncRNA-PNUTS is elevated and correlates with levels of ZEB mRNAs. Thus, PNUTS is a bifunctional RNA encoding both PNUTS mRNA and lncRNA-PNUTS, each eliciting distinct biological functions. While PNUTS mRNA is ubiquitously expressed, lncRNA-PNUTS appears to be tightly regulated dependent on the status of hnRNP E1 and tumour context.

During late M and early G(1), MCM2-7 assembles and is loaded onto chromatin in the final step of prereplicative complex (pre-RC) formation. However, the regulation of MCM assembly remains poorly understood. Cyclin-dependent kinase (CDK)-dependent phosphorylation contributes to DNA replication by initially activating pre-RCs and subsequently inhibiting refiring of origins during S and M phases, thus limiting DNA replication to a single round. Although the precise roles of specific MCM phosphorylation events are poorly characterized, we now demonstrate that CDK1 phosphorylates MCM3 at Ser-112, Ser-611, and Thr-719. In vivo, CDK1-dependent phosphorylation of Ser-112 triggers the assembly of MCM3 with the remaining MCM subunits and subsequent chromatin loading of MCMs. Strikingly, loss of MCM3 triggers the destabilization of other MCM proteins, suggesting that phosphorylation-dependent assembly is essential for stable accumulation of MCM proteins. These data reveal that CDK-dependent MCM3 phosphorylation contributes to the regulated formation of the MCM2-7 complex.

The Nrf2 transcription factor promotes survival following cellular insults that trigger oxidative damage. Nrf2 activity is opposed by the BTB/POZ domain protein Keap1. Keap1 is proposed to regulate Nrf2 activity strictly through its capacity to inhibit Nrf2 nuclear import. Recent work suggests that inhibition of Nrf2 may also depend upon ubiquitin-mediated proteolysis. To address the contribution of Keap1-dependent sequestration versus Nrf2 proteolysis, we identified the E3 ligase that regulates Nrf2 ubiquitination. We demonstrate that Keap1 is not solely a cytosolic anchor; rather, Keap1 is an adaptor that bridges Nrf2 to Cul3. We demonstrate that Cul3-Keap1 complexes regulate Nrf2 polyubiquitination both in vitro and in vivo. Inhibition of either Keap1 or Cul3 increases Nrf2 nuclear accumulation, leading to promiscuous activation of Nrf2-dependent gene expression. Our data demonstrate that Keap1 restrains Nrf2 activity via its capacity to target Nrf2 to a cytoplasmic Cul3-based E3 ligase and suggest a model in which Keap1 coordinately regulates both Nrf2 accumulation and access to target genes.

The accumulation of unfolded proteins elicits a cellular response that triggers both pro-survival and pro-apoptotic signaling events. PERK-dependent activation of NF-E2-related factor-2 (Nrf2) is critical for survival signaling during this response; however, the mechanism whereby Nrf2 confers a protective advantage to stressed cells remains to be defined. We now demonstrate that Nrf2 activation contributes to the maintenance of glutathione levels, which in turn functions as a buffer for the accumulation of reactive oxygen species during the unfolded protein response. The deleterious effects of Nrf2 or PERK deficiencies could be attenuated by the restoration of cellular glutathione levels or Nrf2 activity. In addition, the inhibition of reactive oxygen species production attenuated apoptotic induction following endoplasmic reticulum stress. Our data suggest that perturbations in cellular redox status sensitize cells to the harmful effects of endoplasmic reticulum stress, but that other factors are essential for apoptotic commitment.

Activation of PERK following the accumulation of unfolded proteins in the endoplasmic reticulum (ER) promotes translation inhibition and cell cycle arrest. PERK function is essential for cell survival following exposure of cells to ER stress, but the mechanisms whereby PERK signaling promotes cell survival are not thoroughly understood. We have identified the Nrf2 transcription factor as a novel PERK substrate. In unstressed cells, Nrf2 is maintained in the cytoplasm via association with Keap1. PERK-dependent phosphorylation triggers dissociation of Nrf2/Keap1 complexes and inhibits reassociation of Nrf2/Keap1 complexes in vitro. Activation of PERK via agents that trigger the unfolded protein response is both necessary and sufficient for dissociation of cytoplasmic Nrf2/Keap1 and subsequent Nrf2 nuclear import. Finally, we demonstrate that cells harboring a targeted deletion of Nrf2 exhibit increased cell death relative to wild-type counterparts following exposure to ER stress. Our data demonstrate that Nrf2 is a critical effector of PERK-mediated cell survival.

Transcription factor GATA-1 is essential for erythroid and megakaryocytic maturation. GATA-1 mutations are associated with hematopoietic precursor proliferation and leukemogenesis, suggesting a role in cell cycle control. While numerous GATA-1 target genes specifying mature hematopoietic phenotypes have been identified, how GATA-1 regulates proliferation remains unknown. We used a complementation assay based on synchronous inducible rescue of GATA-1(-) erythroblasts to show that GATA-1 promotes both erythroid maturation and G(1) cell cycle arrest. Molecular studies combined with microarray transcriptome analysis revealed an extensive GATA-1-regulated program of cell cycle control in which numerous growth inhibitors were upregulated and mitogenic genes were repressed. GATA-1 inhibited expression of cyclin-dependent kinase (Cdk) 6 and cyclin D2 and induced the Cdk inhibitors p18(INK4C) and p27(Kip1) with associated inactivation of all G(1) Cdks. These effects were dependent on GATA-1-mediated repression of the c-myc (Myc) proto-oncogene. GATA-1 inhibited Myc expression within 3 h, and chromatin immunoprecipitation studies indicated that GATA-1 occupies the Myc promoter in vivo, suggesting a direct mechanism for gene repression. Surprisingly, enforced expression of Myc prevented GATA-1-induced cell cycle arrest but had minimal effects on erythroid maturation. Our results illustrate how GATA-1, a lineage-determining transcription factor, coordinates proliferation arrest with cellular maturation through distinct, interrelated genetic programs.

The capacity of the cyclin D-dependent kinase to promote G(1) progression through modulation of RB.E2F is well documented. We now demonstrate that the cyclin D1/CDK4 kinase binds to components of the MCM complex. MCM7 and MCM3 were identified as cyclin D1-binding proteins. Catalytically active cyclin D1/CDK4 complexes were incorporated into chromatin-bound protein complexes with the same kinetics as MCM7 and MCM3, where they associated specifically with MCM7. Although the cyclin D1-dependent kinase did not phosphorylate MCM7, active cyclin D1/CDK4, but not cyclin E/CDK2, did catalyze the dissociation of an RB.MCM7 complex. Finally, expression of an active D1/CDK4 kinase but not cyclin E/CDK2 promoted the removal of RB from chromatin-bound protein complexes. Our data suggest that D1/CDK4 complexes play a direct role in altering an inhibitory RB.MCM7 complex possibly allowing for setting of the origin in preparation for DNA replication.

I kappa B-alpha inhibits both DNA-binding and nuclear translocation of dimeric Rel complexes that contain either the RelA or c-Rel proteins. These inhibitory functions of I kappa B-alpha proteins are regulated by both constitutive and inducible phosphorylation. We have mapped the constitutive phosphorylation sites of p40, the avian I kappa B-alpha protein, to a C-terminal acidic serine-rich region that contains four serine residues. Deletions or point mutations that significantly alter the overall negatively charged character of this region abolish association of p40 with Rel proteins in vitro. Serine-to-alanine amino acid substitutions in this region modulate the association of p40 with Rel proteins in vitro and abolish p40-mediated inhibition of DNA-binding by c-Rel. Substitution of aspartic acid residues for the phosphorylated serine residues has no effect on p40-mediated inhibition of DNA-binding. In contrast, the C-terminal acidic serine-rich region is not required for p40-mediated inhibition of nuclear translocation of Rel proteins. Our results demonstrate that p40-mediated inhibition of nuclear translocation and inhibition of DNA-binding by Rel proteins are separable functions. Our results suggest that the phosphorylation status of C-terminal serine residues of I kappa B-alpha proteins will be an important aspect of the autoregulatory feedback loop that enforces temporal control of Rel-regulated gene expression.

Rel proteins are important intracellular mediators of cytokine-induced signal transduction. To understand how cytokines affect different cell populations in the brain, we have characterized Rel activation in astrocytes. A RelA homodimer is uniquely activated in cytokine-stimulated astrocytes. Cytokine-dependent phosphorylation of the RelA inhibitor MAD-3 occurred on discrete peptides prior to its dissociation from RelA. A transient hyperphosphorylation of RelA was also induced. Antioxidant treatment inhibited both RelA activation and phosphorylation of the RelA.MAD-3 complex. These results demonstrate that cytokine-dependent activation of the RelA homodimer involves phosphorylation of both RelA and its associated inhibitor. The sole activation of a RelA homodimer suggests that cytokines will activate a unique set of Rel-regulated genes in astrocytes.

Protein-protein interactions between the CCAAT box enhancer-binding proteins (C/EBP) and the Rel family of transcription factors have been implicated in the regulation of cytokine gene expression. We have used sequence-specific DNA affinity chromatography to purify a complex from avian T cells that binds to a consensus C/EBP motif. Our results provide evidence that Rel-related proteins are components of the C/EBP-DNA complex as a result of protein-protein interactions with the C/EBP proteins. A polyclonal antiserum raised against the Rel homology domain of v-Rel and antisera raised against two human RelA-derived peptides specifically induced a supershift of the C/EBP-DNA complex in mobility shift assays using the affinity-purified C/EBP. In addition, several kappa B-binding proteins copurified with the avian C/EBP complex through two rounds of sequence-specific DNA affinity chromatography. The kappa B-binding proteins are distinct from the C/EBP proteins that directly contact DNA containing the C/EBP binding site. The identification of a protein complex that binds specifically to a consensus C/EBP site and contains both C/EBP and Rel family members suggests a novel mechanism for regulation of gene expression by Rel family proteins.

Regulation of gene expression by members of the NF-kappa B/rel transcription factor family is a central component of signal transduction pathways utilized by many cellular processes, including lymphocyte activation, embryonic development, and oncogenesis. The members of the NF-kappa B/rel transcription factor family are regulated by association with a family of inhibitor (I kappa B) proteins (I kappa B) proteins. To address the importance of the association between rel and I kappa B proteins for oncogenesis by rel proteins, we characterized rel-I kappa B interactions in chicken embryo fibroblasts (CEF) infected with retroviral vectors encoding the avian c-rel (p68c-rel), v-rel (p59v-rel), and I kappa B-beta (pp40I kappa B-beta) proteins. In these experiments, the p59v-rel:pp40I kappa B-beta ratio in coinfected CEF was nearly identical to the p59v-rel:pp40I kappa B-beta ratio in v-rel-transformed cells. The avian I kappa B-beta protein, pp40I kappa B-beta, was able to associate with both the nononcogenic p68c-rel and the oncogenic p59v-rel. Association of p68c-rel with pp40I kappa B-beta in coinfected CEF resulted in inhibition of the DNA-binding activity of p68c-rel. Anti-pp40I kappa B-beta serum was able to restore DNA binding to p68c-rel in the presence of high levels of pp40I kappa B-beta, indicating that pp40I kappa B-beta functions in a trans-acting manner to inhibit DNA binding by p68c-rel. In contrast, sequence-specific DNA binding by the oncogenic v-rel protein, p59v-rel, was not abolished by pp40I kappa B-beta in coinfected CEF. Anti-pp40I kappa B-beta serum did not immunoprecipitate the p59v-rel-DNA adduct or alter the electrophoretic mobility of the p59v-rel-DNA adduct, consistent with the idea that pp40I kappa B-beta and DNA are competitive inhibitors for the same or overlapping domains on rel proteins. Internal v-rel-derived sequences were identified that are responsible for loss of pp40I kappa B-beta-mediated inhibition of DNA binding by p59v-rel. Loss of pp40I kappa B-beta-mediated inhibition of DNA binding by recombinant v/c-rel proteins was not sufficient for oncogenic activation of c-rel. Instead, removal of C-terminal c-rel-derived sequences in addition to loss of pp40I kappa B-beta-mediated inhibition of DNA binding was required for oncogenic activation of c-rel. These results demonstrate the presence of an interaction between internal and C-terminal regions of the c-rel protein that is important for the ability of c-rel to regulate the proliferation of lymphoid cells.