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Original Article The transcription factor Nrf2 might be involved in the process of renal aging

Original Article The transcription factor Nrf2 might be involved in the process of renal aging

of p16 and SA-β-gal increased, whereas the expression of Nrf2 decreased, in the old gr- oup. We showed the importance of SFN-in- duced Nrf2 expression in protection against renal aging. This was also reflected by the sig- nificant reductions in serum urea nitrogen, the urine protein/urine creatinine ratio, and the increase in kidney weight/body weight. In vitro, as the SFN intervention time was extended, the expression of p16 decreased, whereas the expression of Nrf2 increased, in the old re- nal residential cells. Additionally, SFN-induced Nrf2 expression could reduce renal oxidative damage and inflammation both in vivo and in vitro. This evidence suggests that Nrf2 is in- volved in renal aging and that high expression of Nrf2 may inhibit renal aging.
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Nuclear transcription factor Nrf2 suppresses prostate cancer cells growth and migration through upregulating ferroportin

Nuclear transcription factor Nrf2 suppresses prostate cancer cells growth and migration through upregulating ferroportin

The PCR product of the FPN and Nrf2 was constructed in the vector pEGFPC1. SiRNAs for FPN and Nrf2 were designed and synthesized by Guangzhou RiboBio. Plasmids and SiRNAs transfection were performed using Lipofectamine 2000 according to the manufacturer’s instructions (Invitrogen, MA, USA). After 24 hours of incubation, the transfected cells were collected for analysis of mRNA and protein expression. In total, samples were divided into 6 groups: a blank group (cells with no transfection), a vector-NC group (vector negative control, cells transfected with empty vector), a pEGFPC1-FPN group (cells transfected with pEGFPC1-FPN), a Si-Nrf2-group (cells transfected with Nrf2 siRNA), a pEGFPC1-Nrf2 group (cells transfected with pEGFPC1-Nrf2) and a pEGFPC1-Nrf2+Si-FPNgroup (cells transfected with pEGFPC1-Nrf2 and FPN siRNA).
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Transcription factor NRF2 regulates miR 1 and miR 206 to drive tumorigenesis

Transcription factor NRF2 regulates miR 1 and miR 206 to drive tumorigenesis

identified a strong NRF2 binding site at the TALDO1 locus (<1 kb from the TSS), within an intron (2, 49). However, NRF2 binding to the G6PD and PGD loci was not validated in the human lymphoblastoid cell line (49). Last, the NRF2 binding site in the human and murine TKT loci was located at greater than 14 kb upstream of the TSS, suggesting that PPP genes (G6PD, TKT, and PGD) are not direct transcriptional targets of NRF2 (2, 49). Remarkably, we found that PPP activity is regu- lated by miRNAs miR-1 and miR-206, and that NRF2 upregu- lates the expression of PPP enzymes by attenuating the expres- sion of these 2 miRNA species. Investigators in previous studies identified several mechanisms for the cellular regulation of these miRNA species, including epigenetic regulation of miR-1 in lung, prostate, and hepatocellular carcinoma and regulation of miR-206 by nuclear transcription factors, including nuclear receptor subfamily 0, group B member 2, estrogen-related recep- tor γ, yin-yang 1, and activator protein 1 (37, 50). It has been reported that miR-1 expression is downregulated in different types of cancers, including lung, prostate, colon, and hepatocel- lular carcinoma, highlighting its oncosuppressive function. The expression of miR-206 is downregulated in breast cancer (51, 52). In this study, we show that NRF2-dependent miRs, miR-1, and miR-206 play important roles in glucose metabolism by modulating the expression of key rate-limiting enzymes of the PPP, and ectopic expression of miR-1 and miR-206 precursor miRNAs in cancer cells result in reprogramming toward a less malignant phenotype. Since miR-1 and miR-206 affect PPP activity in the opposite manner, it is evident that miR-1 and miR-206 and NRF2 function are reciprocally regulated.
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Role of the redox responsive transcription factor, NRF2 in immune cell function

Role of the redox responsive transcription factor, NRF2 in immune cell function

168 antigenic context. Finally in this study, we highlighted that loss of Nrf2 in LPS- activated DCs resulted in lowered TNFα and IL-12 production. However, we found no differences in IL-2 secretion between Nrf2 +/+ and Nrf2 -/- DCs upon LPS stimulation. This suggests that Nrf2 deficiency induces a lowered Th1 cytokine profile within a DC-mediated Th1 polarising context (Agrawal et al., 2003). Therefore during a bacterial infection, it could be said that Nrf2 deficient DCs may secrete less TNFα and IL-12, resulting in a diminished capacity to prime neighbouring DCs to induce Th1 responses, leading to a reduction in clearance of infection. From a tolerance perspective, it has been previously shown that TNFα- producing iDCs induce the differentiation of antigen-specific CD4 + IL-10-producing regulatory T cells which are known to dampen inappropriate immune responses (Hirata et al., 2010). Therefore, as the Nrf2 deficient iDCs secrete less TNFα, it may be the case that these DCs fail to induce the differentiation of such regulatory T cells, resulting in a diminution of T cell tolerance. Previous studies have demonstrated that under an allergic environment known to induce Th2 responses, Nrf2 DCs exhibited an altered Th1/Th2 cytokine profile skewed towards the Th2 phenotype (Williams et al., 2008; Rangasamy et al., 2010). This highlights a pivotal role for Nrf2 in the regulation of DC Th1/Th2 cytokine production. To further assess the role of Nrf2 in Th1/Th2 differentiation, it would be worthwhile to examine the consequences of this altered DC cytokine secretion on antigen-specific CD4 effector T cell function through the utilisation of OT-II transgenic mouse (Williams et al., 2008). Within this model, the CD4 T cells exclusively express TCR specific for ovalbumin peptide (OVA 323-339 ) (Williams et al., 2008; Hirata et al., 2010). The
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12/15 lipoxygenase–mediated enzymatic lipid oxidation regulates DC maturation and function

12/15 lipoxygenase–mediated enzymatic lipid oxidation regulates DC maturation and function

DCs are able to undergo rapid maturation, which subsequently allows them to initiate and orchestrate T cell–driven immune responses. DC maturation must be tightly controlled in order to avoid random T cell activation and development of autoimmunity. Here, we determined that 12/15-lipoxygenase–meditated (12/15-LO–mediated) enzymatic lipid oxidation regulates DC activation and fine-tunes consecutive T cell responses. Specifically, 12/15-LO activity determined the DC activation threshold via generation of phospholipid oxidation products that induced an antioxidative response dependent on the transcription factor NRF2. Deletion of the 12/15-LO–encoding gene or pharmacologic inhibition of 12/15-LO in murine or human DCs accelerated maturation and shifted the cytokine profile, thereby favoring the differentiation of Th17 cells. Exposure of 12/15-LO–deficient DCs to 12/15-LO–derived oxidized phospholipids attenuated both DC activation and the development of Th17 cells. Analysis of lymphatic tissues from 12/15-LO–deficient mice confirmed enhanced maturation of DCs as well as an increased differentiation of Th17 cells. Moreover, experimental autoimmune
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<p>Transcription factor <em>Nrf2</em> induces the up-regulation of lncRNA <em>TUG1</em> to promote progression and adriamycin resistance in urothelial carcinoma of the bladder</p>

<p>Transcription factor <em>Nrf2</em> induces the up-regulation of lncRNA <em>TUG1</em> to promote progression and adriamycin resistance in urothelial carcinoma of the bladder</p>

and enhanced chemosensitivity through inhibiting enhan- cer of zeste homolog 2/SRY (sex determining region Y)-box 2 axis in BCSCs. 13 Taurine-upregulated gene 1 (TUG1), located at chromosome 22q12, was identi fi ed as an onco- gene in tumorigenesis and was responsible for chemoresistance. 14,15 Previous studies in UCB identi fi ed TUG1 associated with UCB progression. High expression of TUG1 has been documented to be correlated with enhanced UCB cell proliferation and matastasis. 16 Additionally, ADM-resistant acute myeloid leukemia tis- sues and HL60/ADR cells have been shown to express high levels of TUG1, and its knockdown facilitated the sensitivity of HL60/ADR cells to ADM by epigenetically promoting miR-34a expression. 17 A previous paper reported that TUG1 was responsible for the ADM resis- tance of bladder urothelial carcinoma. 18 However, the upstream regulatory mechanism of TUG1-mediated pro- gression and ADM resistance in UCB remains unknown. As the key transcription factor, Nrf2 has been demon- strated to control lncRNA expression in erythroid cells and mammary stem cells. 19,20 Therefore, we speculated that Nrf2-mediated up-regulation of lncRNA TUG1 was crucial to the progression and ADM resistance in urothe- lial carcinoma of the bladder.
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A Horizontally Acquired Transcription Factor Coordinates Salmonella Adaptations to Host Microenvironments

A Horizontally Acquired Transcription Factor Coordinates Salmonella Adaptations to Host Microenvironments

IMPORTANCE Expression of T3SSs typically requires a transcription factor that is linked in a genomic island. Studies of the targets of HilA and SsrB have focused on almost exclusively on T3SS substrates that are either linked or encoded in distinct genomic islands. By broadening our focus, we found that the regulon of SsrB extended considerably beyond T3SS-2 and its substrates, while that of HilA did not. That at least two SsrB-regulated processes streamline existence in the intracellular niche afforded by T3SS-2 seems to be a predictable outcome of evolution and natural selection. However, and importantly, these are the first such functions to be implicated as being SsrB dependent. The concept of T3SS-associated transcription factors coordinating manipu- lations of host cells together with distinct bacterial processes for increased efficiency has unrealized implications for numerous host-pathogen systems.
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Human induced pluripotent stem cell differentiation and direct transdifferentiation into corneal epithelial-like cells

Human induced pluripotent stem cell differentiation and direct transdifferentiation into corneal epithelial-like cells

trideca-1(9),11-dien-8-yl}methyl carbamate; an anticancer drug; Nanog – nanog homeobox, a DNA binding homeobox transcription factor involved in embryonic stem cells (ES) proliferation, reneval and pluripotency; Oct4 – octamer-binding transcription factor 4, Pax6 – paired box gene 6; PBS – phosphate-buffered saline; PCT – lentiviral cocktail containing ΔNp63, C/EBPδ and TCF4 lentiviruses; PCTK – lentiviral cocktail containing PCT plus Klf4; PCTO – lentiviral cocktail containing PCT plus Oct4; PCTOK – lentiviral cocktail containing PCT plus Oct4 and Klf4; PEI – polyethylenimine; PFA – paraformaldehyde; PVDF filters – polyvinylidene fluoride filters; quantitative RT-PCR – real time quantitative reverse transcription polymerase chain reaction; RT-PCR – reverse transcription polymerase chain reaction; Sox2 – transcription factor, also known as SRY –box2 (sex determining region Y)- box 2; TCF4 – transcription factor 4 (immunoglobulin transcription factor 2; ITF-2); ΔNp63α – unique C-termini α isoform of tumor protein p63.
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Genetic analysis of the adenovirus E4 6/7 trans activator: interaction with E2F and induction of a stable DNA-protein complex are critical for activity.

Genetic analysis of the adenovirus E4 6/7 trans activator: interaction with E2F and induction of a stable DNA-protein complex are critical for activity.

DISCUSSION The cellular E2F transcription factor is a critical component of the functional transcription complex that drives adenovirus E2 transcription and is a target for trans activat[r]

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Herpesvirus Saimiri STP-A Oncoprotein Utilizes Src Family Protein Tyrosine Kinase and Tumor Necrosis Factor Receptor-Associated Factors To Elicit Cellular Signal Transduction

Herpesvirus Saimiri STP-A Oncoprotein Utilizes Src Family Protein Tyrosine Kinase and Tumor Necrosis Factor Receptor-Associated Factors To Elicit Cellular Signal Transduction

Src interaction, and the D1 mutant, which is defective in Stat3 interaction, showed diminished levels of Stat3 transcriptional activation, whereas the STP-A YF/D1 mutant, defective in both Stat3 and Src interactions, showed little or no activation of Stat3 transcription activity (9). This indicates that STP-A functions as an adaptor to link Src kinase and the Stat3 tran- scription factor: STP-A recruits Stat3 in the vicinity of Src kinase to allow Stat3 tyrosine phosphorylation and, thereby, its subsequent transcriptional activation. Here we also found that while Fyn and Lck phosphorylated STP-A as strongly as did Src, only Fyn, not Lck, interacted with STP-A as effectively as Src kinase. Furthermore, STP-A interaction likely increased their kinase activities, since STP-A expression enhanced over- all cellular tyrosine phosphorylation when coexpressed with Src or Fyn kinase but not with Lck kinase. Consistently, Src and Fyn coexpression markedly increased STP-A-mediated AP-1 and NF-AT activities, whereas Lck coexpression did so only marginally, indicating the direct correlation between the enhancement of overall tyrosine phosphorylation and the in- crease of AP-1 and NF-AT activities. This suggests that STP-A functions not only as an adaptor to link Src kinase and the Stat3 transcription factor, leading to Stat3 transcription acti- vation, but also as an activator to increase Src and Fyn kinase activities, resulting in AP-1 and NF-AT transcription activa- tion. It is intriguing that the HVS subgroup A oncoprotein STP-A interacts only weakly with Lck, which is a major T-cell non-receptor tyrosine kinase. Besides STP-C, HVS subgroup C carries an additional ORF encoding Tip at the same locus as that encoding STP-A of HVS subgroup A. STP-C interacts with TRAFs but not with tyrosine kinase. Instead, the Tip protein interacts strongly with Lck but only marginally with Fyn, showing a reverse correlation between STP-A and Tip in the repertoire of cellular tyrosine kinase
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Tamoxifen activates Nrf2-dependent SQSTM1 transcription to promote endometrial hyperplasia

Tamoxifen activates Nrf2-dependent SQSTM1 transcription to promote endometrial hyperplasia

SQSTM1/p62 (Sequestosome 1), is an autophagy-related adaptor protein to mediate the degradation of ubiquitinated cargo, via its LC3 interacting region (LIR) and C terminal ubiquitin association (UBA) domain [10-12]. In addition, it can interact with KEAP1 (Kelch-like ECH-Associated protein 1) to disrupt Keap1-Nrf2 interaction, thus stabilizing Nrf2 (nuclear factor erythroid 2-related factor 2, NFE2L2) to trigger the antioxidant response [13, 14]. SQSTM1 can also interact with many other signaling molecules such as TRAF-6 (TNF receptor-associated factor 6) [15, 16] and Raptor [17, 18], leading to the activation of NFκB and mTORC1 (mammalian target of rapamycin complex 1) pathway, respectively. As a proof-of-principle, SQSTM1 was highly expressed to promote the pathogenesis of many tumors. For example, autophagy deficiency promoted tumorigenesis by activating NFκB and Nrf2 signaling in a SQSTM1 dependent manner [19-21]. SQSTM1 expression can also be induced by oncogenic Ras signaling to sustain active NFκB signaling in lung adenocarcinoma and pancreatic ductal adenocarcinoma [22, 23]. Yin Yang 1 (YY1) inhibited miR372 transcription to elevate SQSTM1 expression in breast cancer [24]. Moreover, SQSTM1 can be activated by phosphorylation at serine 351 in hepatocellular carcinoma [25]. However, it remains unknown whether SQSTM1 is relevant to TAM-induced endometrial carcinogenesis.
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Early response genes induced in chondrocytes stimulated with the inflammatory cytokine interleukin 1beta

Early response genes induced in chondrocytes stimulated with the inflammatory cytokine interleukin 1beta

appropriate model for primary chondrocytes in OA [11,20–22]. Second, the amount of total RNA required for microarray analysis precludes the use of primary human chondrocytes for these studies. Third, the inherent genetic variation in primary human chondrocyte cultures could bias the gene expression profile and lead to erroneous conclusions. We found increased expression of a large cohort of transcription factors, cytokines, growth factors, and signaling intermediate genes that are potential regula- tors of metalloproteinase gene expression, proliferation, and sustained inflammation. Alternatively, this was accom- panied by a decrease in a modest number of genes also belonging to these categories, suggesting that IL-1β sub- stantially reprograms gene expression in chondrocytes. A subset of these IL-1β-stimulated genes was then con- firmed by semiquantitative reverse transcriptase poly- merase chain reaction (RT-PCR). This characterization of IL-1β-induced immediate early genes in chondrocytic cells identifies candidate mediators of the expression of colla- genase genes in arthritis.
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The Transcription Factor FoxK Participates with Nup98 To Regulate Antiviral Gene Expression

The Transcription Factor FoxK Participates with Nup98 To Regulate Antiviral Gene Expression

ABSTRACT Upon infection, pathogen recognition leads to a rapidly activated gene expression program that induces antimicro- bial effectors to clear the invader. We recently found that Nup98 regulates the expression of a subset of rapidly activated antiviral genes to restrict disparate RNA virus infections in Drosophila by promoting RNA polymerase occupancy at the promoters of these antiviral genes. How Nup98 specifically targets these loci was unclear; however, it is known that Nup98 participates with transcription factors to regulate developmental-gene activation. We reasoned that additional transcription factors may facilitate the Nup98-dependent expression of antiviral genes. In a genome-wide RNA interference (RNAi) screen, we identified a relatively understudied forkhead transcription factor, FoxK, as active against Sindbis virus (SINV) in Drosophila. Here we find that FoxK is active against the panel of viruses that are restricted by Nup98, including SINV and vesicular stomatitis virus (VSV). Mecha- nistically, we show that FoxK coordinately regulates the Nup98-dependent expression of antiviral genes. Depletion of FoxK sig- nificantly 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. We extended our studies to mammalian cells and found that the mammalian ortholog FOXK1 is antiviral against two disparate RNA viruses, SINV and VSV, in human cells. Interestingly, FOXK1 also plays a role in the expression of antiviral genes in mam- mals: depletion of FOXK1 attenuates virus-inducible interferon-stimulated response element (ISRE) reporter expression. Over- all, our results demonstrate a novel role for FOXK1 in regulating the expression of antiviral genes, from insects to humans.
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Temporal Hierarchy of Gene Expression Mediated by Transcription Factor Binding Affinity and Activation Dynamics

Temporal Hierarchy of Gene Expression Mediated by Transcription Factor Binding Affinity and Activation Dynamics

ABSTRACT Understanding cellular responses to environmental stimuli requires not only the knowledge of specific regulatory components but also the quantitative characterization of the magnitude and timing of regulatory events. The two-component system is one of the major prokaryotic signaling schemes and is the focus of extensive interest in quantitative modeling and in- vestigation of signaling dynamics. Here we report how the binding affinity of the PhoB two-component response regulator (RR) to target promoters impacts the level and timing of expression of PhoB-regulated genes. Information content has often been used to assess the degree of conservation for transcription factor (TF)-binding sites. We show that increasing the information content of PhoB-binding sites in designed phoA promoters increased the binding affinity and that the binding affinity and con- centration of phosphorylated PhoB (PhoB~P) together dictate the level and timing of expression of phoA promoter variants. For various PhoB-regulated promoters with distinct promoter architectures, expression levels appear not to be correlated with TF- binding affinities, in contrast to the intuitive and oversimplified assumption that promoters with higher affinity for a TF tend to have higher expression levels. However, the expression timing of the core set of PhoB-regulated genes correlates well with the binding affinity of PhoB~P to individual promoters and the temporal hierarchy of gene expression appears to be re- lated to the function of gene products during the phosphate starvation response. Modulation of the information content and binding affinity of TF-binding sites may be a common strategy for temporal programming of the expression profile of RR-regulated genes.
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Curcumin targets the TFEB-lysosome pathway for induction of autophagy

Curcumin targets the TFEB-lysosome pathway for induction of autophagy

activation of mTOR, indicating that Curcumin-mediated lysosomal activation is achieved via suppression of mTOR. Third, Curcumin treatment activates transcription factor EB (TFEB), a key nuclear transcription factor in control of autophagy and lysosome biogenesis and function, based on the following observations: (i) Curcumin directly binds to TFEB, (ii) Curcumin promotes TFEB nuclear translocation; and (iii) Curcumin increases transcriptional activity of TFEB. Finally, inhibition of autophagy and lysosome leads to more cell death in Curcumin-treated HCT116 cells, suggesting that autophagy and lysosomal activation serves as a cell survival mechanism to protect against Curcumin-mediated cell death. Taken together, data from our study provide a novel insight into the regulatory mechanisms of Curcumin on autophagy and lysosome, which may facilitate the development of Curcumin as a potential cancer therapeutic agent.
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Ch. 11 Cell Communication Notes.ppt

Ch. 11 Cell Communication Notes.ppt

Figure 11.15 Growth factor Receptor Reception Transduction CYTOPLASM Response Inactive transcription factor Active transcription factor DNA NUCLEUS mRNA Gene Phosphorylation cascade P.. [r]

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Viral delivery of antioxidant genes as a therapeutic strategy in experimental models of amyotrophic lateral sclerosis.

Viral delivery of antioxidant genes as a therapeutic strategy in experimental models of amyotrophic lateral sclerosis.

mice (Charles River Laboratories, Wilmington, MA) for >10 generations. A priori power analysis showed that 15 animals per group was a sufficient sample size to detect a medium effect with an 80% power. Transgenic mice (genotyped according to the Jackson Laboratory protocols) were recruited in subgroups of four (one mouse per group; (i) no treatment, (ii) AAV6-GFP, (iii) AAV6-PRDX3, and (iv) AAV6-NRF2), and they were age-matched and if possible, litter-matched. A total volume of 120 μl of viral vector solution was injected intramuscularly per mouse (30 days of age ± 1 day) in various muscle groups (facial muscles, 20 μl; tongue, 10 μl; intercostal muscles, 15 μl; diaphragm, 15 μl; hind limbs, 60 μl) using isoflurane anesthesia. Multiple injection sites were used per muscle group with a maximum of 5 μl solution per site administered slowly using a 10 μl 33-Gauge Hamilton syringe (ESS Laboratory, Cranston, RI). Behavioral assessment and all in vivo tests were carried out blinded to treatment. All mice were weighed and scored twice per week until they reached 140 days of age, and from that point onwards they were weighed and scored daily. Rotarod tests were performed twice per week (2 trials per test, only best score was recorded). The rotarod was set to accelerate from 4 to 40 rpm (rotations per minute) in 300 seconds, and the latency to fall was recorded in seconds. The maximum time showing no motor impairment was
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Transcription factor FoxM1 is the downstream target of c Myc and contributes to the development of prostate cancer

Transcription factor FoxM1 is the downstream target of c Myc and contributes to the development of prostate cancer

c-Myc, a member of the MYC gene family, is involved in regulating a lot of biological activities [15]. From now on, c- Myc has been found overexpressed in colon cancer, breast cancer, lung cancer, and prostate cancer [16–19]. It is a bidirectional regulatory gene in promoting cell proliferation and inducing cell apoptosis. c-Myc could promote prolifera- tive ability of cells in the stimulation of hematopoietic growth factor. In the absence of hematopoietic growth factor, c-Myc could mediate apoptosis. c-Myc gene also belongs to the apoptosis regulatory gene [20]. In addition, c-Myc could also regulate cell cycle and cell metabolism [21]. In the quiescent cells, the expression level of c-Myc is very low. It accumulates as the initial response gene and maintains at high level throughout the cell cycle when stimulated with growth factors. Once the expression level of c-Myc is out of control, it can lead to tumorigenesis. c-Myc regulates its target genes by directly binding or recruiting histone modification enzyme to the gene’s promoter region [22, 23]. The predicted c-Myc binding sites in FoxM1’s promoter suggested its regulatory role for FoxM1 expression.
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The significance of alternative transcripts for Caenorhabditis elegans transcription factor genes, based on expression pattern analysis

The significance of alternative transcripts for Caenorhabditis elegans transcription factor genes, based on expression pattern analysis

For several other transcription factor genes examined, at least one of the promoters defined by a unique starting exon also appeared to drive expression in the same pattern as the gene in its entirety. For both atf-7 and nhr-46, there are two promoters defined by unique starting exons, the most upstream of each looking dislocated from the rest of what are otherwise compact genes. Nevertheless, when gfp was inserted into either of the unique starting exons for atf-7, the same, strong, very broad specificity, reporter expression pattern, peaking in the L1 stage, was observed (WBIDs Expr9790/9808). For nhr-46, gfp inserted after the transcript a specific start codon, in the proximal of the two unique exons, gave the same expression pattern as when gfp was inserted before the termination codon common to all transcripts; again a broad distribution but peaking this time in the L2 stage (WBIDs Expr9816/9835). For ztf-26 and egl-13, gfp inserted after the initiation codon of the a transcripts, in the more distal unique exon, gave apparently the same reporter expression as when gfp was inserted before the shared termination codon of each gene. While the expression of ztf-26 was broad, including nerve cells, hypodermis and muscle peaking in the L4 stage (WBID Expr9838), that for egl-13 was more restricted, limited to a few nerve cells in the head and tail, and weakly in body wall muscle, but through all postembryonic stages (WBIDs Expr9735/9745). Again, the Promoterome fragment for egl-13 transcript a [17] drove the same but much stronger reporter expression with detectable GFP production in vulval muscle as well as body wall muscle (WBID Expr7672). The recombineered reporter gene fusion to assay egl-13 transcript d, however, gave weak but clear expression in the region of the developing gonad, probably the developing vulval muscle (WBID Expr9746). The impression given is that promoters for egl-13 transcripts a and d both drive expression in the same cells, but with different strengths in different places, the very weak expression from promoter d being detectable in the developing vulva but not elsewhere, with the assay performed. For ztf-26 the recombineered reporter gene fusion for the second promoter, that for transcript b, reveals a subtle distinction in promoter activity that may be more temporal rather than spatial, with GFP expression peaking in the L1 stage (WBID Expr9844).
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When is a transcription factor a NAP?

When is a transcription factor a NAP?

Finally, although FIS (the Factor for Inversion Stimula- tion) is viewed as a NAP, it can function as a conventional transcription factor by recruiting RNA polymerase via protein-protein contacts to initiate transcription [19]. These examples show the challenge in identifying clear distinctions between NAPs and transcription factors. This distinction becomes even more blurred because NAPs are sometimes equivalent to functional domains within transcription factors: NtrC is a prominent example. NtrC is the response regulator partner of the cytosolic NtrB sensor kinase and it activates transcription at s 54 -dependent pro- moters in response to nitrogen stress [20]. These interactions require NtrC to bind to a well-defined enhancer sequence upstream of the target promoter. The DNA-binding domain of NtrC is closely related to the NAP FIS, leading to the proposal, supported by phylogenetic evidence, that FIS evolved from an NtrC-like transcription factor [21]. The fis gene probably arrived in E. coli at the same time as dusB (formerly yhdG ), with which it now forms a dusB-fis operon. The DusB protein is related to NifR3 in Rhodobacter , Rhizobium and the nifR3 gene is co-transcribed in those bacteria with ntrB and ntrC . It has been proposed that dusB/yhdG and fis evolved following horizontal gene transfer of the nifR3 ntrB ntrC nitrogen metabolism operon followed by deletion of all but the fis sequences from ntrC [21]. Here we consider the case of BldC, a recently characterized DNA-binding protein from the Gram-positive bacterium Streptomyces . Streptomycetes are filamentous bacteria that differentiate by producing spore-bearing reproductive structures called aerial hyphae [22,23]. The transition from vegetative to reproductive growth is controlled by the bld (bald) loci, which were identified in classical mutagenic screens. Mutations in bld genes prevent the formation of aerial hyphae, either by blocking entry into development (typically mutations in activators) or by inducing precocious sporulation in the vegetative mycelium (typically mutations in repressors) [24–26]. One of the classic bld genes, bldC , encodes a 68-residue DNA-binding protein related to the DNA-binding domain of MerR-family transcription factors. Recent transcriptional, biochemical and structural analyses have revealed the effect of BldC on global gene expression, how it binds DNA, its wider relationship to previously characterized transcription factors and NAPs, and the diverse modes of DNA binding found among BldC-related proteins. These observations raise further interesting questions about the distinction between NAPs and tran- scription factors, and the evolution of one from the other.
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