Selective destabilization of short-lived mRNAs with the granulocyte-macrophage colony-stimulating factor AU-rich 3' noncoding region is mediated by a cotranslational mechanism

Tumor necrosis factor-alpha induces transcription of the colony-stimulating factor-1 gene in murine osteoblasts

Tumor necrosis factor-alpha (TNF-alpha) stimulates bone resorption both in vitro and in vivo. The cellular mechanisms for this effect are not known but one pathway may be via release of osteoblast derived factors which stimulate osteoclast formation. Because colony-stimulating factor-1 (CSF-1) is essential for osteoclast progenitor proliferation, we examined the effect of TNF-alpha on osteoblast expression of CSF-1. TNF-alpha treatment of MC3T3-E1 or primary mouse osteoblasts stimulated the secretion of an activity that was mitogenic for a CSF-1 responsive cell line and was completely neutralized by antiserum to CSF-1. By Northern analysis, TNF-alpha caused a dose and time (3 to 24 h) dependent increase in CSF-1 transcript expression in MC3T3-E1 cells. mRNA stability studies using actinomycin D revealed that TNF-alpha does not affect CSF-1 mRNA half-life in MC3T3-E1 cells, while nuclear-run off analysis demonstrated that TNF-alpha increases CSF-1 gene transcription. Cycloheximide treatment of MC3T3-E1 cells up-regulated CSF-1 mRNA, and compared to either agent alone, cycloheximide and TNF-alpha in combination resulted in augmentation of CSF-1 expression. A series of studies using both agonists and inhibitors indicated that TNF-alpha-induced CSF-1 expression did not involve the arachidonic acid, PKC, or cAMP pathways. These results suggest that TNF-alpha induces CSF-1 expression in osteoblasts by a transcriptional mechanism which is largely independent of new protein synthesis and of the second messenger pathways examined.

Utilizing the GCN4 leader region to investigate the role of the sequence determinants in nonsense-mediated mRNA decay

In the yeast Saccharomyces cerevisiae, premature translation termination promotes rapid degradation of mRNAs. Accelerated decay requires the presence of specific cis-acting sequences which have been defined as downstream elements. It has been proposed that the role of the downstream element may be to promote translational reinitiation or ribosomal pausing. The GCN4 gene produces an mRNA that contains four short upstream open reading frames (uORFs) preceding the GCN4 protein-coding region in which translational initiation and reinitiation events occur. It was anticipated that these uORFs would function in a manner analogous to nonsense codons, promoting rapid degradation of the mRNA. However, the GCN4 transcript was not degraded by the nonsense-mediated mRNA decay pathway. We have investigated the role of the leader region of the GCN4 transcript in an effort to identify possible sequence elements that inactivate this decay pathway. We show that the GCN4 leader region does not harbor a downstream element needed to promote mRNA decay. In addition, using hybrid GCN4-PGK1 transcripts, we demonstrate that if a translational reinitiation signal precedes a downstream element, the mRNA will no longer be sensitive to nonsense-mediated decay. Furthermore, we demonstrate that the downstream element is functional only after a translational initiation and termination cycle has been completed but is unable to promote nonsense-mediated mRNA decay if it is situated 5' of a translational initiation site. Based on these results, the role of the downstream element will be discussed.

Characterization of adenosine-uridine-rich RNA binding factors

The adenosine-uridine (AU)-rich sequences within the 3' untranslated region (UTR) of many short-lived mRNAs are important in their rapid degradation. We present evidence that human embryonic lung fibroblasts (W138) contain five major proteins of 70, 45, 40, 38, 32.5 kd, which specifically bind the AU-rich region of human granulocyte-macrophage colony-stimulating factor (GM-CSF) 3'UTR containing 7 x AUUUA motifs. The 40 and 38 kd proteins also bound the 3x and 5 x AUUUA cassettes and even more strongly bound to the AUUUUUUUA motif. All five of these proteins showed more abundant localization in the nucleus than the cytoplasm. The 32.5 kd protein was the major cytoplasmic AU-binding protein. Incubation with actinomycin D resulted in a marked increase in binding activity of 45, 40, 38, and 32.5 kd proteins in the cytoplasm, accompanied by decreased binding activity of the 32.5 kd protein in the nucleus. Antibody against heterogeneous nuclear ribonucleoprotein C (hnRNP C) immunoprecipitated the 40 and 38 kd proteins, and antibody against the AU-rich element RNA-binding protein (AUF1) immunoprecipitated the 45, 40, and 38 kd proteins. The present results not only demonstrated that hnRNP C are AU-binding proteins which are present in the cytoplasm as well as the nucleus, but another group of AU-binding proteins (AUF1 [45, 40, 38 kd], and 32.5 kd), which are not hnRNP, have characteristics related to those of hnRNPs. Taken together with our previous results (Akashi et al., 1994, Blood, 83:3182-3187), AU-binding factors including hnRNP C and AUF1, which bind more than 3 x AUUUA motifs, may be involved in rapid degradation of these transcripts. No significant quantitative changes of these proteins in their binding activity to AU-rich sequences occurred in response to several stimuli that stabilize GM-CSF mRNA, indicating that binding of these proteins to their cognate RNA is not responsible for the stabilization of these transcripts.

Cortisol increases interstitial collagenase expression in osteoblasts by post-transcriptional mechanisms

Glucocorticoids regulate both bone formation and bone resorption. In osteoblasts, they inhibit type I collagen synthesis; however, there is limited information about their effects on interstitial collagenase, the enzyme that degrades type I collagen. We used primary cultures of osteoblast-enriched cells from fetal rat calvariae (Ob cells) to study the effects of cortisol on collagenase expression. Northern blot analysis showed that cortisol increased collagenase transcript levels in a dose- and time-dependent manner, which was paralleled by an increase in immunoreactive metalloproteinase in the culture medium. Cortisol increased the half-life of collagenase mRNA from 6 to 12 h in transcription-arrested Ob cells. In contrast, cortisol modestly decreased collagenase gene transcription after 24 h of treatment. The up-regulation of collagenase by cortisol is osteoblast-specific, since the glucocorticoid decreased phorbol 12-myristate 13-acetate-induced collagenase mRNA expression in rat fibroblasts, a result that agrees with other studies of collagenase gene regulation in fibroblastic cells. In conclusion, cortisol increases interstitial collagenase transcript levels by post-transcriptional mechanisms in osteoblastic cells. Our data demonstrate that glucocorticoids regulate collagenase gene expression in a novel tissue-specific manner, further highlighting the differences in gene regulation between osteoblastic and fibroblastic cells.

AU-rich elements: characterization and importance in mRNA degradation

Adenylate/uridylate-rich elements (AREs) are found in the 3' untranslated region (UTR) of many messenger RNAs (mRNAs) that code for proto-oncogenes, nuclear transcription factors and cytokines. They represent the most common determinant of RNA stability in mammalian cells. Moreover, ARE-directed mRNA degradation is influenced by many exogenous factors, including phorbol esters, calcium ionophores, cytokines and transcription inhibitors. These observations suggest that AREs play a critical role in the regulation of gene expression during cell growth and differentiation, and in the immune response.

Characterization of a Human Stromal Cell Line Supporting Hematopoietic Progenitor Cell Proliferation: Effect of HIV Expression

Our objective was to determine the role that bone marrow-derived stromal cells have on human hematopoiesis in HIV infection. In particular, we dissected the heterogeneous bone marrow microenvironment to study the effect HIV expression might have on the cell population capable of producing the cytokines which will support human CD34+ cell differentiation. A stromal cell line, Lof(11-10), was established from human bone marrow by transfecting a plasmid containing the SV40 large T-antigen and isolating foci exhibiting a transformed phenotype. The Lof(11-10) cell line was characterized to determine its susceptibility to HIV infection, to identify its cytokine production profile, and to test the ability of conditioned media from this line to support CD34+ cell differentiation in the presence and absence of HIV expression. Nine cytokines were detected by RT-PCR and ELISA analysis. Conditioned media obtained from the Lof(11-10) cell line was able to support CD34+ celle differentiation. However, because the Lof(11-10) cells are not infectible by HIV, molecular clones of HIV were introduced into these cells by transfection. There was no qualitative difference in the levels of cytokine production between HIV-expressing and control Lof(11-10) cells. Furthermore, conditioned media derived from HIV-expressing and control Lof(11-10) cells added to bone marrow-derived CD34+ progenitor cells yielded similar colony formation in methylcellulose assays. Our data suggest that HIV infection of the cytokine-producing cells within the bone marrow microenvironment, as represented by the Lof(11-10) cell line, results in both normal cytokine production and hematopoiesis in spite of HIV expression. This report adds to the evidence against stromal cells being a significant target of HIV and establishes a system for comparison with more relevant models. Copyright 1995 S. Karger AG, Basel

mRNA stability in mammalian cells

This review concerns how cytoplasmic mRNA half-lives are regulated and how mRNA decay rates influence gene expression. mRNA stability influences gene expression in virtually all organisms, from bacteria to mammals, and the abundance of a particular mRNA can fluctuate manyfold following a change in the mRNA half-life, without any change in transcription. The processes that regulate mRNA half-lives can, in turn, affect how cells grow, differentiate, and respond to their environment. Three major questions are addressed. Which sequences in mRNAs determine their half-lives? Which enzymes degrade mRNAs? Which (trans-acting) factors regulate mRNA stability, and how do they function? The following specific topics are discussed: techniques for measuring eukaryotic mRNA stability and for calculating decay constants, mRNA decay pathways, mRNases, proteins that bind to sequences shared among many mRNAs [like poly(A)- and AU-rich-binding proteins] and proteins that bind to specific mRNAs (like the c-myc coding-region determinant-binding protein), how environmental factors like hormones and growth factors affect mRNA stability, and how translation and mRNA stability are linked. Some perspectives and predictions for future research directions are summarized at the end.

mRNA stability in mammalian cells

This review concerns how cytoplasmic mRNA half-lives are regulated and how mRNA decay rates influence gene expression. mRNA stability influences gene expression in virtually all organisms, from bacteria to mammals, and the abundance of a particular mRNA can fluctuate manyfold following a change in the mRNA half-life, without any change in transcription. The processes that regulate mRNA half-lives can, in turn, affect how cells grow, differentiate, and respond to their environment. Three major questions are addressed. Which sequences in mRNAs determine their half-lives? Which enzymes degrade mRNAs? Which (trans-acting) factors regulate mRNA stability, and how do they function? The following specific topics are discussed: techniques for measuring eukaryotic mRNA stability and for calculating decay constants, mRNA decay pathways, mRNases, proteins that bind to sequences shared among many mRNAs [like poly(A)- and AU-rich-binding proteins] and proteins that bind to specific mRNAs (like the c-myc coding-region determinant-binding protein), how environmental factors like hormones and growth factors affect mRNA stability, and how translation and mRNA stability are linked. Some perspectives and predictions for future research directions are summarized at the end.

Post-transcriptional regulation of human interleukin-2 gene expression at processing of precursor transcripts

Interleukin-2 (IL-2) regulates the clonal expansion of activated T cells and is produced in limited amounts during an immune response. Mitogenic induction of human IL-2 gene expression elicits a transient wave of unstable mRNA. We show here that transcription continues unabated during and well beyond the time when the wave is subsiding, yet few, if any, new mRNA molecules are generated once the wave has reached its maximum. Instead, IL-2 precursor transcripts accumulate, becoming the majority of expressed IL-2 RNA molecules. The flow of precursor transcripts into mature mRNA becomes inhibited in the course of induction. When translation is blocked (e.g. by cycloheximide), expression of IL-2 mRNA can be superinduced by 2 orders of magnitude. This superinduction is completely dependent upon transcription, yet is not accompanied by any significant increase in the rate of primary transcription or in mRNA stability. Instead, the processing of nuclear IL-2 precursor transcripts is greatly facilitated, resulting in pronounced superinduction of cytoplasmic mRNA. Once its transcription has been induced, therefore, expression of the IL-2 gene is down-regulated extensively at the level of precursor RNA processing.

A transient GCN4 mRNA destabilization follows GCN4 translational derepression

Studies based on experimental strategies that utilized either inhibitors or structural alterations point to the existence of an inverse relationship between translation and stability of a given mRNA. In this study we have investigated the potential link between translation and stability of the yeast GCN4 mRNA whose translational rates change with respect to amino acid availability. We observed that under conditions favoring its translation, the steady state levels of the GCN4 mRNA were decreased, but this was not due to a measurable alternation in its decay rate. We have demonstrated that an extensive destabilization of this message is intimately coupled with its increased access to heavy polysomes, which occurs transiently in the process of translational derepression. This transient change in the stability is what readjusts the steady state levels of the GCN4 mRNA. This study demonstrates in vivo the existence of a mechanism of mRNA degradation that is coupled with the process of translation.

Glyceraldehyde-3-phosphate dehydrogenase selectively binds AU-rich RNA in the NAD(+)-binding region (Rossmann fold)

A 36-kDa protein that binds AU-rich RNA was purified from human spleen and identified as glyceraldehyde-3-phosphate dehydrogenase (GAPDH). GAPDH has been previously demonstrated to bind tRNA with high affinity. Competition studies suggested that cytoplasmic GAPDH binds the AU-rich elements (AREs) of lymphokine mRNA 3'-untranslated regions with higher affinity than tRNA. The AUUUA-specific RNA binding activity of GAPDH was inhibited by NAD+, NADH, and ATP in a concentration-dependent manner, suggesting that RNA binding of GAPDH might involve the NAD(+)-binding region, or dinucleotide-binding (Rossmann) fold. This hypothesis was supported by experiments that localized RNA binding to the predicted N-terminal 6.8-kDa peptide, known to be involved in the formation of the NAD(+)-binding domain. The direct demonstration of ARE-specific binding protein activity localized to the NAD(+)-binding region of GAPDH supports the general concept that enzymes containing this domain may exhibit specific RNA binding activity and play additional roles in nucleic acid metabolism. Finally, cytoplasmic GAPDH was found in the polysomal fraction of T lymphocytes. Thus, the RNA binding specificity of GAPDH as well as its localization within the cell merit its strong consideration as a protein important in the regulation of ARE-dependent mRNA turnover and translation in addition to its well described role in glycolysis.

Modulation of cellular macromolecular synthesis by coronavirus: implication for pathogenesis

Infection with the murine coronavirus strain JHM decreases cell surface expression of major histocompatibility complex class I antigens. Northern blots showed that JHM virus infection rapidly reduced the level of actin mRNA, whereas the levels of major histocompatibility complex class I and tubulin mRNAs were reduced only slightly. By contrast, the mRNA levels of interleukin 1 beta, colony-stimulating factor 1 receptor, and tumor necrosis factor alpha increased following infection.

Cloning and characterization of ERF-1, a human member of the Tis11 family of early-response genes

Members of the Tis11 family of early-response genes are characterized by a high degree of sequence similarity around a putative zinc finger motif. They are induced by a variety of cell agonists and polypeptide mitogens, including 12-O-tetradecanoylphorbol-13-acetate (TPA) and epidermal growth factor (EGF). We describe the cloning and sequencing of a human member of this gene family, EGF-response factor 1 (ERF-1), the homolog of the mouse Tis11b/rat cMG1 genes. The human and rodent genes are similar, with 5' UTR, coding sequence, and 3' UTR highly conserved. The promoter/enhancer region and intron sequences contain multiple putative transcription factor binding motifs characteristic of early-response genes. Amino acid sequence comparison of the seven members of the Tis11 family cloned so far identifies a repeated consensus motif of (x+)YKTELC(x+)x5GxCxYGx(x+)CxFxH involving the potential zinc finger. Toward the carboxyterminal end is a region with a high percentage of prolines (15/73) and, partially overlapping, a serine-rich domain (20/54). These may be important as trans-activation and phosphorylation sites. The 3' untranslated region is unusually long, extending over 1,860 bp. The sequence immediately downstream from the translational stop codon has extensive secondary structure potential. The 3' UTR is 60% AT rich, but contains two GC rich (> 70%) regions. In addition there are multiple reiterations of a destabilization sequence, as well as a single UUAUUUAU motif characteristic of mRNAs specifying proteins involved in the inflammatory response. The mRNA contains a consensus polyadenylation signal.

The parathyroid hormone-related protein gene and its expression

Parathyroid hormone-related protein (PTHrP) was originally identified as a tumor product, but it is now established that PTHrP is expressed in many tissues where it exerts paracrine functions. Three potential isoforms of PTHrP, 139, 141 and 173 amino acids in length, have been described and these isoforms result from alternative splicing of the PTHrP gene. The gene is composed of nine exons of which only two are invariant in PTHrP transcripts. The other seven exons may be represented in the PTHrP mRNA complement as a result of alternative splicing, which allows for the production of up to 15 transcripts. Three spatially-distinct promoters, two TATA and one GC-rich region, are responsible for transcription of the gene and these appear to be differentially regulated. The PTHrP gene contains nucleotide sequence motifs in common with members of the immediate-early response gene family, as well as other hallmark features which include induction by growth factors, serum or cycloheximide and relatively short-lived mRNA.

Translational control of cytokine expression by 3' UA-rich sequences

Several messenger RNAs which are transiently expressed contain a conserved uridine-adenosine-rich sequence in their 3' untranslated region. Many of these mRNas encode cytokines, growth factors or oncoproteins. This UA-rich sequence is composed of several interpsersed repeats of the octanucleotide UUAUUUAU and plays a key role in the post-transcriptional regulation of these mRNAs. Known as instability determinants, these UA-rich elements can also strongly affect mRNA translational efficiency. In this report, we review the data which illustrate this translational regulation and give insight the underlying mechanism.

Induction of cytoplasmic factors that bind to the 3' AU-rich region of human interferon beta mRNA during early development of Xenopus laevis

Certain endogenous Xenopus mRNAs, carrying a destabilizing 3' AU-rich sequence, are unusually very stable in oocytes and become unstable only after fertilization. In addition, heterologous short lived mRNA, containing 3' AU-rich sequences, appear to be very stable when injected into Xenopus oocytes. In the present study, a human interferon beta (hu-IFN beta) mRNA, carrying the destabilizing 3' AU-rich element, was used as a probe to identify Xenopus proteins that specifically bind to the 3' AU-rich element as well as to study their relative levels during early embryonic development. While three major proteins that specifically bind to the 3' AU-rich element were detected in human SV80 cells, that naturally express hu-IFN beta (proteins termed AU-F1, F2 and F3), only two proteins, migrating similarly to the SV80 AU-F1 and AU-F3, were detected in cytoplasmic extracts from Xenopus oocytes or eggs. Following fertilization, the intensity of the Xenopus AU-F1 and AU-F3 proteins increased considerably and a new protein, corresponding to SV80 AU-F2, was also detected. Cyclohexamide applied either at the morula or at the early blastula stages reduced the intensity of the AU-binding factors, while actinomycin D did not, indicating that the levels of these factors during these stages are regulated posttranscriptionally. In contrast, application of each of these metabolic inhibitors at the late blastula stage increased the intensity of the AU-binding proteins. The possible function of these AU-binding factors in regulating the expression and half life of AU-rich mRNAs is discussed.

Current applications of COS cell based transient expression systems

An ever increasing number of mammalian expression systems have become available in recent years. Yet a simple and robust mammalian expression system is all that is needed for most routine mammalian expression work. The well established COS cell based expression systems have filled this role and continue to be used to study gene expression, to clone by expression, to produce small quantities of recombinant protein, and to test the efficacy of mammalian expression constructs. Recent applications of COS cell based expression systems in these areas include the following: studies on the role of AU-rich regions localized in the 3' untranslated regions of mRNA transcripts in mRNA half-life; the cloning of the leukocyte antigens CD34 and CD69 as well as the type-II and type-III TGF-beta receptors; and the production of a soluble recombinant form of the gamma delta T-cell receptor and a bispecific Ig fusion protein of the endothelial cell-surface proteins E-selectin and P-selectin.