Endonucleolysis in the turnover of insulin-like growth factor II mRNA

Identification and expression analysis of cDNA encoding insulin-like growth factor 2 in horses

Insulin-like growth factor 2 (IGF2) is responsible for a broad range of physiological processes during fetal development and adulthood, but genomic analyses of IGF2 containing the 5ʹ- and 3ʹ-untranslated regions (UTRs) in equines have been limited. In this study, we characterized the IGF2 mRNA containing the UTRs, and determined its expression pattern in the fetal tissues of horses. The complete equine IGF2 mRNA sequence harboring another exon approximately 2.8 kb upstream from the canonical transcription start site was identified as a new transcript variant. As this upstream exon did not contain the start codon, the amino acid sequence was identical to the canonical variant. Analysis of the deduced amino acid sequence revealed that the protein possessed two major domains, IlGF and IGF2_C, and analysis of IGF2 sequence polymorphism in fetal tissues of Hokkaido native horse and Thoroughbreds revealed a single nucleotide polymorphism (T to C transition) at position 398 in Thoroughbreds, which caused an amino acid substitution at position 133 in the IGF2 sequence. Furthermore, the expression pattern of the IGF2 mRNA in the fetal tissues of horses was determined for the first time, and was found to be consistent with those of other species. Taken together, these results suggested that the transcriptional and translational products of the IGF2 gene have conserved functions in the fetal development of mammals, including horses.

IMP3 RNP safe houses prevent miRNA-directed HMGA2 mRNA decay in cancer and development

The IMP3 RNA-binding protein is associated with metastasis and poor outcome in human cancer. Using solid cancer transcriptome data, we found that IMP3 correlates with HMGA2 mRNA expression. Cytoplasmic IMP3 granules contain HMGA2, and IMP3 dose-dependently increases HMGA2 mRNA. HMGA2 is regulated by let-7, and let-7 antagomiRs make HMGA2 refractory to IMP3. Removal of let-7 target sites eliminates IMP3-dependent stabilization, and IMP3-containing bodies are depleted of Ago1-4 and miRNAs. The relationship between Hmga2 mRNA and IMPs also exists in the developing limb bud, where IMP1-deficient embryos show dose-dependent Hmga2 mRNA downregulation. Finally, IMP3 ribonucleoproteins (RNPs) contain other let-7 target mRNAs, including LIN28B, and a global gene set enrichment analysis demonstrates that miRNA-regulated transcripts in general are upregulated following IMP3 induction. We conclude that IMP3 RNPs may function as cytoplasmic safe houses and prevent miRNA-directed mRNA decay of oncogenes during tumor progression.

Mechanisms of endonuclease-mediated mRNA decay

Endonuclease cleavage was one of the first identified mechanisms of mRNA decay but until recently it was thought to play a minor role to the better-known processes of deadenylation, decapping, and exonuclease-catalyzed decay. Most of the early examples of endonuclease decay came from studies of a particular mRNA whose turnover changed in response to hormone, cytokine, developmental, or nutritional stimuli. Only a few of these examples of endonuclease-mediated mRNA decay progressed to the point where the enzyme responsible for the initiating event was identified and studied in detail. The discovery of microRNAs and RISC-catalyzed endonuclease cleavage followed by the identification of PIN (pilT N-terminal) domains that impart endonuclease activity to a number of the proteins involved in mRNA decay has led to a resurgence of interest in endonuclease-mediated mRNA decay. PIN domains show no substrate selectivity and their involvement in a number of decay pathways highlights a recurring theme that the context in which an endonuclease function is a primary factor in determining whether any given mRNA will be targeted for decay by this or the default exonuclease-mediated decay processes.

Relationship of folate, vitamin B12 and methylation of insulin-like growth factor-II in maternal and cord blood

BACKGROUND/OBJECTIVE

One of the speculated mechanisms underlying fetal origin hypothesis of breast cancer is the possible influence of maternal environment on epigenetic regulation, such as changes in DNA methylation of the insulin-like growth factor-2 (IGF2) gene. The aim of the study is to investigate the relationship between folate, vitamin B(12) and methylation of the IGF2 gene in maternal and cord blood.

SUBJECTS/METHODS

We conducted a cross-sectional study to measure methylation patterns of IGF2 in promoters 2 (P2) and promoters 3 (P3).

RESULTS

The percentage of methylation in IGF2 P3 was higher in maternal blood than in cord blood (P<0.0001), whereas the methylation in P2 was higher in cord blood than in maternal blood (P=0.016). P3 methylation was correlated between maternal and cord blood (P<0.0001), but not P2 (P=0.06). The multivariate linear regression model showed that methylation patterns of both promoters in cord blood were not associated with serum folate levels in either cord or maternal blood, whereas the P3 methylation patterns were associated with serum levels of vitamin B(12) in mother's blood (mean change (MC)=-0.22, P=0.0014). Methylation patterns in P2 of maternal blood were associated with serum levels of vitamin B(12) in mother's blood (MC=-0.23, P=0.012), exposure to passive smoking (MC=0.46, P=0.034) and mother's weight gain during pregnancy (MC=0.23, P=0.019).

CONCLUSIONS

The study suggests that environment influences methylation patterns in maternal blood, and then the maternal patterns influence the methylation status and levels of folate and vitamin B(12) in cord blood.

A reverse transcriptase stop assay revealed diverse quadruplex formations in UTRs in mRNA

Here, we developed a reverse transcriptase based method (RTase stop assay) to characterize quadruplex formations in guanine-rich RNAs with high sensitivity and specificity. By using the RTase stop assay, we also revealed a plausible structural polymorphism in biologically important RNAs. The RTase stop assay would provide helpful insight into RNA quadruplex structures and functions, together with other analytical methods, including various footprinting techniques.

Differential expression of H19 and vitamin D3 upregulated protein 1 as a mechanism of the modulatory effects of high virgin olive oil and high corn oil diets on experimental mammary tumours

Dietary lipids have a role in the aetiology of breast cancer. We have reported earlier that a high corn oil diet downregulates H19 and vitamin D3 upregulated protein 1 (VDUP1) messenger RNA (mRNA) expression in rat dimethylbenz (alpha) anthracene-induced mammary adenocarcinomas in comparison with the control low-fat diet, this effect being associated with a higher degree of tumour malignancy. This result was compatible with the stimulating effect of this diet. In this study we have investigated the influence of a high extra virgin olive diet on H19 and VDUP1 mRNA and/or protein expression. We have shown earlier that this high-fat diet confers to the tumours a more benign phenotype in accordance with its potential protective effect on mammary cancer. We have also analysed the effects on the mRNA and protein expression of insulin-like growth factor-2 , in close relation with H19, and the expression and activity of the thioredoxin protein, negatively regulated by VDUP1. mRNA and protein expression were analysed by chemiluminescent northern blot and western blot, respectively. Thioredoxin activity was determined by the insulin-reducing assay. The results showed that the high olive oil diet does not change the tumour expression of H19 and VDUP1. Moreover, tumours from the animals fed this diet displayed higher levels of the insulin-like growth factor-2 mRNAs, which are related to a higher rate of degradation or a lower traducibility. Finally, tumour expression and activity levels of thioredoxin-1 protein did not change irrespective of the diet. These results suggest that the differential effects of high olive oil and high corn oil diets on mammary cancer are exerted by means of a different, specific influence on gene expression.

IGF-II promoter methylation and ovarian cancer prognosis

PURPOSE

The insulin-like growth factor-II (IGF-II) gene has four promoters that produce distinct transcripts which vary by tissue type and developmental stage. Dysregulation of normal promoter usage has been shown to occur in cancer; DNA methylation regulates promoter use. Thus, we sought to examine if DNA methylation varies among IGF-II promoters in ovarian cancer and if methylation patterns are related to clinical features of the disease.

STUDY DESIGN

Tumor tissue, clinical data, and follow-up information were collected from 215 patients diagnosed with primary epithelial ovarian cancer. DNA extracted from tumor tissues was analyzed for IGF-II promoter methylation with seven methylation specific PCR (MSP) assays: three for promoter 2 (P2) and two assays each for promoters 3 and 4 (P3 and P4).

RESULTS

Methylation was found to vary among the seven assays: 19.3% in P2A, 45.6% in P2B, 50.9% in P2C, 48.4% in P3A, 13.1% in P3B, 5.1% in P4A, and 6.1% in P4B. Methylation in any of the three P2 assays was associated with high tumor grade (P = 0.043), suboptimal debulking (P = 0.036), and disease progression [hazards ratio (HR) = 1.73, 95% confidence interval (CI) 1.09-2.74]. When comparing promoter methylation patterns, differential methylation of P2 and P3 was found to be associated with disease prognosis; patients with P3 but not P2 methylation were less likely to have disease progression (HR = 0.39, 95% CI 0.17-0.91) compared to patients with P2 but not P3 methylation.

CONCLUSIONS

This study shows that methylation varies among three IGF-II promoters in ovarian cancer and that this variation seems to have biologic implications as it relates to clinical features and prognosis of the disease.

Control of fetal growth and neonatal survival by the RasGAP-associated endoribonuclease G3BP

The regulation of mRNA stability plays a major role in the control of gene expression during cell proliferation, differentiation, and development. Here, we show that inactivation of the RasGAP-associated endoribonuclease (G3BP)-encoding gene leads to embryonic lethality and growth retardation. G3BP-/- mice that survived to term exhibited increased apoptotic cell death in the central nervous system and neonatal lethality. Both in mouse embryonic fibroblasts and during development, the absence of G3BP altered the expression of essential growth factors, among which imprinted gene products and growth arrest-specific mRNAs were outstanding. The results demonstrate that G3BP is essential for proper embryonic growth and development by mediating the coordinate expression of multiple imprinted growth-regulatory transcripts.

Organization and promoter analysis of the zebrafish (Danio rerio) interferon gene

Interferon plays important roles in confronting viral infections as the first line of defense. For the purpose of understanding the molecular mechanism which controls transcription of the interferon gene, we cloned and sequenced the interferon promoter region of the zebrafish interferon gene and characterized its activity using firefly luciferase transient transfection expression assays. Different fragments of the zebrafish interferon 5'-flanking region were transfected into ZFL cells. In these cell lines, maximum promoter activity was located in 2.2 kb of the zebrafish interferon 5' flanking region of the ZFL cell line. In this study, we investigated whether the viral replicative intermediate double-stranded RNA (herein we used synthetic polyinosinic-polycytidylic acid [poly(I):poly(C)] modifies the effects of interferon on gene expression. For this purpose, all zebrafish interferon promoter fragments were treated with either 1, 10, or 100 microg/ml poly(I):poly(C). The results showed that after treatment with 10 microg/ml poly(I):poly(C), high promoter activity was observed in the -2.2-kb interferon promoter fragment. Several putative transcription factors were shown in the promoter region, including IRF-1, C/EBP, NFkappaB, and GATA-1. Further study of the in vivo expression of the interferon promoter during development was carried out in transgenic zebrafish expressing an interferon promoter-driven green fluorescent protein (GFP) encoding the GFP cDNA transgene. Morphological studies of transgenic zebrafish indicated that the interferon promoter-driven GFP transcripts appeared in the yolk, head, and lymphoid organs. These results indicate that the interferon promoter is active in a tissue-specific manner, and suggest that the interferon promoter plays an important role in virus resistance during teleost growth.

Regulation of pathways of mRNA destabilization and stabilization

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. Although most studies of gene expression have focused on gene transcription and in the area of eukaryotic mRNA degradation, but to provide a short general discussion of the importance of mRNA degradation and its regulation and a brief overview of recent findings and present knowledge. The overview is followed by a more in-depth discussion of one of the several pathways for mRNA degradation. We concentrate on the pathway for regulated mRNA degradation mediated by mRNA-binding proteins and endonucleases that cleave within the body of mRNAs. As a potential example of this type of control, we focus on the regulated degradation of the egg yolk precursor protein vitellogenin on the mRNA-binding protein vigilin and the mRNA endonuclease polysomal ribonuclease 1 (PMR-1).

Characterization and purification of a mammalian endoribonuclease specific for the alpha -globin mRNA

The alpha-globin mRNA has previously been shown to be the target of an erythroid-enriched endoribonuclease (ErEN) activity which cleaves the mRNA within the 3'-untranslated region. We have currently undertaken a biochemical approach to purify this enzyme and have begun characterization of the enzyme to determine requirements for substrate recognition as well as optimal cleavage conditions. Through mutational analysis and truncations we show that a 26-nucleotide region of the alpha-globin 3'-untranslated region is an autonomous element that is both necessary and sufficient for cleavage by ErEN. Mutations throughout this region abolish cleavage activity by ErEN suggesting that the entire sequence is important for recognition and cleavage. ErEN is most active under biological salt concentrations and temperature and activity of the enzyme does not require cations. The size for ErEN was estimated by denaturing gel filtration analysis and is approximately 40 kDa. Interestingly, the exquisite specificity of ErEN cleavage became compromised with increased purity of the enzyme suggesting the involvement of other proteins in specificity of ErEN cleavage. Nondenaturing gel filtration of MEL extract demonstrated that ErEN is a component of an approximately 160 kDa complex implying that additional proteins may regulate ErEN activity and provide increased cleavage specificity.

Characterization of nuclear RNases that cleave hepatitis B virus RNA near the La protein binding site

Hepatitis B virus (HBV) RNA is downregulated by inflammatory cytokines induced in the liver by adoptively transferred HBV-specific cytotoxic T lymphocytes (CTLs) and during murine cytomegalovirus (MCMV) infections of the livers of HBV transgenic mice. The disappearance of HBV RNA is tightly associated with the cytokine-induced proteolytic cleavage of a previously defined HBV RNA-binding protein known as La autoantigen. La binds to a predicted stem-loop structure at the 5' end of the posttranscriptional regulatory element of HBV RNA between nucleotides 1243 and 1333. In the present study, we searched for nuclear RNase activities that might be involved in HBV RNA decay. Nuclear extracts derived from control livers and CTL-injected and MCMV-infected livers were analyzed for the ability to cleave HBV RNA. Endonucleolytic activity that cleaved HBV RNA at positions 1269 to 1270 and 1271 to 1272, immediately 5' of the stem-loop bound by the La protein (positions 1272 to 1293), was detected. Furthermore, we provide evidence that the cytokine-dependent downregulation of HBV RNA following MCMV infection is temporally associated with the upregulation of the endonucleolytic activity herein described. Collectively, these results suggest a model in which the steady-state HBV RNA content is controlled by the stabilizing influence of La and the destabilizing influence of nuclear RNase activities.

Dexamethasone inhibits macrophage accumulation after balloon arterial injury in cholesterol fed rabbits

Macrophages play a critical role in the development and progression of atherosclerosis. This study was designed to examine the effect of the glucocorticoid, dexamethasone, (Dex), on macrophage accumulation after acute arterial injury. Twenty New Zealand white rabbits were fed a 2% cholesterol, 6% peanut oil, rabbit chow diet for one month prior to bilateral balloon dilatation of the femoral arteries. Ten rabbits received Dex (1 mg/kg, im.) the day before and then daily for 7 days after arterial injury; control rabbits received vehicle only. Seven days after injury, Dex treatment resulted in a 96% and 77% reduction (P < 0.002) in the mean number of macrophages accumulating in the intima and media, respectively. This effect was apparently not due to a reduction in the number of circulating monocytes or to the ability of monocytes from Dex treated animals to adhere to endothelium or migrate in response to a chemotactic signal, determined in vitro under static conditions. It was associated with a 61% reduction in monocyte chemoattractant protein-1 (MCP-1) antigen (P < 0.004) in the injured arterial wall (media+intima). Glucocorticoids may be useful in attenuating the inflammatory response and subsequent foam-cell accumulation after arterial injury.

Mechanisms and control of mRNA decapping in Saccharomyces cerevisiae

The process of mRNA turnover is a critical component of the regulation of gene expression. In the past few years a discrete set of pathways for the degradation of polyadenylated mRNAs in eukaryotic cells have been described. A major pathway of mRNA degradation in yeast occurs by deadenylation of the mRNA, which leads to a decapping reaction, thereby exposing the mRNA to rapid 5' to 3' exonucleolytic degradation. A critical step in this pathway is decapping, since it effectively terminates the existence of the mRNA and is the site of numerous control inputs. In this review, we discuss the properties of the decapping enzyme and how its activity is regulated to give rise to differential mRNA turnover. A key point is that decapping appears to be controlled by access of the enzyme to the cap structure in a competition with the translation initiation complex. Strikingly, several proteins required for mRNA decapping show interactions with the translation machinery and suggest possible mechanisms for the triggering of mRNA decapping.

Distinct RNA structural domains cooperate to maintain a specific cleavage site in the 3'-UTR of IGF-II mRNAs

The insulin-like growth factor II mRNAs are targets for site-specific endonucleolytic cleavage in the 3'-UTR, which results in a very stable 3' cleavage product of 1.8 kb, consisting of 3'-UTR sequences and a poly(A) tail. The 5' cleavage product contains the coding region and is rapidly degraded. Thus, cleavage is thought to provide an additional way to control IGF-II protein synthesis. We had established that cleavage requires two widely separated sequence elements (I and II) in the 3'-UTR that form a stable duplex of 83 nucleotides. The cleavage-site itself is located in an internal loop preceded by two stable stem-loop structures. Furthermore, in a study which was based on RNA folding algorithms, we have shown that there are specific sequence and structural requirements for the cleavage reaction. Here, the functions of the different structural domains in cleavage were assessed by deletion/mutational analyses, and biochemical structure probing assays were performed to characterize better the RNA structures formed and to verify the computer folding predictions. The data suggest that the stem-loop domain contributes to maintain a highly specific c leavage-site by preventing the formation of alternative structures in the cleavage-site domain. Involvement of the nucleotides in the cleavage-site loop itself in non-Watson-Crick interactions may be important for providing a specific recognition surface for an endoribonuclease activity.

Regulatory role of the 3' untranslated region of luteinizing hormone receptor: effect on mRNA stability

Posttranscriptional regulation of luteinizing hormone receptor (LHR) mRNA has a significant role in regulating cell surface receptor expression during ovarian cycle. In order to gain insight into the mechanism of posttranscriptional regulation, the cis-acting elements in the 3' untranslated region (3' UTR) of LHR mRNA were examined by transfection studies followed by measurements of the receptor expression and receptor mRNA half-life. The results show that the inhibitory effect exerted by the 3.51 kb 3' UTR of the LHR resides in the distal 1.98 kb region. Half-life measurement of LHR mRNA showed that the inhibitory effect of the 3' UTR was due to a decrease in receptor mRNA stability. Deletion studies revealed that the entire 1.98 kb region is required for LHR mRNA destabilization. Although the 3.51 kb 3' UTR of LHR contains 11 AUUUA motifs, their removal had no effect on mRNA stability or receptor expression. Thus, although AUUUA motifs have been implicated in mRNA stability, these motifs do not appear to play an inhibitory role in LHR expression. The 3' UTR of LHR was also able to decrease the expression of a reporter gene indicating that the inhibitory effect of 3' UTR is not unique to the open reading frame of LHR. The present studies show that the distal 1.98 kb portion of the 3' UTR exerts an inhibitory effect on the expression of LHR by decreasing the receptor mRNA half-life. The inhibitory effect of 3' UTR might play a role in the maintenance of the steady state levels of the receptor mRNA under different physiological states.

Posttranscriptional Regulation of Acute Phase Serum Amyloid A2 Expression by the 5′- and 3′-Untranslated Regions of Its mRNA

Human acute-phase serum amyloid A protein (A-SAA) is a major acute phase reactant, the concentration of which increases dramatically as part of the body’s early response to inflammation. A-SAA is the product of two almost identical genes, SAA1 and SAA2, which are induced by the pro-inflammatory cytokines, IL-1 and IL-6. In this study, we examine the roles played by the 5′- and 3′-untranslated regions (UTRs) of the SAA2 mRNA in regulating A-SAA2 expression. SAA2 promoter-driven luciferase reporter gene constructs carrying the SAA2 5′-UTR and/or 3′-UTR were transiently transfected into the HepG2 human hepatoma cell line. After induction of chimeric mRNA with IL-1β and IL-6, the SAA2 5′- and 3′-UTRs were both able to posttranscriptionally modify the expression of the luciferase reporter. The SAA2 5′-UTR promotes efficient translation of the chimeric luciferase transcripts, whereas the SAA2 3′-UTR shares this property and also significantly accelerates the rate of reporter mRNA degradation. Our data strongly suggest that the SAA2 5′- and 3′-UTRs each play significant independent roles in the posttranscriptional regulation of A-SAA2 protein synthesis.

Transcriptional pulsing approaches for analysis of mRNA turnover in mammalian cells

Modulation of mRNA stability provides a powerful means for controlling gene expression during the cell cycle, cell differentiation, the immune response, as well as many other physiological transitions. Through the years, many different methods have been developed for measuring mRNA stability. Frequently mRNA stability is studied indirectly by analyzing the steady-state level of mRNA. Therefore by inference, changes in mRNA abundance are thought to affect only the stability of the mRNA, an assumption that is not always correct. Alternatively, direct measurements of mRNA decay are performed in a number of ways, including kinetic labeling techniques and administration of transcriptional inhibitors. Due to the nature of these techniques, they either are technically demanding or introduce a significant change in cell physiology. In addition, many critical mechanistic issues as to deadenylation kinetics, decay intermediates, and precursor-product relationships cannot be readily addressed by these methods. Here, we describe and discuss in detail two different transcriptional pulsing methods based on the c-fos serum-inducible promoter and the tetracycline-regulated promoter systems as an effort to better elucidate the mechanistic steps and regulation underlying differential and selective mRNA turnover in mammalian cells. Both systems allow unequivocal monitoring of deadenylation and decay kinetics as well as determination of precursor-product relationship. In addition, decay rate constants and half-lives are determined and used in both methods to quantitatively denote the mRNA stability. Thus, they provide a reliable way to determine subtle yet physiologically meaningful changes in mRNA stability. Application of one method or the other covers the study of mRNA turnover in most mammalian cell types under a wide range of physiological conditions.

Insulin-like growth factor II promoter expression in cultured rodent osteoblasts and adult rat bone

Insulin-like growth factor (IGF)-II stimulates bone formation by increasing the replication of cells of the osteoblastic lineage and by enhancing the differentiated function of the osteoblast. Although IGF-II is synthesized by skeletal cells, little is known about the mechanisms involved and its regulation by growth factors. IGF-II expression is tissue specific and is developmentally regulated. In the present study, we examined the expression of IGF-II in fetal rat, newborn mouse and MC3T3-E1 osteoblastic (Ob) cells, and in adult rat calvariae. We also determined mechanisms involved in the regulation of IGF-II by platelet-derived growth factor (PDGF) BB, fibroblast growth factor-2 (FGF-2), and transforming growth factor (TGF) beta1. Northern analysis revealed IGF-II transcripts of 3.6 and 1.2 kb in osteoblastic cells and adult rat calvariae. Ribonuclease (RNase) protection assay using probes specific to the three known IGF-II promoters, P1, P2, and P3, demonstrated messenger RNA (mRNA) expression driven by P3 in osteoblasts and adult rat calvariae, but no expression of P1 or P2 transcripts. PDGF BB, FGF-2, and TGF beta1 inhibited the expression of IGF-II P3 mRNA by 50%. PDGF BB, FGF-2, and TGF beta1 also decreased the rates of IGF-II transcription in rat Ob cells as determined by nuclear run-on assays and did not modify the decay of IGF-II in transcriptionally arrested rat Ob cells. In conclusion, the synthesis of IGF-II in osteoblastic cells and in adult rat calvariae is driven by IGF-II P3 and is regulated by skeletal growth factors acting at the transcriptional level using the IGF-II P3.

Isolation and characterization of tilapia (Oreochromis mossambicus) insulin-like growth factors gene and proximal promoter region

To understand the molecular mechanism which controls the transcription of the insulin-like growth factors (IGFs) gene, we have cloned and sequenced the cDNA for the proximal promoter region of the tilapia IGFs gene and have characterized its activity by chloramphenicol acetyltransferase (CAT) transient transfected expression assays. Tilapia (Oreochromis mossambicus) IGF-I cDNA (549 bp) was amplified by PCR from single-stranded cDNA of growth hormone (GH)-induced liver RNA using a pair of oligonucleotides specific for fish IGF-I as amplification primers. Tilapia IGF-I and IGF-II 5' termini were analyzed by rapid amplification of cDNA 5' ends (5'RACE). Analysis of the 5'RACE results revealed two transcription start sites in IGF-I and one transcription start site in IGF-II. Different fragments of the 5' flanking region were transfected into human lung adenocarcinoma cells. In the cell line, maximum promoter activity was located in the distal 657 basepairs of the IGF-I 5' flanking region and in the distal 450 basepairs of the IGF-II 5' flanking region. The in vivo actions of the IGFs promoter on developmental stage expression were investigated further in transgenic zebrafish in which an IGFs promoter-driven green fluorescent protein (GFP) encoding the cDNA transgene was microinjected into embryos. Morphologic and RT-PCR studies of the transgenic zebrafish indicated that IGF-I promoter-driven GFP transcripts appeared for the first time in the 1-K-cell stage and the IGF-II promoter-driven GFP transcripts appeared for the first time in the 32-cell stage. Fluorescent (GFP) distribution was apparent within 48 h in IGF-II-transgenic zebrafish embryos, especially in eye, muscle, corpuscle, floor plate, horizontal myoseptum, yolk sac extension, and yolk sac. These results indicate that the IGF-I and IGF-II promoters are active in tissue and in a development-specific manner. Our findings also indicate that the IGF-II promoter influences the growth of fish embryos earlier than does IGF-I, and IGF-II has higher levels of expression than does IGF-I. These results suggest that the IGF-II promoter plays a growth factor role in teleost embryo development.

Deadenylation-dependent and -independent decay pathways for alpha1-tubulin mRNA in Chlamydomonas reinhardtii

The alpha- and beta-tubulin mRNAs of Chlamydomonas reinhardtii exhibit different half-lives under different conditions: when expressed constitutively, they degrade with half-lives of about 1 h, whereas when induced by deflagellation, they degrade with half-lives of only 10 to 15 min. To investigate the decay pathway(s) used under these two conditions, an alpha1-tubulin gene construct which included an insert of 30 guanidylate residues within the 3' untranslated region was introduced into cells. This transgene was efficiently expressed in stably transformed cells, and the mRNA exhibited constitutive and postinduction half-lives like those of the alpha1-tubulin mRNA. Northern blot analysis revealed the occurrence of a 3' RNA fragment derived from the poly(G)-containing alpha1-tubulin transcripts. The 3' fragment was shown to accumulate as full-length mRNA disappeared in actinomycin D-treated cells, indicating a precursor-product relationship. Insertion of a second poly(G) tract upstream of the first resulted in accumulation of only a longer 3' fragment, suggesting that the decay intermediate is generated by 5'-to-3' exonucleolytic digestion. A translational requirement for generation of the 3' fragment was demonstrated by experiments in which cells were deflagellated in the presence of cycloheximide. Analysis of fragment poly(A) length revealed that the fragments were, at most, oligoadenylated in nondeflagellated cells but had a long poly(A) tail in deflagellated cells. These findings suggest that the oligoadenylated fragment is a decay intermediate in a deadenylation-dependent, constitutive degradation pathway and that the requirement for deadenylation is bypassed in deflagellated cells. This represents the first example in which a single transcript has been shown to be targeted to different decay pathways under different cellular conditions.

A broader role for AU-rich element-mediated mRNA turnover revealed by a new transcriptional pulse strategy

The widespread occurrence of AU-rich elements (AREs) in mRNAs encoding proteins with diversified functions and synthesized under a vast variety of physiological conditions suggests that AREs are involved in finely tuned and stringent control of gene expression. Thus it is important to investigate the regulation of ARE-mediated mRNA decay in a variety of mammalian cells in different physiological states. The tetracycline (Tet)-regulatory promoter system appears appropriate for these investigations. However, we found that efficient degradation of mRNAs bearing different AREs cannot be observed simply by blocking constitutive transcription from the Tet-regulated promoter with Tet, possibly due to saturation of the cellular decay machinery. In addition, deadenylation kinetics and their relationship to mRNA decay cannot be adequately measured under these conditions. To overcome these obstacles we have developed a new strategy that employs the Tet-regulated promoter system to achieve a transient burst of transcription that results in synthesis of a population of cytoplasmic mRNAs fairly homogeneous in size. Using this new system we show that ARE-destabilizing function, necessary for down-regulating mRNAs for cytokines, growth factors and transcription factors, is maintained in quiescent or growth-arrested cells as well as in saturation density-arrested NIH 3T3 cells. We also demonstrate that the ARE-mediated decay pathway is conserved between NIH 3T3 fibroblasts and K562 erythroblasts. These in vivo observations support a broader role for AREs in the control of cell growth and differentiation. In addition, we observed that there is a significant difference in deadenylation and decay rates for beta-globin mRNA expressed in these two cell lines. Deadenylation and decay of beta-globin mRNA in K562 cells is extraordinarily slow compared with NIH 3T3 cells, suggesting that the increased stability gained by beta-globin mRNA in K562 cells is mainly controlled at the deadenylation step. Our strategy for studying mammalian mRNA turnover now permits a more general application to different cell lines harboring the Tet-regulated system under various physiological conditions.

Distinct repression of translation by wortmannin and rapamycin

The role of phosphatidylinositol 3-kinase and FK506-binding protein rapamycin-associated protein (FRAP) in translational control has been examined by treating RD-rhabdomyosarcoma cells with wortmannin and rapamycin and studying the effects on cell-growth, translation initiation, and protein synthesis. Whereas wortmannin and rapamycin exhibit subtle effects on global translation, examination of individual mRNAs in sucrose gradients and of individual proteins in two-dimensional polyacrylamide gels reveals that wortmannin and rapamycin exhibit distinct effects on the translation of individual mRNAs. Wortmannin represses the synthesis of a third of cellular proteins, whereas rapamycin affects a subset of these proteins. Since ribosomal protein S6 was rapidly dephosphorylated following wortmannin and rapamycin treatment, and the phosphorylation status of the eukaryotic initiation factor 4E was unchanged, our data imply that the p70 signalling pathway has at least one branch-point upstream of FRAP leading to an additional route of translational control.

Structure and expression of the gene encoding secretor-type galactoside 2-alpha-L-fucosyltransferase (FUT2)

The expression and secretion of ABO antigens in epithelial cells of glands are controlled by secretor-type alpha (1,2)fucosyltransferase activity. We have examined the expression of the secretor-type alpha(1,2)fucosyltransferase gene (FUT2) and a pseudogene of FUT2 (Sec1) in several tumor cell lines by northern blot and/or reverse-transcription-PCR (RT-PCR) analyses. Transcripts of FUT2 were found in total RNA from ovarian, gastric and colonic cancer cell lines but not from six leukemic cell lines, including erythroleukemic HEL cells, by RT-PCR. On the other hand, RT-PCR indicated that Sec1 was expressed in all these tumor cells, including all hematopoietic cells studied. Northern blot analysis indicated that FUT2 transcripts with a similar size (3.3 kb) were expressed in cancer cell lines. Rapid amplification of cDNA ends suggested that the entire FUT2 cDNA is 3.1-kb long and has two Alu repetitive elements in its 3' untranslated region, including an inverted repeat. The mRNA, therefore, may form a large stem-and-loop structure (1.2 kb). Each stem contains about 300 bases, the loop contains 640 bases, and the percentage of complementary nucleotide sequences in the stem region is 85%. The presence of a large stem-and-loop structure in the 3' untranslated region may regulate the level of the FUT2 transcript by affecting the stability of the mRNA.

Human CD46 aberrant splicing in transgenic mice

RNA analysis of mice transgenic for human CD46 reveals almost undetectable levels of the expected transcript and the accumulation of a 900 nt shorter species. cDNA cloning and sequence analysis of this variant demonstrate an aberrant splicing of the transgene RNA. This aberrant splicing is present at low levels in cells that normally express the gene, suggesting that the transgene is lacking regulatory elements influencing the abundance of the shorter transcript.

Regulation of eukaryotic messenger RNA turnover

We have demonstrated the existence of multiple mRNA binding proteins that interact specifically with defined regions in posttranscriptionally regulated mRNAs. These domains appear to be destabilizers whose function can be attenuated by the interaction with the specific binding proteins. Thus, the ability to alter mRNA decay rates on demand, given different environmental or intracellular conditions, appears to be mediated by controlling the localization, activity, and overall function of the cognate binding protein. Based on our limited experience, we predict that most, if not all, of similarly regulated mRNAs will ultimately be found to interact with regulatory mRNA binding proteins. Under conditions whereby the mRNA binding proteins are constitutively active (e.g., tumor cell lines), abnormal mRNA decay will result, with accumulation and overtranslation. Such appears to be the case for cytokines and possibly amyloid protein precursor mRNAs in cancer and Alzheimer's disease, respectively. Conversely, mutagenesis of these critical 3' untranslated region elements will likely have comparable deleterious effects on the regulation of gene expression. To the extent that such derangements exist in human disease, attention to understanding the mechanistic detail at this level may provide insights into the development of appropriate therapeutics or treatment strategies.

Control of messenger RNA stability in higher eukaryotes

The mRNA decay rate (half-life) is a major determinant of mRNA abundance in organisms from bacteria to mammals. mRNA levels can fluctuate many-fold following a change in mRNA half-life, without any change in transcription, and these fluctuations affect how a cell grows, differentiates and responds to its environment. The half-lives of many mRNAs vary tenfold or more in response to cytokines, hormones, starvation, hypoxia, or viral infection. Three major questions regarding mRNA stability are currently being addressed. What sequences in mRNAs determine half-lives? What enzymes degrade mRNAs? What (trans-acting) factors regulate mRNA stability and how do they function? This review focuses on RNA-binding or regulatory proteins and on candidate messenger ribonucleases (mRNases).

Differential stability of Xenopus c-myc RNA during oogenesis in axolotl Involvement of the 3' untranslated region in vivo

We have used the axolotl oocyte (Ambystoma mexicanum Shaw) to study the stability of exogenously injected Xenopus RNAs. Three different cellular developmental stages have been analysed: (1) the growing oocyte (stage III-IV of vitellogenesis), (2) the full-grown oocyte at the end of vitellogenesis (stage VI) and (3) the progesterone-matured stage VI oocyte. Three exogenous RNAs have been synthesized in vitro from a c-myc Xenopus cDNA clone. One transcript is 2.3 kb long (full length), the second is 1.5 kb long, with most of the 3' untranslated region (3'UTR) removed, and the third corresponds to the 3'UTR (0.8 kb). After injection or coinjection of these exogenous Xenopus RNAs into axolotl oocytes, the stability of the molecules was studied after 5 min, 6 h and 21 h by extraction of total RNA and Northern blot analysis.Results show a difference in Xenopus RNA stability during axolotl oogenesis. In growing oocytes, the three synthetic transcripts are gradually degraded. The absence of the 3'UTR is not therefore sufficient to stabilize the transcript during early oogenesis. No degradation is observed in full-grown oocytes, suggesting the existence of stabilizing factors at the end of oogenesis. When stage VI oocytes are induced to mature by progesterone, only the 2.3 and 1.5 kb Xenopus RNAs disappear. This suggests a role for germinal vesicle breakdown in this degradation process as well as the existence of a factor present in the nucleus and involved in the specific destabilization of these RNAs after oocyte maturation. This degradation might implicate several destabilizing sequences localized in the coding or in the 3'UTR of the c-myc gene. In contrast, the 0.8 kb transcript (3'UTR) is not degraded during this period and remains very stable. Therefore, degradation appears distinct from one transcript to another and from one region to another within the same molecule. During maturation, the behaviour of the 2.3 and 1.5 kb transcripts is different when coinjected with the 3'UTR, suggesting a role in trans of this untranslated molecule in c-myc stability. Our approach allows us to analyse the role of the coding and 3'UTR regions of the c-myc RNA in the control of mRNA degradation in vivo.

Growth-dependent translation of IGF-II mRNA by a rapamycin-sensitive pathway

Insulin-like growth factor (IGF)-II is important for fetal growth and development. The human IGF-II gene generates multiple mature transcripts with different 5' untranslated regions (5'UTRs) but identical coding regions and 3'UTRs. We have previously shown that a minor 4.8-kilobase messenger RNA was engaged in the synthesis of preproIGF-II, and a major 6.0-kb mRNA was untranslated and stored in a 100S ribonucleoprotein particle. Here we demonstrate that the 6.0-kb mRNA is selectively mobilized and translated in dispersed exponentially growing cells. Translational activation is prevented by rapamycin and mimicked by anisomycin, which suggests that translation of the 6.0-kb mRNA is regulated by the p70S6k/85S6k kinase signalling pathway. Therefore, the minor 4.8-kb mRNA generates a constitutive production of prepro-IGF-II, whereas the major 6.0-kb mRNA provides a post-transcriptionally regulated species.

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.

Diversity of cytoplasmic functions for the 3' untranslated region of eukaryotic transcripts

The 3' untranslated region (3' UTR) can control gene expression by affecting the localization, stability and translation of mRNAs. The recent finding that 3' UTRs can control the decapping rate of mRNAs, in combination with their ability to influence the initiation of translation, suggests that 3' UTRs act through a direct or indirect interaction between the 3' and 5' ends of mRNAs.

Degradation of mRNA in eukaryotes

Based on the above mechanisms of mRNA degradation, an integrated model of mRNA turnover can be proposed (Figure 1). In this model, all polyadenylated mRNAs would be degraded by the deadenylation-dependent pathway at some rate. In addition to this default pathway, another layer of complexity would come from degradation mechanisms specific to individual mRNAs or to classes of mRNAs. Such mRNA-specific mechanisms would include sequence-specific endonuclease cleavage and deadenylation-independent decapping. Thus, the overall decay rate of an individual transcript will be a function of its susceptibility to these turnover pathways. In addition, cis-acting sequences that specify mRNA decay rate, as well as regulatory inputs that control mRNA turnover, are likely to affect all the steps of these decay pathways. One important goal in future work will be to identify the gene products that are responsible for the nucleolytic events in these pathways and to delineate how specific mRNA features act to affect the function of these degradative activities. The identification of distinct mRNA decay pathways should allow, genetic and biochemical approaches that can be designed to identify these gene products. A second important goal is to understand the nature of the interaction between the 5' and 3' termini, which may also be critical for efficient translation.

Purification and characterization of an estrogen-regulated Xenopus liver polysomal nuclease involved in the selective destabilization of albumin mRNA

A previous report from this laboratory described an estrogen-regulated endoribonuclease activity on Xenopus liver polysomes which had properties one might expect for a messenger ribonuclease involved in the regulated destabilization of albumin mRNA (Pastori, R. L., Moskaitis, J. E., and Schoenberg, D. R. (1991) Biochemistry 30, 10490-10498). This report describes the purification and properties of this ribonuclease. The purified nuclease fraction contained a doublet of 62 and 64 kDa and a small amount of a 40-kDa peptide. In situ analysis on both denaturing and nondenaturing gels using an albumin transcript as substrate showed all three proteins possess nuclease activity. Peptide mapping and Western blot with a polyclonal antiserum showed the 62- and 64-kDa peptides to be isoforms, and the 40-kDa peptide to be a degradation product of the larger species. Two-dimensional gel electrophoresis further separated the 62- and 64-kDa species into three pairs of proteins, with isoelectric points of 9.6, 9.8, and 9.8. The purified ribonuclease rapidly degraded a full-length albumin transcript, yet had no effect on either a full-length albumin antisense transcript or full-length ferritin transcript. A number of properties of the purified nuclease were characterized, including the effects of salt, divalent cations, EDTA, sulfhydryl reagents, and temperature. Treatment of the polysomal nuclease with micrococcal nuclease had no effect, indicating that this enzyme does not require an RNA cofactor for activity. Finally, primer extension mapped the major cleavage site to an overlapping repeated sequence APyrUGA, with cleavage between and adjacent to the two pyrimidine residues generating fragments with 5'-hydroxyls.

Discriminating translation of insulin-like growth factor-II (IGF-II) during mouse embryogenesis

The problem is to discover which of the promoters of the insulin-like growth factor-II gene stimulate the transcription of mRNA which is translated into protein. Three alternative leader exons are attached to the coding sequences in RNA transcribed from this gene in other systems, and it is mainly the paternal allele which is expressed in mouse development. Transcripts bearing each of the three leader exons were found in the RNA from the chorio-allantoic placenta, visceral yolk sac, and embryo, starting at 9.5 days. A varying proportion of one abundant transcript was disengaged from the polysomes at different days of development. This transcript was prefixed by the longest of the three alternative untranslated 5' leader exons (exon 2), and it was consistently associated with polysomes in the choroid plexus and leptomeninges of the brain. Many exon 2 transcripts were abbreviated by endonucleolytic cleavage and lacked a poly(A) tail. In contrast, the transcripts with the shortest leader (exon 3) were mainly displayed on polysomes at all the stages of development which were examined. During mouse development, the production of IGF-II protein must be partly controlled by the mechanisms which regulate translation.

Mechanisms of mRNA degradation in eukaryotes

Recent experiments have identified distinct mechanisms of eukaryotic RNA turnover. In one mechanism, deadenylation triggers decapping, exposing the messenger RNA to 5' to 3' degradation. This pathway may act at different rates on the majority of messenger RNAs. There are also degradation mechanisms, such as endonucleolytic cleavage, limited to messenger RNAs containing specific sequence elements.

Measurement of gut hormone gene expression: mRNA and peptides

During the past decade numerous methods for measurement of mRNA and peptides have been developed. Since the expression cascade from DNA to protein is regulated at all levels, the methods should be carefully designed to accomplish the purpose of the analysis. Regulation of the nuclear processing, the translational activity and the decay of a particular mRNA changes the proportionality between transcriptional activity and production of prepropeptide. Moreover, the post-translational maturation of the pro-hormones may be attenuated. Detection of mRNA is valuable and feasible because it is easy to generate cDNA probes for most hormones, and because mRNA demonstration unequivocally indicates the cellular site of gene expression. The deduction of preprohormone structures has also made it possible to improve the versatility of radioimmunoassays (RIA). Monospecific antibodies and pure tracers have allowed the development of sequence-specific RIA libraries for bioactive peptides and their precursors. Recently we have introduced a simple processing-independent analysis (PIA) for clinical use, since the post-translational maturation of gut peptides may be changed in gastrointestinal diseases. So far PIA has improved the diagnostic sensitivity for gut hormone tumours.

Insulin-like growth factors

The purpose of this review has been to emphasize, in general terms, the major aspects of the structure, expression, and regulation of the IGF-I and IGF-II genes. The complex organization of these genes provides ample opportunities for control of gene expression at multiple levels. It is important to realize that regulation at one level can influence regulation at a different level. While such regulatory interactions are characteristic of both the IGF-I and IGF-II genes, they are particularly evident in the case of IGF-I gene expression. For example, the choice of transcription start site influences the length and the sequence of the 5'-UTR, which can influence mRNA translatability and prepeptide sequence, which may influence the amounts of protein produced and, potentially, the intracellular processing and secretion of the final gene product, the mature hormone. Another example is provided by the alternative splicing of E-peptide-encoding exons, which determines the primary structure of the prohormone, which could influence its processing, stability, or function. Thus, this complex gene organization may reflect the need to carefully control, through a multilevel process, the synthesis, processing, and secretion of these important regulatory peptides.

The molecular and cellular biology of insulin-like growth factor II

Insulin-like growth factor II (IGF-II) is a 67 amino acid polypeptide that belongs to the family of insulin-like peptides. The IGF-II gene is coupled to the insulin gene and paternally imprinted. Multiple IGF-II mRNAs with identical coding regions and 3' untranslated regions (UTRs) but different 5' UTRs are generated from 3 promoters. The transcripts are translationally discriminated and inactivated by a specific endonucleolytic cleavage in their 3' UTR. These features may be important in the control of IGF-II production. IGF-II functions in an auto- and paracrine manner and binds to two types of receptors. The IGF-I receptor that is a tyrosine kinase and closely related with the insulin receptor and the IGF-II/mannose 6-phosphate (IGF-II/Man 6-P) receptor that is identical with the cation-independent mannose 6-phosphate receptor. The mitogenic and metabolic actions of IGF-II are propagated by the IGF-I receptor. In contrast, the IGF-II/Man 6-P receptor, that target lysosomal enzymes from the Golgi apparatus or the plasma membrane to the lysosomes, mediates the rapid internalization and degradation of IGF-II. IGF-II is expressed at high levels during foetal life and it is a major growth factor for the foetus in rodents. The developmental profiles and tissue distribution of the IGF-I and the maternally imprinted IGF-II/Man 6-P receptors both parallel that of IGF-II. In this scenario IGF-II promotes the growth of the embryo through the IGF-I receptor, whereas the IGF-II/Man 6-P receptor balance the activity by controlling the extracellular level of IGF-II.