Promoter-associated small double-stranded RNA interacts with heterogeneous nuclear ribonucleoprotein A2/B1 to induce transcriptional activation

2012 ◽  
Vol 447 (3) ◽  
pp. 407-416 ◽  
Author(s):  
Jia Hu ◽  
Zhong Chen ◽  
Ding Xia ◽  
Jia Wu ◽  
Hua Xu ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
Transcriptional Activation ◽  
Mammalian Cells ◽  
Kinase Inhibitor ◽  
Suppressor Gene ◽  
Tumour Suppressor Gene ◽  
Double Stranded Rna ◽  
P21 Promoter

Several recent reports have demonstrated that small activating dsRNA [double-stranded RNA; saRNA (small activating dsRNA)] complementary to promoter regions can up-regulate gene expression in mammalian cells, a phenomenon termed RNAa (RNA activation). However, the mechanism of RNAa remains obscure with regard to what is the target molecule for promoter-targeted saRNA and what are the proteins involved in this process. p21Waf1/Cip1 (p21) [CDKN1A (cyclin-dependent kinase inhibitor 1A)], an important tumour suppressor gene, is among the genes that can be activated by RNAa in tumour cells. In the present study, we provide direct evidence that p21 promoter-targeted saRNA interact with its intended target on the p21 promoter to activate p21 expression. This process is associated with recruitment of RNA polymerase II and AGO2 (argonaute 2) protein to the saRNA-target site. Additionally, we found that several hnRNPs (heterogeneous nuclear ribonucleoproteins) (A1, A2/B1 and C1/C2) are associated with saRNA. Further studies show that hnRNPA2/B1 interacts with the saRNA in vivo and in vitro and is required for RNAa activity. These findings indicate that RNAa results from specific targeting of promoters and reveals additional mechanistic details of RNAa.

scholarly journals Autophosphorylation sites participate in the activation of the double-stranded-RNA-activated protein kinase PKR.

1996 ◽  
Vol 16 (11) ◽  
pp. 6295-6302 ◽  
Author(s):  
D R Taylor ◽  
S B Lee ◽  
P R Romano ◽  
D R Marshak ◽  
A G Hinnebusch ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Mammalian Cells ◽  
Rna Binding ◽  
Initiation Factor ◽  
Double Stranded Rna ◽  
Catalytic Domains ◽  
Dependent Protein ◽  
Mutant Kinase

The interferon-induced RNA-dependent protein kinase PKR is found in cells in a latent state. In response to the binding of double-stranded RNA, the enzyme becomes activated and autophosphorylated on several serine and threonine residues. Consequently, it has been postulated that autophosphorylation is a prerequisite for activation of the kinase. We report the identification of PKR sites that are autophosphorylated in vitro concomitantly with activation and examine their roles in the activation of PKR. Mutation of one site, threonine 258, results in a kinase that is less efficient in autophosphorylation and in phosphorylating its substrate, the initiation factor eIF2, in vitro. The mutant kinase is also impaired in vivo, displaying reduced ability to inhibit protein synthesis in yeast and mammalian cells and to induce a slow-growth phenotype in Saccharomyces cerevisiae. Mutations at two neighboring sites, serine 242 and threonine 255, exacerbated the effect. Taken together with earlier results (S. B. Lee, S. R. Green, M. B. Mathews, and M. Esteban, Proc. Natl. Acad. Sci. USA 91:10551-10555, 1994), these data suggest that the central part of the PKR molecule, lying between its RNA-binding and catalytic domains, regulates kinase activity via autophosphorylation.

scholarly journals Yeast NC2 Associates with the RNA Polymerase II Preinitiation Complex and Selectively Affects Transcription In Vivo

2001 ◽  
Vol 21 (8) ◽  
pp. 2736-2742 ◽  
Author(s):  
Joseph V. Geisberg ◽  
Frank C. Holstege ◽  
Richard A. Young ◽  
Kevin Struhl
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcriptional Activation ◽  
Negative Regulator ◽  
Preinitiation Complex ◽  
Positive Role ◽  
Pol Ii ◽  
Basal Transcription Factors

ABSTRACT NC2 (Dr1-Drap1 or Bur6-Ydr1) has been characterized in vitro as a general negative regulator of RNA polymerase II (Pol II) transcription that interacts with TATA-binding protein (TBP) and inhibits its function. Here, we show that NC2 associates with promoters in vivo in a manner that correlates with transcriptional activity and with occupancy by basal transcription factors. NC2 rapidly associates with promoters in response to transcriptional activation, and it remains associated under conditions in which transcription is blocked after assembly of the Pol II preinitiation complex. NC2 positively and negatively affects approximately 17% of Saccharomyces cerevisiaegenes in a pattern that resembles the response to general environmental stress. Relative to TBP, NC2 occupancy is high at promoters where NC2 is positively required for normal levels of transcription. Thus, NC2 is associated with the Pol II preinitiation complex, and it can play a direct and positive role at certain promoters in vivo.

scholarly journals The Gcn4p Activation Domain Interacts Specifically In Vitro with RNA Polymerase II Holoenzyme, TFIID, and the Adap-Gcn5p Coactivator Complex

1998 ◽  
Vol 18 (3) ◽  
pp. 1711-1724 ◽  
Author(s):  
Connie M. Drysdale ◽  
Belinda M. Jackson ◽  
Richard McVeigh ◽  
Edward R. Klebanow ◽  
Yu Bai ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
Transcriptional Activation ◽  
Adapter Proteins ◽  
Activation Domain ◽  
Hydrophobic Residues ◽  
Cell Extracts ◽  
Tata Box Binding Protein ◽  
Rna Polymerase Ii Holoenzyme

ABSTRACT The Gcn4p activation domain contains seven clusters of hydrophobic residues that make additive contributions to transcriptional activation in vivo. We observed efficient binding of a glutathioneS-transferase (GST)–Gcn4p fusion protein to components of three different coactivator complexes in Saccharomyces cerevisiae cell extracts, including subunits of transcription factor IID (TFIID) (yeast TAFII20 [yTAFII20], yTAFII60, and yTAFII90), the holoenzyme mediator (Srb2p, Srb4p, and Srb7p), and the Adap-Gcn5p complex (Ada2p and Ada3p). The binding to these coactivator subunits was completely dependent on the hydrophobic clusters in the Gcn4p activation domain. Alanine substitutions in single clusters led to moderate reductions in binding, double-cluster substitutions generally led to greater reductions in binding than the corresponding single-cluster mutations, and mutations in four or more clusters reduced binding to all of the coactivator proteins to background levels. The additive effects of these mutations on binding of coactivator proteins correlated with their cumulative effects on transcriptional activation by Gcn4p in vivo, particularly with Ada3p, suggesting that recruitment of these coactivator complexes to the promoter is a cardinal function of the Gcn4p activation domain. As judged by immunoprecipitation analysis, components of the mediator were not associated with constituents of TFIID and Adap-Gcn5p in the extracts, implying that GST-Gcn4p interacted with the mediator independently of these other coactivators. Unexpectedly, a proportion of Ada2p coimmunoprecipitated with yTAFII90, and the yTAFII20, -60, and -90 proteins were coimmunoprecipitated with Ada3p, revealing a stable interaction between components of TFIID and the Adap-Gcn5p complex. Because GST-Gcn4p did not bind specifically to highly purified TFIID, Gcn4p may interact with TFIID via the Adap-Gcn5p complex or some other adapter proteins. The ability of Gcn4p to interact with several distinct coactivator complexes that are physically and genetically linked to TATA box-binding protein can provide an explanation for the observation that yTAFII proteins are dispensable for activation by Gcn4p in vivo.

scholarly journals The Anti-apoptotic Function of Hsp70 in the Interferon-inducible Double-stranded RNA-dependent Protein Kinase-mediated Death Signaling Pathway Requires the Fanconi Anemia Protein, FANCC

2002 ◽  
Vol 277 (51) ◽  
pp. 49638-49643 ◽  
Author(s):  
Qishen Pang ◽  
Tracy A. Christianson ◽  
Winifred Keeble ◽  
Tara Koretsky ◽  
Grover C. Bagby
Keyword(s):  
Protein Kinase ◽  
Fanconi Anemia ◽  
Mammalian Cells ◽  
Physical Interaction ◽  
Dependent Protein Kinase ◽  
Double Stranded Rna ◽  
Multimeric Complex ◽  
Dependent Protein

Proteins encoded by five of the six known Fanconi anemia (FA) genes form a heteromeric complex that facilitates repair of DNA damage induced by cross-linking agents. A certain number of these proteins, notably FANCC, also function independently to modulate apoptotic signaling, at least in part, by suppressing ground state activation of the pro-apoptotic interferon-inducible double-stranded RNA-dependent protein kinase (PKR). Because certain FANCC mutations interdict its anti-apoptotic function without interfering with the capacity of FANCC to participate functionally in the FA multimeric complex, we suspected that FANCC enhances cell survival independent of its participation in the complex. By investigating this function in both mammalian cells and in yeast, an organism with no FA orthologs, we show that FANCC inhibited the kinase activity of PKR bothin vivoandin vitro, and this effect depended upon a physical interaction between FANCC and Hsp70 but not on interactions of FANCC with other Fanconi proteins. Hsp70, FANCC, and PKR form a ternary complex in lymphoblasts and in yeast expressing PKR. We conclude that Hsp70 requires the cooperation of FANCC to suppress PKR activity and support survival of hematopoietic cells and that FANCC does not require the multimeric FA complex to exert this function.

CLL Tumours with a Deletion of 11q Form Two Functional Subgroups Based on the Mutation Status of the Remaining ATM Allele.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 710-710
Author(s):  
Belinda Austen ◽  
Maria Podinovskaia ◽  
Claire Almond ◽  
Graham Fews ◽  
Anne Gardiner ◽  
...  
Keyword(s):  
Dna Damage ◽  
Suppressor Gene ◽  
Tumour Suppressor Gene ◽  
Fish Analysis ◽  
Wild Type ◽  
Atm Gene ◽  
Atm Protein ◽  
11Q Deletion

Abstract Deletions in chromosome 11q are an established prognostic marker in CLL. One copy of the ATM gene is deleted in these tumours, as detected by FISH analysis. However, it remains unclear whether the ATM gene is the main tumour suppressor gene that is accounting for the poor outcome in tumours with 11q deletions. We have recently reported that patients whose tumours have mutations in the ATM gene have an impaired overall and treatment free survival. In our large cohort of 155 patients, tumours with an ATM mutation only partly correlated with tumours with an 11q deletion. We have therefore investigated the relationship between 11q deletions and mutations in the ATM gene. Using the highly sensitive DHPLC method, we have screened the 60 ATM coding exons for mutations in a cohort of 46 tumours, all with a deletion of chromosome 11q. We have found ATM mutations in 19 tumours, indicating a prevalence of 41%. The ATM protein is vital in the cell’s response to DNA damage including that induced by chemotherapy. ATM acts upstream from p53 and defects in ATM function, like p53, lead to impaired DNA damage induced apoptosis. Furthermore, we have previously shown that loss of ATM function is associated with both in vitro and in vivo chemo-resistance. Therefore, we next assessed whether the status of the remaining ATM allele in the 11q deleted tumours affected the response to DNA damage. Firstly we induced DNA damage with irradiation and measured both the phosphorylation of ATM protein targets and the induction of p53 dependent transcription responses in representative samples. We found that 11q deleted tumours with a remaining wild type ATM allele had responses that were similar to those seen in tumours with two wild type ATM alleles. In contrast, 11q deleted tumours with a mutation in the remaining ATM allele had defective DNA damage induced responses. We then analysed the effects of in vitro treatment with Fludarabine. First we demonstrated that fludarabine induces ATM dependent phophosphorylation responses in CLL tumours. Then we analysed its effect in the two 11q deleted CLL subgroups. We showed defective phosphorylation responses to fludarabine in the tumours with a mutation in the second ATM allele, but normal responses in those with a second wild type ATM allele. In summary, we have shown that approximately 40% of CLL tumours with an 11q deletion have a mutation in their remaining ATM allele. Furthermore, we have demonstrated that the 11q deleted tumours appear to form two functional subgroups based on the presence of a mutation in the remaining ATM allele. In contrast to the subgroup with a wild type ATM allele, CLL tumours with a mutant ATM allele have defective in vitro responses to DNA damage with both irradiation and fludarabine. We expect that the functional differences between the two 11q deleted subsets will translate into differences in clinical outcome.

scholarly journals Low GAS5 expression may predict poor survival and cisplatin resistance in cervical cancer

2020 ◽  
Vol 11 (7) ◽  
Author(s):  
Xingyu Fang ◽  
Guanglei Zhong ◽  
Yuhan Wang ◽  
Zhongqiu Lin ◽  
Rongchun Lin ◽  
...  
Keyword(s):  
Cervical Cancer ◽  
Animal Studies ◽  
Cisplatin Resistance ◽  
Suppressor Gene ◽  
Tumour Suppressor Gene ◽  
Luciferase Reporter ◽  
Poor Overall Survival ◽  
Cisplatin Sensitivity

Abstract Cisplatin resistance is a major challenge in cervical cancer (CC) chemotherapy. Growth arrest‐specific 5 (GAS5) has been reported to be a tumour suppressor gene in CC. However, the mechanism of GAS5 in chemoresistance remains undetermined. Our research evaluated GAS5 expression in normal and CC tissues by qPCR and in situ hybridization (ISH). Statistical analysis was conducted to analyse the association of GAS5 expression with survival. Biochemical methods were used to screen upstream and downstream regulators of GAS5. Then, interactions were confirmed by ChIP, RNA pull-down, RNA immunoprecipitation (RIP), dual-luciferase reporter and real-time PCR assays. The cisplatin sensitivity of GAS5-overexpressing CC cells was demonstrated in vitro and in vivo. The results showed that low GAS5 expression was correlated with poor overall survival. Mechanistically, GAS5 was transcriptionally modulated by P-STAT3 and served as a competing endogenous RNA (ceRNA) of miR-21 to indirectly affect cisplatin sensitivity through PDCD4 regulation in CC cells. Animal studies confirmed that GAS5 enhanced cisplatin sensitivity and promoted PDCD4 expression in vivo. GAS5 was regulated by P-STAT3 and affected the sensitivity of CC to cisplatin-based chemotherapy through the miR-21/PDCD4 axis. This result may provide new insight into cisplatin-based therapy.

scholarly journals In vivo binding of NF-κB to the IκBβ promoter is insufficient for transcriptional activation

2006 ◽  
Vol 400 (1) ◽  
pp. 115-125 ◽  
Author(s):  
Bryan D. Griffin ◽  
Paul N. Moynagh
Keyword(s):  
Gene Regulation ◽  
Transcription Factor ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcriptional Activation ◽  
Nuclear Factor Κb ◽  
Transcriptional Initiation ◽  
Il Interleukin

Despite certain structural and biochemical similarities, differences exist in the function of the NF-κB (nuclear factor κB) inhibitory proteins IκBα (inhibitory κBα) and IκBβ. The functional disparity arises in part from variance at the level of gene regulation, and in particular from the substantial induction of IκBα, but not IκBβ, gene expression post-NF-κB activation. In the present study, we probe the differential effects of IL (interleukin)-1β on induction of IκBα and perform the first characterization of the human IκBβ promoter. A consensus NF-κB-binding site, capable of binding NF-κB both in vitro and in vivo, is found in the IκBβ gene 5′ flanking region. However, the IκBβ promoter was not substantially activated by pro-inflammatory cytokines, such as IL-1β and tumour necrosis factor α, that are known to cause strong activation of NF-κB. Furthermore, in contrast with IκBα, NF-κB activation did not increase expression of endogenous IκBβ as assessed by analysis of mRNA and protein levels. Unlike κB-responsive promoters, IκBβ promoter-bound p65 inefficiently recruits RNA polymerase II, which stalls at the promoter. We present evidence that this stalling is likely due to the absence of transcription factor IIH engagement, a prerequisite for RNA polymerase II phosphorylation and transcriptional initiation. Differences in the conformation of promoter-bound NF-κB may underlie the variation in the ability to engage the basal transcriptional apparatus at the IκBβ and κB-responsive promoters. This accounts for the differential expression of IκB family members in response to NF-κB activation and furthers our understanding of the mechanisms involved in transcription factor activity and IκBβ gene regulation.

scholarly journals Epigenetic silencing of the XAF1 gene is mediated by the loss of CTCF binding

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Georgina Victoria-Acosta ◽  
Karla Vazquez-Santillan ◽  
Luis Jimenez-Hernandez ◽  
Laura Muñoz-Galindo ◽  
Vilma Maldonado ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Cell Cycle Progression ◽  
Molecular Mechanisms ◽  
Suppressor Gene ◽  
Tumour Suppressor Gene ◽  
Epigenetic Silencing ◽  
Ctcf Binding ◽  
Open Chromatin ◽  
Cpg Dinucleotide

Abstract XAF1 is a tumour suppressor gene that compromises cell viability by modulating different cellular events such as mitosis, cell cycle progression and apoptosis. In cancer, the XAF1 gene is commonly silenced by CpG-dinucleotide hypermethylation of its promoter. DNA demethylating agents induce transcriptional reactivation of XAF1, sensitizing cancer cells to therapy. The molecular mechanisms that mediate promoter CpG methylation have not been previously studied. Here, we demonstrate that CTCF interacts with the XAF1 promoter in vivo in a methylation-sensitive manner. By transgene assays, we demonstrate that CTCF mediates the open-chromatin configuration of the XAF1 promoter, inhibiting both CpG-dinucleotide methylation and repressive histone posttranslational modifications. In addition, the absence of CTCF in the XAF1 promoter inhibits transcriptional activation induced by well-known apoptosis activators. We report for the first time that epigenetic silencing of the XAF1 gene is a consequence of the loss of CTCF binding.

scholarly journals TFIIS Enhances Transcriptional Elongation through an Artificial Arrest Site In Vivo

2001 ◽  
Vol 21 (13) ◽  
pp. 4162-4168 ◽  
Author(s):  
Dmitry Kulish ◽  
Kevin Struhl
Keyword(s):  
Rna Polymerase Ii ◽  
Transcriptional Activation ◽  
Chromatin Immunoprecipitation ◽  
Transcriptional Analysis ◽  
Transcriptional Elongation ◽  
Specific Assay ◽  
Physical Evidence ◽  
Reduced Temperature

ABSTRACT Transcriptional elongation by RNA polymerase II has been well studied in vitro, but understanding of this process in vivo has been limited by the lack of a direct and specific assay. Here, we designed a specific assay for transcriptional elongation in vivo that involves an artificial arrest (ARTAR) site designed from a thermodynamic theory of DNA-dependent transcriptional arrest in vitro. Transcriptional analysis and chromatin immunoprecipitation experiments indicate that the ARTAR site can arrest Pol II in vivo at a position far from the promoter. TFIIS can counteract this arrest, thereby demonstrating that it possesses transcriptional antiarrest activity in vivo. Unexpectedly, the ARTAR site does not function under conditions of high transcriptional activation unless cells are exposed to conditions (6-azauracil or reduced temperature) that are presumed to affect elongation in vivo. Conversely, TFIIS affects gene expression under conditions of high, but not low, transcriptional activation. Our results provide physical evidence for the discontinuity of transcription elongation in vivo, and they suggest that the functional importance of transcriptional arrest sites and TFIIS is strongly influenced by the level of transcriptional activation.

scholarly journals Adenovirus E1B 55K Represses p53 Activation In Vitro

1998 ◽  
Vol 72 (4) ◽  
pp. 3146-3154 ◽  
Author(s):  
Michelle E. D. Martin ◽  
Arnold J. Berk
Keyword(s):  
Rna Polymerase Ii ◽  
Transcriptional Activation ◽  
Expression System ◽  
Gel Filtration ◽  
Velocity Sedimentation ◽  
Nuclear Extracts ◽  
P53 Activation ◽  
Adenovirus E1b

ABSTRACT Adenovirus E1B 55K protein cooperates with E1A gene products to induce cell transformation. E1B 55K mediates its effects by binding to and inhibiting the transcriptional activation and growth-suppression functions of the tumor suppressor p53. Previous studies in vivo have suggested that E1B 55K has an active role in repressing p53 transcriptional activation and that this repression function is directed to specific promoters through E1B 55K’s interaction with DNA-bound p53. Flag-tagged E1B 55K (e55K) was expressed with the baculovirus expression system and immunopurified. Gel filtration, velocity sedimentation centrifugation, and glutaraldehyde cross-linking indicated that e55K is a dimer with a nonglobular conformation. e55K bound directly to purified p53, causing an ∼10-fold increase in p53 affinity for tandem binding sites. Using in vitro transcription assays reconstituted with purified p53, e55K, and HeLa cell nuclear extracts, we found that e55K specifically repressed p53 activation. These results demonstrate that as postulated from earlier transient expression experiments, E1B 55K is a specific repressor of transcription from a promoter with bound p53. Since HeLa nuclear extracts contain little detectable histone protein, E1B 55K probably represses transcription through direct or indirect interactions with the RNA polymerase II transcription machinery.

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