RNA Gel Mobility Shift Assays Research Articles

RplI interacts with 5' UTR of exsA to repress its translation and type III secretion system in Pseudomonas aeruginosa.

Pseudomonas aeruginosa is an important opportunistic pathogen capable of causing variety of infections in humans. The type III secretion system (T3SS) is a critical virulence determinant of P. aeruginosa in the host infections. Expression of the T3SS is regulated by ExsA, a master regulator that activates the expression of all known T3SS genes. Expression of the exsA gene is controlled at both transcriptional and posttranscriptional levels. Here, we screened a P. aeruginosa transposon (Tn5) insertional mutant library and found rplI, a gene coding for the ribosomal large subunit protein L9, to be a repressor for the T3SS gene expression. Combining real-time quantitative PCR (qPCR), western blotting and lacZ fusion assays, we show that RplI controls the expression of exsA at the posttranscriptional level. Further genetic experiments demonstrated that RplI mediated control of the exsA translation involves 5’ untranslated region (5’ UTR). A ribosome immunoprecipitation assay and qPCR revealed higher amounts of a 24 nt fragment from exsA mRNA being associated with ribosomes in the ΔrplI mutant. An interaction between RplI and exsA mRNA harboring its 24 nt, but not 12 nt, 5’ UTR was confirmed by RNA Gel Mobility Shift and Microscale Thermophoresis assays. Overall, this study identifies the ribosomal large subunit protein L9 as a novel T3SS repressor that inhibits ExsA translation in P. aeruginosa.

Post-Transcriptional Regulation of Endothelial Nitric Oxide Synthase Expression by Polypyrimidine Tract-Binding Protein 1.

Endothelial nitric oxide synthase (eNOS) is an important regulator of vascular function and its expression is regulated at post-transcriptional levels through a yet unknown mechanism. The purpose of this study is to elucidate the post-transcriptional factors regulating eNOS expression and function in endothelium. To elucidate the molecular basis of tumor necrosis factor (TNF)-α-mediated eNOS mRNA instability, biotinylated eNOS 3'-untranslational region (UTR) was used to purify its associated proteins by RNA affinity chromatography from cytosolic fractions of TNF-α-stimulated human umbilical vein endothelial cells (HUVECs). We identified 2 cytosolic proteins, with molecular weight of 52 and 57 kDa, which specifically bind to eNOS 3'-UTR in response to TNF-α stimulation. Matrix-assisted laser desorption ionization time-of-flight mass spectrometric analysis identified the 57-kDa protein as polypyrimidine tract-binding protein 1 (PTB1). RNA gel mobility shift and UV cross-linking assays demonstrated that PTB1 binds to a UCUU-rich sequence in eNOS 3'-UTR, and the C-terminal half of PTB1 is critical to this interaction. Importantly, PTB1 overexpression leads to decreased activity of luciferase gene fused with eNOS 3'-UTR as well as reduced eNOS expression and activity in human ECs. In HUVECs, we show that TNF-α markedly increased PTB1 expression, whereas adenovirus-mediated PTB1 overexpression decreased eNOS mRNA stability and reduced protein expression and endothelium-dependent relaxation. Furthermore, knockdown of PTB1 substantially attenuated TNF-α-induced destabilization of eNOS transcript and downregulation of eNOS expression. These results indicate that PTB1 is essential for regulating eNOS expression at post-transcriptional levels and suggest a novel therapeutic target for treatment of vascular diseases associated with inflammatory endothelial dysfunction.

PDGF-BB enhances monocyte chemoattractant protein-1 mRNA stability in smooth muscle cells by downregulating ribonuclease activity

Platelet-derived growth factor (PDGF) has protean manifestations, including the regulation of growth and migration, in many cell types. We have previously reported that PDGF-BB induces the accumulation of monocyte chemoattractant protein (MCP)-1 mRNA in smooth muscle cells (SMC), in large part due to an increase in mRNA stability. To elucidate the mechanism by which PDGF-BB stabilizes MCP-1 mRNA, we have employed in vitro RNA gel mobility shift and decay assays. Cytoplasmic extracts from PDGF-BB-treated SMC increased the half-life of in vitro transcribed MCP-1 mRNA from ≈45 min to >2 h. PDGF-BB-inhibitable degradation was not dependent on specific regions of the MCP-1 mRNA and was equally effective on a variety of in vitro transcribed mRNAs. Angiotensin II had a similar effect on MCP-1 mRNA stability, whereas tumor necrosis factor-α and basic fibroblast growth factor did not. The PDGF-BB-inhibitable RNAse activity was active at pH 6.6 and heat stable, but was sensitive to proteinase K. Extracts from PDGF-BB- or angiotensin II-treated cells inhibited the RNAse activity of control extracts, suggesting that the effect of PDGF-BB and angiotensin II are due to activation of a soluble inhibitor of the RNAse. The effect of PDGF-BB was blocked by inhibitors of tyrosine phosphorylation, but not by inhibitors of phosphatidylinositol 3-kinase or mitogen-activated protein kinases. These studies provide new insights into the mechanisms by which PDGF-BB enhances mRNA accumulation.

Expression of the SH2D1A gene is regulated by a combination of transcriptional and post-transcriptional mechanisms.

The SH2D1A gene, which is altered or deleted in patients with X-linked lymphoproliferative disease, encodes the small protein SAP (for SLAM-associated protein) that is expressed in T and NK cells. A 22-bp fragment in close proximity to an initiator-like site was defined as the basal promoter of mouse SH2D1A, and a highly homologous 33-bp segment was defined as the human basal promoter. When an Ets consensus site was mutated, no reporter activity was detectable. Gel mobility supershift assays revealed that the two transcription factors Ets-1 and Ets-2 bind to the human and mouse sequences. The involvement of Ets-1 and Ets-2 in expression of SH2D1A was functionally confirmed by overexpression studies of their dominant-negative forms. We also found that SH2D1A mRNA decays very rapidly in mouse T cells, and its 3' untranslated region (UTR) has RNA-destabilizing activity in transfection studies with reporter/3' UTR constructs. As judged by RNA-gel mobility shift assays, this rapid degradation of SH2D1A mRNA was due to a balance in binding of the factors AUF1 and HuR to its 3' UTR. Although the SH2D1A mRNA level decreased upon triggering of the T cell receptor (TCR), the RNA degradation rate itself was not altered by TCR engagement.

Epstein-Barr virus nuclear antigen 1 is a DNA-binding protein with strong RNA-binding activity.

Epstein-Barr virus (EBV) nuclear antigen 1 (EBNA-1) plays key roles in both the regulation of gene expression and the replication of the EBV genome in latently infected cells. To characterize the RNA-binding activity of EBNA-1, it was demonstrated that EBNA-1 binds efficiently to RNA homopolymers that are composed of poly(G) and weakly to those composed of poly(U). All three RGG boxes of EBNA-1 contributed additively to poly(G)-binding activity and could mediate RNA binding when attached to a heterologous protein in an RNA gel mobility-shift assay. In vitro-transcribed EBV and non-EBV RNA probes revealed that EBNA-1 bound to most RNAs examined and the affinity increased as the content of G and U increased, as demonstrated in competition assays. Among these probes, the 5' non-coding region (NCR) (nt 131-278) of hepatitis C virus RNA appeared to be the strongest competitor for EBNA-1 binding to the EBV-encoded small nuclear RNA 1 (EBER1) probe, whereas a mutant 5' NCR RNA with partially disrupted secondary structure was a weak competitor. Furthermore, the interaction of endogenous EBNA-1 and EBER1 in EBV-infected cells was demonstrated by a ribonucleoprotein immunoprecipitation assay. These results revealed that EBNA-1 is a DNA-binding protein with strong binding activity to a relatively broad spectrum of RNA and suggested an additional biological impact of EBNA-1 through its ability to bind to RNA.

Taxol- and okadaic acid-induced destabilization of bcl-2 mRNA is associated with decreased binding of proteins to a bcl-2 instability element

The observation that overexpression of the anti-apoptotic protein Bcl-2 is associated with both cancer development and anti-cancer drug resistance suggests that factors which regulate bcl-2 expression may be important therapeutic targets. We report here that taxol or okadaic acid (OA) treatment of HL-60 cells reduced bcl-2 mRNA steady state levels to 50% of control cell levels in 20–24 hr of treatment. The 3′-untranslated region of bcl-2 mRNA contains four potential A+U-rich elements (AREs), which are associated with mRNA destabilization. RNA gel mobility shift assays revealed that HL-60 cell extracts contain proteins that bind to RNA transcripts containing the first bcl-2 ARE (ARE 1). ARE 1 binding activity was substantially reduced in extracts of cells treated for 20 hr with taxol or OA and was abolished after 32 hr of treatment. UV-induced RNA cross-linking assays revealed that untreated HL-60 cell extracts contain approximately eight proteins, ranging in size from 32 to 100 kDa, that bind to ARE 1 RNA. Following 20 hr of taxol or OA treatment, RNA cross-linking to ∼70 and ∼38 kDa proteins was greatly reduced, and cross-linking to four proteins of 45–60 kDa sizes was progressively reduced with 10–34 hr of OA or taxol treatment. Collectively, these results suggest a novel action of taxol and OA on bcl-2 expression, which involves bcl-2 mRNA downregulation through inactivation of bcl-2 mRNA stabilizing factors.

RNA Gel Shift Assays for Analysis of Hormone Control of mRNA Stability

Publisher Summary This chapter focuses on the regulation of the cytoplasmic stability of specific mRNAs. The level of an mRNA in the cytoplasm represents a balance between the rate at which the mRNA precursor is synthesized in the nucleus and the rates of nuclear RNA processing, and export and cytoplasmic mRNA degradation. While it has long been known that steroid hormones regulate mRNA stability, until the past few years progress in this area was limited by the dearth of information on the general pathways of eukaryotic mRNA degradation, the lack of suitable cell culture models, and the absence of appropriate tools for analyzing mRNA stability and the protein–nucleic acid interactions that control this process. Studies of the hormone regulation of mRNA degradation employ an evolving constellation of technologies. The chapter focuses on the use of RNA gel mobility shift assays to monitor the levels of hormone-regulated mRNA-binding proteins and to study their interactions with specific mRNAs. Hormones regulate the levels of a number of mRNA-binding proteins, and thereby modulate mRNA stability. RNA gel shift assays show that polysome salt extracts from liver cells of estrogen-treated Xenopus exhibit increased binding of vigilin to a crucial segment of the vitellogenin mRNA 3′-untranslated region. The basic principle of DNA and RNA gel mobility shift assays is that polyacrylamide gel electrophoresis is used to separate a labeled nucleic acid probe from the protein–nucleic acid complex.

Translational Regulation of Prostaglandin Endoperoxide H Synthase-1 mRNA in Megakaryocytic MEG-01 Cells: SPECIFIC PROTEIN BINDING TO A CONSERVED 20-NUCLEOTIDE CISELEMENT IN THE 3′-UNTRANSLATED REGION

Prostaglandin endoperoxide H synthase-1 (PGHS-1) is an abundant enzyme in platelets, where it plays a key role in the cascade of prostanoid formation. In platelets, the primary site of PGHS-1 synthesis is in precursor megakaryocytic cells. We have previously shown that in megakaryocytic MEG-01 cells, TPA induces an increase of PGHS-1 mRNA within a few hours, whereas protein increase occurs after several days of treatment. We now report that the delayed increase in PGHS-1 protein is caused by translational regulation. De novo PGHS-1 synthesis, measured using [(35)S]methionine pulse labeling followed by immunoprecipitation, was detected at day 4 after TPA treatment but not at day 1. To identify a potential element of PGHS-1 mRNA controlling translation, we compared the 3'-untranslated region from different species and identified a 20-nt segment perfectly conserved. The 20-nt segment was used as a probe in RNA gel mobility-shift assays using MEG-01 extracts from control cells or from TPA-treated cells. Four complexes were formed with extracts from control cells or cells treated with TPA for 1 day but were not observed with extracts from cells treated for 4 days. Of the 4 complexes, one was sequence-specific and binding involved uridylate residues and interactions with a 45-kDa protein and a protein doublet of 116 kDa. Binding of this 45/116-kDa complex to the 20-nt conserved cis element most likely regulates negatively PGHS-1 protein accumulation. We have provided evidence that the PGHS-1 gene is regulated at the translational level.

Identification of critical amino acid residues on human dihydrofolate reductase protein that mediate RNA recognition.

Previous studies have shown that human dihydrofolate reductase (DHFR) acts as an RNA-binding protein, in which it binds to its own mRNA and, in so doing, results in translational repression. In this study, we used RNA gel mobility shift and nitrocellulose filter-binding assays to further investigate the specificity of the interaction between human DHFR protein and human DHFR mRNA. Site-directed mutagenesis was used to identify the critical amino acid residues on DHFR protein required for RNA recognition. Human His-Tag DHFR protein specifically binds to human DHFR mRNA, while unrelated proteins including thymidylate synthase, p53 and glutathione-S-transferase were unable to form a ribonucleoprotein complex with DHFR mRNA. The Cys6 residue is essential for RNA recognition, as mutation at this amino acid with either an alanine (C6A) or serine (C6S) residue almost completely abrogated RNA-binding activity. Neither one of the cysteine mutant proteins was able to repress the in vitro translation of human DHFR mRNA. Mutations at amino acids Ile7, Arg28 and Phe34, significantly reduced RNA-binding activity. An RNA footprinting analysis identified three different RNA sequences, bound to DHFR protein, ranging in size from 16 to 45 nt, while a UV cross-linking analysis isolated an approximately 16 nt RNA sequence bound to DHFR. These studies begin to identify the critical amino acid residues on human DHFR that mediate RNA binding either through forming direct contact points with RNA or through maintaining the protein in an optimal structure that allows for the critical RNA-binding domain to be accessible.

Fibrillarin binds to a 3 ′cis-regulatory element in pre-mRNA of uvi15+ in fission yeast

uvi 15 + is induced by various stresses including exposure to UV-light. Previously, we demonstrated that the UV-induction is mainly regulated at the post-transcriptional level through a cis-acting element in the pre-mRNA. Here we show that deletion analyses define an 18-nt element responsible for the UV-induction. RNA gel mobility shift assay showed that a specific protein(s) could form a complex with the 54-nt element but its binding ability is moderately decreased in response to UV-light. Using yeast three-hybrid screen, we isolated a homolog of fibrillarin as a protein interacting with the 54-nt element, which is a key nucleolar protein for pre-rRNA processing. We further showed that the recombinant fibrillarin specifically binds to the element in a sequence-specific manner. Thus, the data suggest that fission yeast fibrillarin might regulate uvi 15 + mRNA stability via binding with the 54-nt element in the pre-mRNA, implying that fibrillarin is involved in both pre-mRNA and pre-rRNA processing.

Tumor necrosis factor-alpha induces fibronectin synthesis in coronary artery smooth muscle cells by a nitric oxide-dependent posttranscriptional mechanism.

Postcardiac transplant coronary arteriopathy is associated with tumor necrosis factor-alpha (TNF-alpha) induction of fibronectin-dependent smooth muscle cell (SMC) migration into the subendothelium, resulting in occlusive neointimal formation. Because expression of inducible nitric oxide synthase (iNOS) is elevated in neointimal formation after transplantation and upregulated in vascular SMCs by TNF-alpha, we investigated whether TNF-alpha induction of fibronectin synthesis in coronary artery (CA) SMCs is mediated by nitric oxide (NO). TNF-alpha caused a dose-dependent increase in reactive oxygen and nitrogen intermediates in CA SMCs (P<0.05). This correlated with increased NO production (P<0.05) and fibronectin synthesis (P<0.05). TNF-alpha induction of fibronectin synthesis was abrogated by the NOS inhibitor N(G)-monomethyl-L-arginine (L-NMMA) (P<0.05) or the flavonoid-containing enzyme inhibitor diphenyleneiodonium (DPI) (P<0.05) and reproduced with the NO donor S-nitroso-N-acetyl-penicillamine (SNAP) (P<0.05). Northern blotting showed no effect of TNF-alpha on steady-state fibronectin mRNA levels. TNF-alpha increased expression of light chain 3 (LC-3), a protein shown previously to facilitate fibronectin mRNA translation through its interaction with an adenosine-uracil rich element (ARE) in the 3'-untranslated region of fibronectin mRNA. RNA gel mobility shift and UV cross-linking assays using CA SMC lysates revealed protein binding complexes with radiolabeled oligonucleotide containing the ARE, similar to those generated with recombinant LC-3. One of these complexes increased after TNF-alpha treatment, an effect inhibited with L-NMMA or DPI. These data demonstrate a novel paradigm whereby cytokines regulate mRNA translation of extracellular matrix proteins through NO-dependent modulation of RNA binding protein interaction with mRNA.

Identification of the RNA Binding Domain of T4 RegA Protein by Structure-based Mutagenesis

The T4 translational repressor RegA protein folds into two structural domains, as revealed by the crystal structure (Kang, C.-H. , Chan, R., Berger, I., Lockshin, C., Green, L., Gold, L., and Rich, A. (1995) Science 268, 1170-1173). Domain I of the RegA protein contains a four-stranded beta-sheet and two alpha-helices. Domain II contains a four-stranded beta-sheet and an unusual 3/10 helix. Since beta-sheet residues play a role in a number of protein-RNA interactions, one or both of the beta-sheet regions in RegA protein may be involved in RNA binding. To test this possibility, mutagenesis of residues on both beta-sheets was performed, and the effects on the RNA binding affinities of RegA protein were measured. Additional sites for mutagenesis were selected from molecular modeling of RegA protein. The RNA binding affinities of three purified mutant RegA proteins were evaluated by fluorescence quenching equilibrium binding assays. The activities of the remainder of the mutant proteins were evaluated by quantitative RNA gel mobility shift assays using lysed cell supernatants. The results of this mutagenesis study ruled out the participation of beta-sheet residues. Instead, the RNA binding site was found to be a surface pocket formed by residues on two loops and an alpha-helix. Thus, RegA protein appears to use a unique structural motif in binding RNA, which may be related to its unusual RNA recognition properties.

Specific in vitro association between the hepatitis C viral genome and core protein

Little is known about the molecular interactions required for hepatitis C virion assembly. The 5′ noncoding region (5′NCR) of the RNA genome is highly conserved and has extensive secondary structure. The highly basic core protein is rich in arginine and lysine residues. We postulate that a specific interaction between these structures may be important for virion assembly. Using an RNA gel mobility shift assay, a specific interaction has been demonstrated between the RNA of the 5′NCR and recombinant core protein. Proteins from other regions of the virus do not interact with the viral RNA. The interaction is inhibited competitively by unlabelled sense polarity RNA, but antisense 5′NCR RNA and nonspecific RNAs compete only at much higher concentrations. These data suggest that there is a specific interaction between the 5′NCR of the hepatitis C virus (HCV) genome and HCV core protein. This interaction may be important for the specific encapsidation of the viral genome during HCV replication. J. Med. Virol. 59:131–134, 1999. © 1999 Wiley-Liss, Inc.

Specific in vitro association between the hepatitis C viral genome and core protein

Little is known about the molecular interactions required for hepatitis C virion assembly. The 5' noncoding region (5'NCR) of the RNA genome is highly conserved and has extensive secondary structure. The highly basic core protein is rich in arginine and lysine residues. We postulate that a specific interaction between these structures may be important for virion assembly. Using an RNA gel mobility shift assay, a specific interaction has been demonstrated between the RNA of the 5'NCR and recombinant core protein. Proteins from other regions of the virus do not interact with the viral RNA. The interaction is inhibited competitively by unlabelled sense polarity RNA, but antisense 5'NCR RNA and nonspecific RNAs compete only at much higher concentrations. These data suggest that there is a specific interaction between the 5'NCR of the hepatitis C virus (HCV) genome and HCV core protein. This interaction may be important for the specific encapsidation of the viral genome during HCV replication.

Nitric oxide mediates LC-3-dependent regulation of fibronectin in ductus arteriosus intimal cushion formation.

Ductus arteriosus intimal cushion formation is characterized by fibronectin-dependent smooth muscle cell (SMC) migration. Enhanced fibronectin synthesis in ductus SMC is regulated by the interaction of LC-3, a microtubule-associated protein, with an AU-rich element (ARE) in the 3'-untranslated region of fibronectin mRNA, facilitating its recruitment to polyribosomes for translation. Since nitric oxide (NO) is implicated in posttranscriptional gene regulation and is produced in the ductus, we investigated its mechanistic role in LC-3-mediated fibronectin synthesis. NO production was sevenfold higher in ductus vs. aortic SMC (P<0.005) associated with increased neuronal NO synthase (nNOS) expression. The NOS inhibitor L-NMMA decreased fibronectin synthesis by approximately 45-50% (P<0.05), whereas the NO donor, SNAP, increased ductus fibronectin synthesis approximately onefold (P<0.05); neither agent altered fibronectin mRNA levels. Immunoblotting revealed that SNAP increased and L-NMMA reduced a membrane-associated phosphorylated form of LC-3. RNA gel mobility shift assays confirmed that NO enhanced LC-3 binding to the fibronectin mRNA ARE. Our studies indicate a tissue-specific program in the ductus arteriosus whereby elevated nNOS expression and NO production regulate the posttranscriptional increase in fibronectin synthesis required for SMC motility.

Cytoplasmic proteins interact with a translational control element in the protein-coding region of proopiomelanocortin mRNA.

Previous studies have indicated that proopiomelanocortin (POMC) is translationally regulated. We proposed that the regulatory mechanism involves an interaction between trans-acting protein factors and a cis-acting stem-loop structure in the coding region of POMC mRNA. Functional interactions were tested by examining the translation of mouse POMC mRNA in a rabbit reticulocyte system. Specific binding was demonstrated with ultraviolet-crosslinking and RNA gel mobility shift assays. The evidence presented supports our hypothesis that the translational regulation of POMC gene expression involves recognition of the stem-loop by RNA-binding proteins. Furthermore, POMC stem-loop RNA-binding proteins specifically recognized a predicted stem-loop found in the coding region of corticotropin-releasing hormone, suggesting a novel mechanism of gene regulation that may extend to other neuropeptides as well.

HnRNP C increases amyloid precursor protein (APP) production by stabilizing APP mRNA.

We have previously shown that heterogeneous nuclear ribonucleoprotein C (hnRNP C) and nucleolin bound specifically to a 29 nt sequence in the 3'-untranslated region of amyloid precursor protein (APP) mRNA. Upon activation of peripheral blood mononuclear cells, hnRNP C and nucleolin acquired APP mRNA binding activity, concurrent with APP mRNA stabilization. These data suggested that the regulated interaction of hnRNP C and nucleolin with APP mRNA controlled its stability. Here we have directly examined the role of the cis element and trans factors in the turnover and translation of APP mRNA in vitro . In a rabbit reticulocyte lysate (RRL) translation system, a mutant APP mRNA lacking the 29 nt element was 3-4-fold more stable and synthesized 2-4-fold more APP as wild-type APP mRNA. Therefore, the 29 nt element functioned as an APP mRNA destabilizer. RNA gel mobility shift assays with the RRL suggested the presence of endogenous nucleolin, but failed to show hnRNP C binding activity. However, wild-type APP mRNA was stabilized and coded for 6-fold more APP when translated in an RRL system supplemented with exogenous active hnRNP C. Control mRNAs lacking the 29 nt element were unaffected by hnRNP C supplementation. Therefore, occupancy of the 29 nt element by hnRNP C stabilized APP mRNA and enhanced its translation.

Properties and purification of a glucose-inducible human fatty acid synthase mRNA-binding protein.

Glucose stabilizes the mRNA for human fatty acid synthase (FAS), an enzyme relevant to diverse human disorders, including hyperlipidemia, obesity, and malignancy. To determine the underlying mechanisms, RNA gel mobility shift assays were used to demonstrate that human Hep G2 cells contain a cytoplasmic factor that binds specifically to the 3'-terminus of the human FAS mRNA. D-Glucose increased RNA-binding activity by 2.02-fold (P = 0.0033), with activity peaking 3 h after glucose feeding. Boiling or treatment of extracts with proteinase K abolished binding. Ultraviolet cross-linking of the FAS mRNA-binding factor followed by SDS-PAGE resolved a proteinase K-sensitive band with an apparent molecular mass of 178 +/- 7 kDa. The protein was purified to homogeneity using nondenaturing polyacrylamide gels as an affinity matrix. Acid phosphatase treatment of the protein prevented binding to the FAS mRNA, but binding activity was unaffected by modification of sulfhydryl groups and was not Mg2+ or Ca2+ dependent. Deletion and RNase T1 mapping localized the binding site of the protein to 37 nucleotides characterized by the repetitive motif ACCCC and found within the first 65 bases of the 3'-UTR. Hybridization of the FAS transcript with an oligonucleotide antisense to this sequence abolished binding. These findings indicate that a 178-kDa glucose-inducible phosphoprotein binds to an (ACCCC)n-containing sequence in the 3'-UTR of the FAS mRNA within the same time frame that glucose stabilizes the FAS message. This protein may participate in the posttranscriptional control of FAS gene expression.

Vigilin, a Ubiquitous Protein with 14 K Homology Domains, Is the Estrogen-inducible Vitellogenin mRNA 3′-Untranslated Region-binding Protein

RNA-binding proteins containing KH domains are widely distributed. One KH domain protein of unknown function, vigilin (also known as the high density lipoprotein-binding protein), contains 14 KH domains and is ubiquitous in vertebrate cells. We previously used RNA gel mobility shift assays to describe an estrogen-inducible protein which binds specifically to a segment of the 3'-untranslated region (3'-UTR) of vitellogenin mRNA, an area which has been implicated in the estrogen-mediated stabilization of vitellogenin mRNA. Here we show that the vitellogenin mRNA-binding protein (VitRNABP) is vigilin. The VitRNABP was isolated as a 150-155-kDa protein on a vitellogenin mRNA 3'-UTR affinity column. Peptide microsequencing revealed that the purified protein was vigilin, a conclusion confirmed in Western blot analysis with antibodies to vigilin. Direct confirmation that vigilin is the VitRNABP was obtained from RNA gel mobility shift assays which demonstrated that antibodies to chicken vigilin supershifted the Xenopus VitRNABP band. Xenopus liver vigilin mRNA and the VitRNABP exhibited similar induction by estrogen, providing additional confirmation that vigilin is the estrogen-inducible protein which binds to the 3'-UTR of estrogen-stabilized vitellogenin mRNA. These data support a role for vigilin in the hormonal control of mRNA metabolism.

Differential Activity of ELAV-like RNA-binding Proteins in Human Neuroblastoma

Many short-lived mRNAs contain AU-rich instability elements within their 3'-untranslated region. Cellular factors that bind to these elements are thought to play a role in the regulation of mRNA degradation. In the accompanying paper (Chagnovich, D., and Cohn, S. L. (1996) J. Biol. Chem. 271, 33580-33586) we characterized the binding activity of a 40-kDa protein (p40) that interacts with high specificity with at least two AU-rich elements located within the 3'-untranslated region of N-myc. p40 activity correlates with N-myc mRNA stability in subclones of the NBL-W neuroblastoma cells line (W-N and W-S). In an effort to determine the identity of p40 we performed immunoblotting studies, immunoprecipitation experiments, and RNA gel mobility shift assays using antibodies that are directed against known RNA-binding proteins. In this paper we demonstrate that in W-N and W-S cells, p40 activity parallels the expression of embryonic letal abnormal vision (ELAV)-like proteins, and that antibodies directed against this family of RNA-binding proteins recognize p40. We also show that purified ELAV-like proteins (HuD and Hel-N1) bind with high specificity to the same N-myc 3'-untranslated region sequences as p40. Our data indicate that p40 is a member of the ELAV-like family, and suggest that this family of RNA-binding proteins may regulate N-myc mRNA turnover.