Structure and genomic organization of the human AUF1 gene: alternative pre-mRNA splicing generates four protein isoforms

Androgen regulates the level and subcellular distribution of the AU-rich ribonucleic acid-binding protein HuR both in vitro and in vivo

HuR, a member of the ELAV family of AU-rich RNA-binding proteins, is present in a variety of tissues and is directly involved in stabilizing labile AU-rich messenger RNAS: We have found that treating the human HepG2 cell line with 10 nM dihydrotestosterone (DHT) for 48 h decreases the total level of HuR by 75%. DHT decreases both cytosolic and nuclear HuR levels in HepG2 cells, but increases HuR levels in polyribosomes by 325%. In BALB/c mice, HuR levels in the submaxillary salivary gland (SMG) and the kidney display a dramatic sexual dimorphism, but those in the spleen and thyroid do not. DHT (200 microg) causes total HuR levels in female SMG and kidney to fall progressively, whereas, conversely, orchiectomy of males causes HuR levels to rise in these two tissues by 800% and 200%, respectively. As an internal control we probed the same blots for AUF1, a destabilizing AU-binding protein, and confirmed our previous findings showing that the cytosolic p37 isoform of AUF1 shows the opposite responses of cytosolic HuR in the SMG, and that the level of AUF1 in the kidney does not respond to DHT. In polyribosomes from female mouse SMG, HuR levels doubled after 6 h of DHT, but decreased by 80% after 24- and 48-h DHT treatment. Thus, the total level of HuR is regulated in two different androgen-responsive systems, as is the shuttling of HuR between different subcellular compartments. As AUF1 is responsive to androgen in the mouse SMG, but not in the kidney, tissue-specific posttranscriptional regulation of AU-rich messenger RNA metabolism could be mediated in part by differential androgen-dependent regulation of HuR and AUF1.

The cap-to-tail guide to mRNA turnover

The levels of cellular messenger RNA transcripts can be regulated by controlling the rate at which the mRNA decays. Because decay rates affect the expression of specific genes, they provide a cell with flexibility in effecting rapid change. Moreover, many clinically relevant mRNAs--including several encoding cytokines, growth factors and proto-oncogenes--are regulated by differential RNA stability. But what are the sequence elements and factors that control the half-lives of mRNAs?

Folding of A+U-rich RNA elements modulates AUF1 binding. Potential roles in regulation of mRNA turnover

In mammals, A+U-rich elements (AREs) are potent cis-acting determinants of rapid cytoplasmic mRNA turnover. Recognition of these sequences by AUF1 is associated with acceleration of mRNA decay, likely involving recruitment or assembly of multi-subunit trans-acting complexes. Previously, we demonstrated that AUF1 deletion mutants formed tetramers on U-rich RNA substrates by sequential addition of protein dimers (Wilson, G. M., Sun, Y., Lu, H., and Brewer, G. (1999) J. Biol. Chem. 274, 33374-33381). Here, we show that binding of the full-length p37 isoform of AUF1 to these RNAs proceeds via a similar mechanism, allowing delineation of equilibrium binding constants for both stages of tetramer assembly. However, association of AUF1 with the ARE from tumor necrosis factor (TNFalpha) mRNA was significantly inhibited by magnesium ions. Further fluorescence and hydrodynamic experiments indicated that Mg(2+) induced or stabilized a conformational change in the TNFalpha ARE. Based on the solution of parameters describing both the protein-RNA and Mg(2+)-RNA equilibria, we present a dynamic, global equilibrium binding model describing the relationship between Mg(2+) and AUF1 binding to the TNFalpha ARE. These studies provide the first evidence that some AREs may adopt higher order RNA structures that regulate their interaction with trans-acting factors and indicate that mRNA structural remodeling has the potential to modulate the turnover rates of some ARE-containing mRNAs.

Synchronous and regulated expression of two AU-binding proteins, AUF1 and HuR, throughout murine development

The AUF1 (hnRNPD) and HuR (ELAV-like) proteins, potential trans-acting factors for regulated mRNA decay, bind in vitro to A+U-rich elements (AREs) found in the 3' untranslated region (3' UTR) of many labile transcripts. In an effort to determine whether these trans-acting factors are likely to play a role in embryogenesis, we have analysed their expression during mouse development both at the mRNA and protein levels. We show that AUF1 and HuR are expressed at all the developmental stages analysed from day 8.5 of embryonic development to adulthood. Expression levels are dynamic, varying between tissues and developmental stages. However, a strong positive correlation between AUF1 and HuR protein levels was observed in all examined tissues. Finally, we compared AUF1 and HuR expression with accumulation of one common target mRNA, c-myc. The similar spatio-temporal distribution of these proteins and of c-myc mRNA is in agreement with a potential concerted role in ARE-mediated control of mRNA stability.

Down-regulation of cyclin D1 expression by prostaglandin A(2) is mediated by enhanced cyclin D1 mRNA turnover

Prostaglandin A(2) (PGA(2)), an experimental chemotherapeutic agent, causes growth arrest associated with decreased cyclin D1 expression in several cancer cell lines. Here, using human non-small-cell lung carcinoma H1299 cells, we investigated the mechanisms whereby PGA(2) down-regulates cyclin D1 expression. Transcription rates of the cyclin D1 gene, studied using a cyclin D1 promoter-luciferase construct and nuclear run-on assays, were not affected by PGA(2) treatment. Instead, the cyclin D1 mRNA was rendered unstable after exposure to PGA(2). Since the stability of labile mRNA is modulated through binding of proteins to specific mRNA sequences, we sought to identify protein(s) recognizing the cyclin D1 mRNA. In electrophoretic mobility-shift assays using radiolabeled RNA probes derived from different regions of cyclin D1 mRNA, we observed that (i) lysates prepared from PGA(2)-treated cells exhibited enhanced protein-cyclin D1 RNA complex formation; (ii) the kinetics of complex formation correlated closely with that of cyclin D1 mRNA loss; and (iii) binding occurred within a 390-base cyclin D1 3' untranslated region (UTR) (K12). This binding activity could be cross-linked, revealing proteins ranging from 30 to 47 kDa. The RNA-binding protein AUF1, previously associated with the degradation of target mRNAs, bound cyclin D1 mRNA, because anti-AUF1 antibodies were capable of supershifting or immunoprecipitating cyclin D1 mRNA-protein complexes. Finally, insertion of K12 in the 3'UTR of reporter genes markedly reduced the expression and half-life of the resulting chimeric mRNAs in transfected, PGA(2)-treated cells. Our data demonstrate that PGA(2) down-regulates cyclin D1 expression by decreasing cyclin D1 mRNA stability and implicates a 390-base element in the 3'UTR in this regulation.

A nuclear matrix-associated factor, SAF-B, interacts with specific isoforms of AUF1/hnRNP D

One class of heterogeneous nuclear ribonucleoproteins (hnRNPs), AUF1/hnRNP D, consists of four isoform proteins (p45, p42, p40, and p37) which are generated by alternative splicing. The present study was therefore undertaken to clarify any isoform-specific differences in terms of their functions and nucleocytoplasmic localization. All isoforms primarily localized in the nucleus. However, heterokaryon analysis and a study using RNA polymerase II inhibitor revealed that p40/p37 exhibited a continuous shuttling between the nucleus and cytoplasm. Constant nuclear retention activity was mapped to the p45/p42-specific sequence at the C-terminal region, which is retained by alternative splicing. Using this domain as a probe, we performed a yeast two-hybrid screening and we found that scaffold attachment factor B (SAF-B), a nuclear matrix-associated protein, exhibits protein-protein interaction to this region. Colocalization of p45/p42 and SAF-B was observed as a speckle in the nucleus. Interestingly, p45/p42 isoforms appeared to act as a negative regulator in gene expression by forming a complex with SAF-B. Thus, the present study revealed that the isoform-specific functions of AUF1/hnRNP D are defined by intracellular shuttling capacity.

Interleukin-1-mediated stabilization of mouse KC mRNA depends on sequences in both 5'- and 3'-untranslated regions

mRNA transcribed from the mouse KC chemokine gene accumulated to significantly higher levels in multiple cell types after treatment with interleukin 1alpha (IL-1alpha) as compared with tumor necrosis factor-alpha (TNFalpha). Although TNFalpha and IL-1alpha both signaled the activation of nuclear factor kappaB and enhanced transcription of the KC gene with equal potency, only IL-1alpha treatment resulted in stabilization of KC mRNA. Nucleotide sequences that confer sensitivity for IL-1alpha-mediated mRNA stabilization were identified within the 5'- and 3'-untranslated regions (UTRs) of KC mRNA using transient transfection of chimeric plasmids containing specific portions of KC mRNA linked to the chloramphenicol acetyltransferase (CAT) gene. When plasmids containing either the 3'- or 5'-UTR of KC mRNA were used, the half-life of CAT mRNA was unaltered either in untreated or IL-1alpha-stimulated cells. In contrast, CAT mRNA transcribed from plasmids that contained both the 5'- and 3'-UTRs of the KC mRNA decayed more rapidly than control CAT mRNA, and this enhanced decay was prevented in cells treated with IL-1alpha. A cluster of four overlapping AUUUA motifs within the 3'-UTR was required, whereas the 5'-UTR region exhibited orientation dependence. These findings indicate that cooperative function of the two nucleotide sequences involves a distinct signaling pathway used by IL-1alpha but not TNFalpha.

Purification and characterization of beta-adrenergic receptor mRNA-binding proteins

Beta-adrenergic receptors (beta-ARs), like other G-protein-coupled receptors, can undergo post-transciptional regulation at the level of mRNA stability. In particular, the human beta(1)- and beta(2)-ARs and the hamster beta(2)-AR mRNA undergo beta-agonist-mediated destabilization. By UV cross-linking, we have previously described an approximately M(r) 36,000 mRNA-binding protein, betaARB, that binds to A/C+U-rich nucleotide regions within 3'-untranslated regions. Further, we have demonstrated previously that betaARB is immunologically distinct from AUF1/heterogeneous nuclear ribonucleoprotein (hnRNP) D, another mRNA-binding protein associated with destabilization of A+U-rich mRNAs (Pende, A., Tremmel, K. D., DeMaria, C. T., Blaxall, B. C., Minobe, W., Sherman, J. A., Bisognano, J., Bristow, M. R., Brewer, G., and Port, J. D. (1996) J. Biol. Chem. 271, 8493-8501). In this report, we describe the peptide composition of betaARB. Mass spectrometric analysis of an approximately M(r) 36,000 band isolated from ribosomal salt wash proteins revealed the presence of two mRNA-binding proteins, hnRNP A1, and the elav-like protein, HuR, both of which are known to bind to A+U-rich nucleotide regions. By immunoprecipitation, HuR appears to be the biologically dominant RNA binding component of betaARB. Although hnRNP A1 and HuR can both be immunoprecipitated from ribosomal salt wash proteins, the composition of betaARB (HuR alone versus HuR and hnRNP A1) appears to be dependent on the mRNA probe used. The exact role of HuR and hnRNP A1 in the regulation of beta-AR mRNA stability remains to be determined.

Testosterone and dihydrotestosterone regulate AUF1 isoforms in a tissue-specific fashion in the mouse

The sex difference in the metabolism of certain mRNAs in the murine submaxillary gland (SMG) prompted us to determine whether androgens regulate the expression of any of the four isoforms of AUF1, proteins that bind differentially to AU-rich RNA. We found that cytosol from female SMGs contains two major isoforms (p45 and p40), whereas cytosol from male SMGs contains a prominent p37 and a weaker p42. Injecting female mice with testosterone decreases p45 levels by 81% after 7 days (P < 0.05, n = 4), whereas p42 and p37 increase 74 and 449% at 7 days (P < 0.05, n = 4, for both). Orchiectomy, conversely, decreases p37 levels in the male SMG by 91% (P < 0.006) while increasing p45 5-fold and p40 2.5-fold (P < 0.05, n = 5 for both). Both male and female kidney cytosol contains a prominent p37 and a faint band of approximately 42 kDa, but neither shows a significant change when circulating androgen levels are altered. Dihydrotestosterone (DHT) changes the pattern of AUF1 isoforms in female SMG cytosol more rapidly than does testosterone. Nuclear extracts from female SMG contain predominantly p45, and DHT decreases its level slightly (35%, P < 0.05 at 24 h). Polysomal extracts from female SMG contain p45 and p42, and DHT increases p45 levels 58% (P < 0.02, n = 6) at 24 h. In certain nonreproductive tissues, androgens may differentially regulate AUF1 isoform levels to modulate the metabolism of AU-rich mRNAs posttranscriptionally.

Characterization of the binding of the RNA-binding protein AUF1 to the human AT(1) receptor mRNA

An important mechanism of regulation of the expression of the AT(1) receptors is the modulation of the mRNA stability. AUF1, a human RNA-binding protein, may play an important role. Since AUF1 seems to bind to AU-rich regions of the 3'-untranslated region of the mRNAs, we verified the nucleotide sequence of human AT(1) receptor 3'-untranslated region and we found possible binding sites. In addition we evaluated the expression of the AUF1 protein in human vascular smooth muscle cells: the administration of both isoproterenol and angiotensin II induced a significant increase of total anti-AUF1 immunoreactive isoforms. At the same time angiotensin II induced a significant decrease in the AT(1) receptor mRNA abundance. Moreover, we found that recombinant human AUF1 protein binds to human AT(1) receptor riboprobes. The protein was able to bind to the distal portion of the 3'-untranslated region, and also to the coding region. Since the clinically relevant AT(1) receptor polymorphism is located in the 3'-untranslated region, we created two DNAs, corresponding to the A and C polymorphism, without any differences. Our data demonstrate the presence of AUF1 in human vascular smooth muscle cells and its modulation by activation of the beta-adrenergic and the AT(1) pathways, a and specific binding of AUF1 to the human AT(1) receptor mRNA, suggesting a role of this protein in the modulation of the AT(1) receptor expression.

Developmental regulation of RNA transcript destabilization by A + U-rich elements is AUF1-dependent

The developmental immaturity of neonatal phagocytic function is associated with decreased accumulation and half-life (t((1)/(2))) of granulocyte/macrophage colony-stimulating factor (GM-CSF) mRNA in mononuclear cells (MNC) from the neonatal umbilical cord compared with adult peripheral blood. The in vivo t((1)/(2)) of GM-CSF mRNA is 3-fold shorter in neonatal (30 min) than in adult (100 min) MNC. Turnover of mRNA containing a 3'-untranslated region (3'-UTR) A + U-rich element (ARE), which regulates GM-CSF mRNA stability, is accelerated in vitro by protein fractions enriched for AUF1, an ARE-specific binding factor. The data reported here demonstrate that the ARE significantly accelerates in vitro decay of the GM-CSF 3'-UTR in the presence of either neonatal or adult MNC protein. Decay intermediates of the GM-CSF 3'-UTR are generated that are truncated at either end of the ARE. Furthermore, the t((1)/(2)) of the ARE-containing 3'-UTR is 4-fold shorter in the presence of neonatal (19 min) than adult (79 min) MNC protein, reconstituting developmental regulation in a cell-free system. Finally, accelerated ARE-dependent decay of the GM-CSF 3'-UTR in vitro by neonatal MNC protein is significantly attenuated by immunodepletion of AUF1, providing new evidence that this accelerated turnover is ARE- and AUF1-dependent.

Assembly of AUF1 oligomers on U-rich RNA targets by sequential dimer association

Many labile mammalian mRNAs are targeted for rapid cytoplasmic turnover by the presence of A + U-rich elements (AREs) within their 3'-untranslated regions. These elements are selectively recognized by AUF1, a component of a multisubunit complex that may participate in the initiation of mRNA decay. In this study, we have investigated the recognition of AREs by AUF1 in vitro using oligoribonucleotide substrates. Gel mobility shift assays demonstrated that U-rich RNA targets were specifically bound by AUF1, generating two distinct RNA-protein complexes in a concentration-dependent manner. Chemical cross-linking revealed the interaction of AUF1 dimers to form tetrameric structures involving protein-protein interactions in the presence of high affinity RNA targets. From these data, a model of AUF1 association with AREs involving sequential dimer binding was developed. Using fluorescent RNA substrates, binding parameters of AUF1 dimer-ARE and tetramer-ARE equilibria were evaluated in solution by fluorescence anisotropy measurements. Using two AUF1 deletion mutants, sequences C-terminal to the RNA recognition motifs are shown to contribute to the formation of the AUF1 tetramer.ARE complex but are not obligate for RNA binding activity. Kinetic studies demonstrated rapid turnover of AUF1.ARE complexes in solution, suggesting that these interactions are very dynamic in character. Taken together, these data support a model where ARE-dependent oligomerization of AUF1 may function to nucleate the formation of a trans-acting, RNA-destabilizing complex in vivo.

Unraveling a cytoplasmic role for hnRNP D in the in vivo mRNA destabilization directed by the AU-rich element

AU-rich RNA-destabilizing elements (AREs) have become a paradigm for studying cytoplasmic mRNA turnover in mammalian cells. Though many RNA-binding proteins have been shown to bind to AREs in vitro, trans-acting factors that participate in the in vivo destabilization of cytoplasmic RNA by AREs remains unknown. Experiments were performed to investigate the cellular mechanisms and to identify potential trans-acting factors for ARE-directed mRNA decay. These experiments identified hnRNP D, a heterogeneous nuclear ribonucleoprotein (hnRNP) capable of shuttling between the nucleus and cytoplasm, as an RNA destabilizing protein in vivo in ARE-mediated rapid mRNA decay. Our results show that the ARE destabilizing function is dramatically impeded during hemin-induced erythroid differentiation and not in TPA-induced megakaryocytic differentiation of human erythroleukemic K562 cells. A sequestration of hnRNP D into a hemin-induced protein complex, termed hemin-regulated factor or HRF, correlates well with the loss of ARE-destabilizing function in the cytoplasm. Further experiments show that in hemin-treated cells, ectopic expression of hnRNP D restores the rapid decay directed by the ARE. The extent of destabilizing effect varies among the four isoforms of hnRNP D, with p37 and p42 displaying the most profound effect. These results demonstrate a specific cytoplasmic function for hnRNP D as an RNA-destabilizing protein in ARE-mediated decay pathway. These in vivo findings support an emerging idea that shuttling hnRNP proteins have not only a nuclear but also a cytoplasmic function in mRNA metabolism. The data further imply that shuttling hnRNP proteins define, at least in part, the nuclear history of individual mRNAs and thereby influence their cytoplasmic fate.

Regulation of AUF1 expression via conserved alternatively spliced elements in the 3' untranslated region

The A+U-rich RNA-binding factor AUF1 exhibits characteristics of a trans-acting factor contributing to the rapid turnover of many cellular mRNAs. Structural mapping of the AUF1 gene and its transcribed mRNA has revealed alternative splicing events within the 3' untranslated region (3'-UTR). In K562 erythroleukemia cells, we have identified four alternatively spliced AUF1 3'-UTR variants, including a population of AUF1 mRNA containing a highly conserved 107-nucleotide (nt) 3'-UTR exon (exon 9) and the adjacent downstream intron (intron 9). Functional analyses using luciferase-AUF1 3'-UTR chimeric transcripts demonstrated that the presence of either a spliceable or an unspliceable intron 9 in the 3'-UTR repressed luciferase expression in cis, indicating that intron 9 sequences may down-regulate gene expression by two distinct mechanisms. In the case of the unspliceable intron, repression of luciferase expression likely involved two AUF1-binding sequences, since luciferase expression was increased by deletion of these sites. However, inclusion of the spliceable intron in the luciferase 3'-UTR down-regulated expression independent of the AUF1-binding sequences. This is likely due to nonsense-mediated mRNA decay (NMD) owing to the generation of exon-exon junctions more than 50 nt downstream of the luciferase termination codon. AUF1 mRNA splice variants generated by selective excision of intron 9 are thus also likely to be subject to NMD since intron 9 is always positioned >137 nt downstream of the stop codon. The distribution of alternatively spliced AUF1 transcripts in K562 cells is consistent with this model of regulated AUF1 expression.

Characterization of two human beta1-adrenergic receptor transcripts: cloning and alterations in the failing heart

Two human beta1-adrenergic receptor cDNAs, approximately 2.75 kb and approximately 3 kb in length, were isolated from a placenta phage library. Both transcripts are collinear with the previously isolated genomic sequence. Additionally, all clones begin between -274 and -236 bp relative to the translational start site, which is consistent with the previously identified transcriptional start site at -263. Furthermore, the 2.75 and 3 kb transcripts utilize conserved polyadenylation consensus sites at +2469 and +2751, respectively. Thus, this is the first report of the identification of full-length human beta1-AR cDNA clones. Both transcripts are expressed in placenta, heart, cerebral cortex, and lung with the 3 kb transcript more highly expressed than the 2.75 kb transcript in all tissues. RNase protection analysis utilizing left ventricular heart RNA isolated from patients with idiopathic dilated cardiomyopathy demonstrates 2.1-fold and 2.7-fold decreases of the 2. 75 and 3 kb transcripts, respectively, as compared with nonfailing controls. Thus, in heart failure patients the 3 kb transcript decreases to a significantly greater extent than the 2.75 kb transcript. This preferential reduction may be the result of differences in mRNA stability mediated by putative AU-rich elements specific to the 3'-untranslated region of the larger transcript.

Control of mRNA decay by heat shock-ubiquitin-proteasome pathway

Cytokine and proto-oncogene messenger RNAs (mRNAs) are rapidly degraded through AU-rich elements in the 3' untranslated region. Rapid decay involves AU-rich binding protein AUF1, which complexes with heat shock proteins hsc70-hsp70, translation initiation factor eIF4G, and poly(A) binding protein. AU-rich mRNA decay is associated with displacement of eIF4G from AUF1, ubiquitination of AUF1, and degradation of AUF1 by proteasomes. Induction of hsp70 by heat shock, down-regulation of the ubiquitin-proteasome network, or inactivation of ubiquitinating enzyme E1 all result in hsp70 sequestration of AUF1 in the perinucleus-nucleus, and all three processes block decay of AU-rich mRNAs and AUF1 protein. These results link the rapid degradation of cytokine mRNAs to the ubiquitin-proteasome pathway.

Two forms of expression and genomic structure of the human heterogeneous nuclear ribonucleoprotein D-like JKTBP gene (HNRPDL)

The human DNA- and RNA-binding protein JKTBP is a member of a 2xRNA-binding domain (RBD)-glycine family of heterogeneous nuclear ribonucleoproteins that are involved in mRNA biogenesis. Northern and Western blottings revealed that mRNAs of approx. 1.4 and 2.8kb and proteins of approx. 38 and 53kDa were present in HL-60 cells and various tissues. Cloning and characterization of a previously unknown cDNA for the 2.8kb mRNA indicated that the cDNA encodes a 420 amino acid JKTBP polypeptide. Isolation and characterization of the genomic DNA showed that the gene (HNRPDL) had nine exons and had two separate transcription start sites for the two transcripts. The features of the 5' flanking sequences of these sites showed that the gene is a housekeeping gene. Fluorescence in situ hybridization mapped the gene to 4q13-q21. From its gene organization, the JKTBP seems to be most closely related to hnRNP D/AUF1.

Identification and characterization of proteins binding A + U-rich elements

A + U-Rich elements (AREs) have been extensively investigated as cis-acting determinants of rapid mRNA turnover. Recently, a number of RNA-binding proteins interacting with AREs have been described. This article presents strategies and techniques used by our laboratory to identify and characterize a family of ARE-binding proteins collectively termed AUF1. However, these techniques may be applied to the study of any protein displaying sequence-specific RNA binding activity. The techniques described here include the purification of native AUF1 from cultured cells as well as the preparation of recombinant AUF1 proteins using a bacterial expression system. Analyses of RNA-protein interactions are also described, including the use of gel mobility shift assays with synthetic RNA probes to monitor specific RNA binding activity in cell extracts or with recombinant proteins. Variations of this technique are also described to evaluate the RNA binding affinity of recombinant proteins and the use of specific RNA competitors to assess RNA determinants of protein binding specificity. Other techniques presented include the identification of specific proteins in RNA:protein complexes using antibody supershifts and the estimation of molecular weights of RNA-binding proteins by UV crosslinking. Results of individual experiments are presented as examples of some techniques. Throughout the article, suggestions are included to avoid commonly encountered problems and to assist in the optimization of these techniques for the study of other RNA-binding proteins.