Stability of nuclear RNA in mammalian cells

A mechanistic pan-cancer pathway model informed by multi-omics data interprets stochastic cell fate responses to drugs and mitogens

Most cancer cells harbor multiple drivers whose epistasis and interactions with expression context clouds drug and drug combination sensitivity prediction. We constructed a mechanistic computational model that is context-tailored by omics data to capture regulation of stochastic proliferation and death by pan-cancer driver pathways. Simulations and experiments explore how the coordinated dynamics of RAF/MEK/ERK and PI-3K/AKT kinase activities in response to synergistic mitogen or drug combinations control cell fate in a specific cellular context. In this MCF10A cell context, simulations suggest that synergistic ERK and AKT inhibitor-induced death is likely mediated by BIM rather than BAD, which is supported by prior experimental studies. AKT dynamics explain S-phase entry synergy between EGF and insulin, but simulations suggest that stochastic ERK, and not AKT, dynamics seem to drive cell-to-cell proliferation variability, which in simulations is predictable from pre-stimulus fluctuations in C-Raf/B-Raf levels. Simulations suggest MEK alteration negligibly influences transformation, consistent with clinical data. Tailoring the model to an alternate cell expression and mutation context, a glioma cell line, allows prediction of increased sensitivity of cell death to AKT inhibition. Our model mechanistically interprets context-specific landscapes between driver pathways and cell fates, providing a framework for designing more rational cancer combination therapy.

Cancer is a complex and diverse disease. Two people with the same cancer type often respond differently to the same treatment. These differences are primarily driven by the fact that two type-matched tumors can possess distinct sets of mutations and gene expression profiles, provoking differential sensitivity to drugs. Over the past few decades, we have seen a shift away from more broadly cytotoxic drugs to more targeted molecules therapies; but how to match a patient with a specific drug or drug cocktail remains a difficult problem. Here, we build a mechanistic ordinary differential equation model describing the interactions between commonly mutated pan-cancer signaling pathways—receptor tyrosine kinases, Ras/RAF/ERK, PI3K/AKT, mTOR, cell cycle, DNA damage, and apoptosis. We develop methods for how to tailor the model to multi-omics data from a specific biological context, devise a novel stochastic algorithm to induce non-genetic cell-to-cell fluctuations in mRNA and protein quantities over time, and train the model against a wealth of biochemical and cell fate data to gain insight into the systems-level, context-specific control of proliferation and death. One day, we hope models of this kind could be tailored to patient-derived tumor mRNA sequencing data and used to prioritize patient-specific drug regimens.

Two's company: studying interspecies relationships with dual RNA-seq

Organisms do not exist isolated from each other, but constantly interact. Cells can sense the presence of interaction partners by a range of receptors and, via complex regulatory networks, specifically react by changing the expression of many of their genes. Technological advances in next-generation sequencing over the recent years now allow us to apply RNA sequencing to two species at the same time (dual RNA-seq), and thus to directly study the gene expression of two interacting species without the need to physically separate cells or RNA. In this review, we give an overview over the latest studies in interspecies interactions made possible by dual RNA-seq, ranging from pathogenic to symbiotic relationships. We summarize state-of-the-art experimental techniques, bioinformatic data analysis and data interpretation, while also highlighting potential problems and pitfalls starting from the selection of meaningful time points and number of reads to matters of rRNA depletion. A short outlook on new trends in the field of dual RNA-seq concludes this review, looking at sequencing of non-coding RNAs during host-pathogen interactions and the prediction of molecular interspecies interactions networks.

Self-organization and entropy reduction in a living cell

In this paper we discuss the entropy and information aspects of a living cell. Particular attention is paid to the information gain on assembling and maintaining a living state. Numerical estimates of the information and entropy reduction are given and discussed in the context of the cell's metabolic activity. We discuss a solution to an apparent paradox that there is less information content in DNA than in the proteins that are assembled based on the genetic code encrypted in DNA. When energy input required for protein synthesis is accounted for, the paradox is clearly resolved. Finally, differences between biological information and instruction are discussed.

In vivo kinetics of U4/U6·U5 tri-snRNP formation in Cajal bodies

The U4/U6·U5 tri-small nuclear ribonucleoprotein particle (tri-snRNP) is an essential pre-mRNA splicing factor, which is assembled in a stepwise manner before each round of splicing. It was previously shown that the tri-snRNP is formed in Cajal bodies (CBs), but little is known about the dynamics of this process. Here we created a mathematical model of tri-snRNP assembly in CBs and used it to fit kinetics of individual snRNPs monitored by fluorescence recovery after photobleaching. A global fitting of all kinetic data determined key reaction constants of tri-snRNP assembly. Our model predicts that the rates of di-snRNP and tri-snRNP assemblies are similar and that ∼230 tri-snRNPs are assembled in one CB per minute. Our analysis further indicates that tri-snRNP assembly is approximately 10-fold faster in CBs than in the surrounding nucleoplasm, which is fully consistent with the importance of CBs for snRNP formation in rapidly developing biological systems. Finally, the model predicted binding between SART3 and a CB component. We tested this prediction by Förster resonance energy transfer and revealed an interaction between SART3 and coilin in CBs.

Development, validation and field application of an RNA-based growth index in juvenile plaice Pleuronectes platessa

A general mechanism relating RNA concentration and growth rate is derived from four physiological assumptions and developed into a growth index for juvenile plaice Pleuronectes platessa. The index describing instantaneous growth rates (G, day⁻¹) in the laboratory with the lowest Akaike information criterion with small-sample bias adjustment was a function of RNA concentration (R, g(RNA)g⁻¹(wet mass)), temperature (T, ° K), body mass (M, g) and DNA concentration (D, g(DNA)g⁻¹(wet mass)): G = β₀ + β(R) R + β(T)T + β(T2)T² + β(M)M + β(D)D + β(RT)RT. RNA concentration began to respond to changes in feeding conditions within 8 days, suggesting that the index reflects growth rate in the short-term. Furthermore, the index distinguished between rapid growth and negative growth of juvenile P. platessa measured directly in laboratory and field enclosures, respectively. An application of the RNA-based growth index at two beaches on the west coast of Scotland suggested that the growth of juvenile P. platessa varies considerably in space and time and is submaximum in late summer.

The many pathways of RNA degradation

From the earliest comparisons of RNA production with steady-state levels, it has been clear that cells transcribe more RNA than they accumulate, implying the existence of active RNA degradation systems. In general, RNA is degraded at the end of its useful life, which is long for a ribosomal RNA but very short for excised introns or spacer fragments, and is closely regulated for most mRNA species. RNA molecules with defects in processing, folding, or assembly with proteins are identified and rapidly degraded by the surveillance machinery. Because RNA degradation is ubiquitous in all cells, it is clear that it must be carefully controlled to accurately recognize target RNAs. How this is achieved is perhaps the most pressing question in the field.

Validation of immuno-laser capture microdissection coupled with quantitative RT-PCR to probe blood-brain barrier gene expression in situ

Laser capture microdissection (LCM) holds great potential for analyzing gene expression profiles in situ. Most recently, this laboratory employed a novel immunostain-based LCM protocol (immuno-LCM) to selectively retrieve brain microvascular endothelial cells (BMEC) from intimately associated perivascular cells. However, before this protocol can be confidently coupled to downstream analytical platforms, it must be demonstrated that any variability associated with it is minimal, so as not to obscure data interpretation. As various factors could contribute to variability, this study focused on determining whether technical inconsistency and/or biological diversity of sample populations, played such a role. Specifically, two separate immuno-LCM-derived BMEC samples derived from adjacent tissue sections of a single mouse (to detect only technical variability), and from analogous tissue sections of three different mice (to detect technical and biological variability) were compared for their relative expression of 16 genes, using quantitative-RT-PCR (qRT-PCR). Both significant linear and rank-order correlations were observed between different sections from the same animal, underscoring lack of technical variability in this LCM application. Furthermore, a three-dimensional scatter plot of gene expression profiles from the three animals was linear, and ANOVA showed absence of statistically significant differences between any of the animals, confirming lack of biological variability. These findings argue that immuno-LCM coupled to qRT-PCR affords a reproducible means to assay gene expression in situ.

In vitro human keratinocyte migration rates are associated with SNPs in the KRT1 interval

Efforts to develop effective therapeutic treatments for promoting fast wound healing after injury to the epidermis are hindered by a lack of understanding of the factors involved. Re-epithelialization is an essential step of wound healing involving the migration of epidermal keratinocytes over the wound site. Here, we examine genetic variants in the keratin-1 (KRT1) locus for association with migration rates of human epidermal keratinocytes (HEK) isolated from different individuals. Although the role of intermediate filament genes, including KRT1, in wound activated keratinocytes is well established, this is the first study to examine if genetic variants in humans contribute to differences in the migration rates of these cells. Using an in vitro scratch wound assay we observe quantifiable variation in HEK migration rates in two independent sets of samples; 24 samples in the first set and 17 samples in the second set. We analyze genetic variants in the KRT1 interval and identify SNPs significantly associated with HEK migration rates in both samples sets. Additionally, we show in the first set of samples that the average migration rate of HEK cells homozygous for one common haplotype pattern in the KRT1 interval is significantly faster than that of HEK cells homozygous for a second common haplotype pattern. Our study demonstrates that genetic variants in the KRT1 interval contribute to quantifiable differences in the migration rates of keratinocytes isolated from different individuals. Furthermore we show that in vitro cell assays can successfully be used to deconstruct complex traits into simple biological model systems for genetic association studies.

Fiber-optic microarray for simultaneous detection of multiple harmful algal bloom species

Harmful algal blooms (HABs) are a serious threat to coastal resources, causing a variety of impacts on public health, regional economies, and ecosystems. Plankton analysis is a valuable component of many HAB monitoring and research programs, but the diversity of plankton poses a problem in discriminating toxic from nontoxic species using conventional detection methods. Here we describe a sensitive and specific sandwich hybridization assay that combines fiber-optic microarrays with oligonucleotide probes to detect and enumerate the HAB species Alexandrium fundyense, Alexandrium ostenfeldii, and Pseudo-nitzschia australis. Microarrays were prepared by loading oligonucleotide probe-coupled microspheres (diameter, 3 mum) onto the distal ends of chemically etched imaging fiber bundles. Hybridization of target rRNA from HAB cells to immobilized probes on the microspheres was visualized using Cy3-labeled secondary probes in a sandwich-type assay format. We applied these microarrays to the detection and enumeration of HAB cells in both cultured and field samples. Our study demonstrated a detection limit of approximately 5 cells for all three target organisms within 45 min, without a separate amplification step, in both sample types. We also developed a multiplexed microarray to detect the three HAB species simultaneously, which successfully detected the target organisms, alone and in combination, without cross-reactivity. Our study suggests that fiber-optic microarrays can be used for rapid and sensitive detection and potential enumeration of HAB species in the environment.

RNA stability in terminally differentiating fibre cells of the ocular lens

During terminal differentiation of lens fibre cells all cytoplasmic organelles are degraded abruptly. This process eliminates light-scattering elements from the optical axis of the lens and thereby ensures the transparency of the tissue. With the breakdown of the nucleus, transcription ceases, but the degree to which extant RNA is translated in the anucleated cells is uncertain. Previous studies indicated that fibre cell mRNA is unusually stable. For example, full-length delta-crystallin transcripts have been detected in core fibres months after transcription in these cells ceased. In the present study, we used the embryonic chicken lens as a model to examine the fate of RNA in the period immediately before and after organelle degradation. We mapped the tissue distribution of ribosomal RNA (rRNA) using acridine orange staining, in situ hybridization, and direct visualization of ribosomes by electron microscopy. These experiments suggested that rRNA decayed in the anucleated core fibre cells with a half-life of approximately 2.5 days. Similarly, in situ hybridization analysis of polyadenylated transcripts, beta-actin, or GAPDH mRNA indicated that these sequences were not stable in the core fibre cells. However, in agreement with earlier findings, we detected a strong in situ hybridization signal for delta-crystallin in the lens core, many days after transcription had ceased. We used quantitative PCR to compare the levels of GAPDH, L14 and delta-crystallin transcripts in the core region during development. Surprisingly, all three mRNAs decayed with indistinguishable kinetics. We conclude that the persistent delta-crystallin hybridization signal was not evidence of an unusually stable mRNA but, rather, reflected the extraordinary initial abundance of this transcript. Taken together, our data indicate that the half-life of both mRNA and the protein synthetic machinery in the lens core is only a few days. Given that, in vertebrate lenses, nuclei in this region of the lens are degraded during embryonic development, protein synthesis in central lens fibre cells is probably completed well before birth.

Turnover of primary transcripts is a major step in the regulation of mouse H19 gene expression

In the gene expression pathway, RNA biogenesis is a central multi-step process where both message fidelity and steady-state levels of the mature RNA have to be ascertained. An emerging question is whether RNA levels could be regulated at the precursor stage. Until recently, because it was technically very difficult to determine the level of a pre-mRNA, discrimination between changes in transcriptional activity and in pre-mRNA metabolism was extremely difficult. H19 RNA, the untranslated product of an imprinted gene, undergoes post-transcriptional regulation. Here, using a quantitative real-time RT-PCR approach, we accurately quantify its precursor RNA levels and compare these with the transcriptional activity of the gene, assessed by run-on assays. We find that the levels of H19 precursor RNA are regulated during physiological processes and this regulation appears to be related to RNA polymerase II transcription termination. Our results provide direct evidence that turnover of polymerase II primary transcripts can regulate gene expression in mammals.

Further evidence for the role of fibrosis in the pathobiology of rhinophyma

Recent evidence suggests that fibrosis may play an important role in the pathobiology of rhinophyma. The fibrogenic cytokine transforming growth factor (TGF)-beta2 has been reported to be up-regulated in rhinophyma tissue. Of the three common isoforms of TGF-beta, TGF-beta1 and TGF-beta2 are considered fibrogenic, whereas TGF-beta3 has antiscarring properties. To provide further evidence for the role of fibrosis in the pathobiology of rhinophyma, specimens from 8 patients with rhinophyma were compared with nine specimens of normal nasal skin. Immunohistochemistry was used to compare intensity levels of TGFbeta1 and TGFbeta3 proteins, and quantitative reverse transcription-polymerase chain reaction was used to determine messenger ribonucleic acid (mRNA) expression levels of TGFbeta1 and TGFbeta3. TGF-beta1 was elevated significantly in rhinophyma tissue (p < 0.001), whereas TGF-beta3 was no different in the rhinophyma specimens compared with normal nasal skin (p = 0.06). TGFbeta1 mRNA expression was five-fold higher in rhinophyma tissue compared with normal skin (p < 0.001). The mRNA expression of TGF-beta3 was the same for both pathological and normal tissue (p < 0.09). These data, together with previously published observations, present further evidence that fibrosis mediated by the fibrogenic cytokines TGFbeta1 and TGFbeta2 play a role in the pathobiology of rhinophyma and suggest a means of treatment by neutralizing or down-regulating these cytokines.

Epstein-Barr virus nuclear antigen 5 inhibits pre-mRNA cleavage and polyadenylation

The long-standing suspicion that Epstein-Barr virus nuclear antigen 5 (EBNA5) is involved in transcription regulation was recently confirmed by the observation by several groups that EBNA5 cooperates with EBNA2 in activation of the LMP1 promoter. In attempts to elucidate the molecular basis for the EBNA5-mediated enhancement of EBNA2 transactivation, we obtained evidence of an additional function of EBNA5: at high but still biologically relevant levels, EBNA5 acted as a repressor of gene expression by interfering with the processing of pre-mRNA. Transient transfections with reporter plasmids revealed that EBNA5 repressed reporter mRNA and protein expression in the cytoplasm, but did not lower the steady-state level of reporter RNA in the total cellular RNA fraction. We have excluded that repression occurred as a consequence of cell death induced by EBNA5. Using the RNase protection assay with a probe comprising the pre-mRNA cleavage and polyadenylation site, EBNA5 was found to inhibit 3'-end cleavage and polyadenylation of pre-mRNAs from the reporter plasmids investigated. The effect of inhibitory levels of EBNA5 on chromosomal genes was examined in transient transfections by expression profiling using a cDNA microarray panel containing 588 genes. The results showed that EBNA5 could also inhibit the expression of chromosomal genes and did it in a discriminatory manner. This is consistent with the notion that a regulatory mechanism exists in the cell that confers specificity to the selection by EBNA5 of target genes for repression.

Assessment of the total number of human transcription units

Variation in the estimates of the number of genes encoded by the human genome (28,000-120,000) attests to the difficulty of systematically identifying human genes. Sequencing of human chromosome 22 (Chr22) provided the first comprehensive, unbiased view of an entire human chromosome, and intensive analysis of this sequence identified 545 genes and 134 pseudogenes that had similarity or identity to known proteins and/or ESTs and which were listed in the gene annotation (http://www.sanger.ac.uk/HGP/Chr22). This analysis yielded an estimate of approximately 36,000 functional expressed genes in the human genome (and 9000 pseudogenes). However, a key uncertainty in this estimate was that hundreds of additional genes beyond those annotated in the Chr22 sequence are predicted by the gene prediction program Genscan, an unknown number of which might represent additional expressed genes. To determine what fraction of these "predicted novel genes" (PNGs) represents expressed human genes, we used a sensitive RT-PCR assay to detect predicted transcripts in 17 tissues and one cell line. Our results indicate that at least 5000-9000 additional human genes which lack similarity to known genes or proteins exist in the human genome, increasing baseline gene estimates to approximately 41,000-45,000.

Identification of a regulated pathway for nuclear pre-mRNA turnover

We have identified a nuclear pathway that rapidly degrades unspliced pre-mRNAs in yeast. This involves 3'-->5' degradation by the exosome complex and 5'-->3' degradation by the exonuclease Rat1p. 3'-->5' degradation is normally the major pathway and is regulated in response to carbon source. Inhibition of pre-mRNA degradation resulted in increased levels of pre-mRNAs and spliced mRNAs. When splicing was inhibited by mutation of a splicing factor, inhibition of turnover resulted in 20- to 50-fold accumulation of pre-mRNAs, accompanied by increased mRNA production. Splicing of a reporter construct with a 3' splice site mutation was also increased on inhibition of turnover, showing competition between degradation and splicing. We propose that nuclear pre-mRNA turnover represents a novel step in the regulation of gene expression.

Changes in the expression of extracellular matrix (ECM) and matrix metalloproteinases (MMP) of proliferating rat parotid acinar cells

Tissue morphogenesis, development, and maintenance of function are mediated by signals generated through the composition of the extracellular matrix. The regulation of the composition of matrix is determined by enzymes specific for their degradation, the matrix metalloproteinases. Chronic injections of the beta-adrenergic receptor agonist, isoproterenol, result in a non-neoplastic hypertrophy and hyperplasia of the rat parotid gland. The activity of matrix metalloproteinases, as measured by gelatin zymography and enzymatic digestion of Azocoll substrates by gland lysates, decreased significantly (P < 0.05) following 24 hrs of agonist treatment, and slowly recovered to control values by 6 days of treatment. Daily administration of the broad-spectrum matrix metalloproteinase inhibitor Galardin for 3 days in combination with isoproterenol resulted in enhanced gland hypertrophy compared with that produced by isoproterenol alone. Given alone, Galardin also caused hypertrophy. The relative abundance of mRNA for the extracellular matrix molecules, collagens I and III and fibronectin, declined rapidly following the initiation of beta-agonist treatment in vivo, while laminin B1 and B2 mRNA levels increased initially before declining below control levels. These changes in patterns of mRNA levels also were observed in the concentrations of glandular protein when Western dot blot analysis of collagens I and III and laminin, respectively, was used. The importance of laminin, in vivo, was demonstrated by coinjection of anti-laminin antibody along with isoproterenol, which resulted in the inhibition of beta-agonist-induced parotid gland hypertrophy and hyperplasia. These data suggest that modulation of the ECM is associated with isoproterenol-induced salivary gland hypertrophy and hyperplasia. It is likely that this modulation of the ECM takes place through transcriptional regulation of some ECM genes and regulation of matrix-degrading enzyme activity.

Extracellular-matrix gene expression during mouse submandibular gland development

Early morphogenesis of mouse submandibular glands begins on late day 11 of fetal development when the epithelium begins to bud from the surrounding mandibular mesenchyme. Using total RNA collected from fetal BALB/c submandibular glands, steady-state levels of mRNA expression for extracellular matrix molecules were measured using quantitative competitive reverse transcription-polymerase chain reaction (RT-PCR). By comparing the PCR amplification products of both the cellular mRNA and a synthetic template, pMATRIX, it was possible to measure the direct expression of collagens alpha2(I), alpha1(III), alpha1(IV), fibronectin, laminin B2, elastin and lysyl oxidase genes. There was an observed trend for an increasing concentration of collagen alpha2(I), collagen alpha1(III) and lysyl oxidase mRNA molecules per cell on day 16 of development. The relative abundance of elastin mRNA was detectable only on day 16. Fibronectin and laminin B2 were more constitutively present but had their highest copy number per cell on day 16. The presence of extracellular-matrix protein was confirmed by immunohistochemistry using day-16 fetal glands and adult glands. With the construction of the pMATRIX supertemplate and the advent of quantitative, competitive RT-PCR technology, it has been possible to measure small changes in the steady-state concentrations for extracellular-matrix mRNA during salivary gland development.

Induction of apoptosis and CPP32 expression by thyroid hormone in a myoblastic cell line derived from tadpole tail

During amphibian metamorphosis, the tail and gills that are useful in aquatic life but inappropriate for terrestrial activity are induced to degenerate completely in several days by endogenous thyroid hormone (TH). The dramatic resorption of the tadpole tail has attracted a good deal of attention as an experimental system of cell death, but the mechanism has not been well characterized. To facilitate in vitro analysis, we have established a myoblast cell line (XLT-15) derived from the Xenopus laevis tadpole tail. This cultured cell line died in response to TH and exhibited positive TUNEL reaction and internucleosomal DNA cleavage. Simultaneously, expression of the Xenopus CPP32/apopain/Yama gene was up-regulated by TH in the cell line as it is in regressing tadpole tail, whereas interleukin-1beta-converting enzyme (ICE) mRNA is around 1 copy/cell in tail and undetectable in XLT-15 cells. A CPP32/apopain/Yama inhibitor (acetyl-Asp-Glu-Val-Asp-aldehyde) prevented TH-induced apoptosis of XLT-15 cells, but an ICE inhibitor (acetyl-Tyr-Val-Ala-Asp-aldehyde) did not. These results suggested that an increase of CPP32/apopain/Yama gene expression is involved in TH-dependent apoptosis of XLT-15 and tadpole tail resorption during metamorphosis.

Title aggregation patterns of argyrophilic nucleolar organizer regions induced by 5-fluorouracil in the nuclei of MCF-7 human breast cancer cells

The effects of tamoxifen and 5-fluorouracil (5-FU) on the patterns of argyrophilic nucleolar organizer regions (AgNORs) in MCF7 human breast cancer cells were studied. Tamoxifen and 5-FU both inhibited the growth of MCF-7 cells by 18% by day 3 of culture, but each had different effects on the AgNORs. Whereas no significant changes were induced by tamoxifen, effects on the AgNORs of MCF-7 cells by 5-FU were dramatic: 5-FU treatment changed the pattern of AgNORs, reducing the number of satellites by aggregation, typically to a single aggregation around nucleoli in a sphenoidal fashion. We named these morphological changes: fluorouracil induced AgNOR aggregations (FAA). Following treatment with 500 ng/ml 5-FU, FAA developed rapidly. AgNORs forming two or three aggregates in 24% (6 h), 24% (12 h), 40% (24 h) and 34% (48 h) of cells, compared to a control rate of 14%. Single large aggregate was rarely found in untreated cultures but after 6, 12, 24 and 48 h treatment with 500 ng/ml 5-FU, AgNORs had formed a single aggregate in 6, 8, 16 and 22% of cells, respectively. FAA were observed at a concentration of 100 ng/ml 5-FU; 48 h treatment resulted in cells in which two or three aggregates were increased by 24% and single aggregate by 16%. These large single aggregates were larger than nucleoli stained by Papanicolau staining.

Analysis of beta-adrenergic receptor mRNA levels in human ventricular biopsy specimens by quantitative polymerase chain reactions: progressive reduction of beta 1-adrenergic receptor mRNA in heart failure

OBJECTIVES

This study investigated the relation between the severity of heart failure and the extent of the reduction of beta 1-adrenergic receptor messenger ribonucleic acid (mRNA) levels in biopsy specimens from the ventricular septum obtained during cardiac catheterization of patients with various degrees of heart failure.

BACKGROUND

Heart failure is accompanied by desensitization of the beta-adrenergic receptor system, which is in part due to downregulation of beta 1-adrenergic receptors. Downregulation of beta 1-adrenergic receptors has been suggested to be caused by reductions in mRNA levels.

METHODS

Because biopsy specimens were small and receptor mRNAs not abundant, mRNA levels were determined by quantitative reverse transcription/polymerase chain reactions. This method was validated by measuring synthetic ribonucleic acid (RNA) standards and samples from explanted hearts by solution hybridization assays. Both methods yielded similar results, but the polymerase chain reaction method was approximately 1,000-fold more sensitive. Sources of variations in the polymerase chain reaction were quantitated and found to be best controlled for by determination of the glyceraldehyde phosphate dehydrogenase mRNA as an endogenous control.

RESULTS

Beta 1-adrenergic receptor mRNA levels in the biopsy specimens were decreased by 7% in mild (New York Heart Association functional class II), 26% in moderate (functional class III) and > 50% in severe heart failure (functional class IV). There was a good correlation between hemodynamic indicators of heart failure and beta 1-adrenergic receptor mRNA levels. In contrast, beta 2-adrenergic receptor mRNA levels were apparently unaffected by heart failure.

CONCLUSIONS

Reduced beta 1-adrenergic receptor mRNA levels occur early in heart failure and can be detected in septal biopsy specimens during right heart catheterization. The reduction in beta 1-adrenergic receptor expression may contribute to further loss of cardiac function.

Subcellular distribution of rRNA and poly(A) RNA in hippocampal neurons in culture

In situ hybridization was used to assess the subcellular distribution of rRNA and poly(A) RNA in hippocampal neurons maintained in culture. Labeling produced with 35S-labeled probes to either rRNA or poly(A) was heaviest over the cell body with lighter, patchy labeling of proximal dendrites. In contrast, 3H-labeled probes labeled dendrites throughout their length, and the ratio of dendritic to cell body labeling was higher with 3H-labeled probes. There was no detectable labeling of axons of mature neurons with either probe. The pattern of hybridization produced by 35S-labeled oligonucleotide probes to rRNA varied depending on the concentration of the oligonucleotide. These studies provide the first detailed study of the subcellular distribution of rRNA and poly(A) RNA in neurons, and highlight technical issues to consider when evaluating results of hybridizations carried out with 35S- and 3H-labeled probes on cells in culture.

Characterization of a beta-nerve growth factor expression vector for mammalian cells

A mammalian expression vector that directs expression of murine beta-nerve growth factor (beta-NGF) from a murine sarcoma virus long terminal repeat (LTR) promoter element was constructed and characterized. The vector, designated pLTRSNGF, was stably transfected into murine L-cells, and beta-NGF mRNA and protein levels were quantified and compared to endogenous levels in control L-cells. Transfection of pLTRSNGF resulted in an approximate doubling of both beta-NGF mRNA and mature beta-NGF protein secreted into the media. Transfection of pLTRSNGF into rat PC 12 cells resulted in colonies of autocrine-differentiating cells that extended dense networks of neurites in the absence of added NGF, indicating that the beta-NGF produced from the vector is biologically active.

Inhibitors of RNA and protein synthesis stabilize messenger RNA for the RII beta subunit of protein kinase A in different cellular compartments

Messenger RNA for RII beta is transiently induced (greater than 50-fold) by cAMP analogs in primary cultures of rat Sertoli cells. The induction is dependent on protein synthesis. We have previously shown that mRNA for RII beta is stabilized by cAMP, as well as inhibitors of transcription and translation. This indicated that rapid degradation of RII beta mRNA involved a protein with a rapid turnover and its corresponding mRNA. The two RNA synthesis inhibitors used in the present study stabilized both nuclear and cytoplasmic RII beta mRNA, whereas inhibition of protein synthesis stabilized RII beta mRNA in the cytoplasm only. These results indicate that only cytoplasmic degradation of RII beta mRNA is dependent on a protein with high turnover. In contrast, nuclear degradation appears to be dependent on an RNA with a short half-life, not involving protein synthesis.

Transcriptional and posttranscriptional mechanisms in uncoupling protein mRNA response to cold

Three mechanisms account for the rapid elevation and maintenance of uncoupling protein (UCP) mRNA levels in cold-exposed rats, namely, an increase in the rate of transcription initiation, an increase in the fraction of nascent UCP transcripts undergoing elongation, and stabilization of the mature UCP mRNA. The second mechanism precedes and outlasts the increase in the rate of UCP gene transcription, which is brisk but short lived. After 48 h of cold exposure, mature UCP mRNA levels are maintained elevated solely on the basis of stabilization, since the levels of both transcription initiation and fifth intron-containing transcripts (precursors) have returned to basal. Results in hypothyroid rats given 3,5,3'-triiodothyronine (T3) and in dispersed brown adipocytes show that T3 is involved both in the increase in UCP mRNA precursor level and stabilization of mature UCP mRNA. These mechanisms are rapidly reversed when the rats are returned to thermoneutrality. These coordinated transcriptional and post-transcriptional mechanisms modulating UCP gene expression ensure a rapid increase in the concentration of UCP and prevent further accumulation of the protein as physiologically adequate levels are attained.

All three human ras genes are expressed in a wide range of tissues

We examined the expression of the ras gene family (Ha-ras, Ki-ras, N-ras) in human fetal tissues (14 week) and in several human tumor cell lines. Dot blot hybridization showed that the three ras genes were expressed in all of the samples analysed, with a range of expression between 10 and 180 molecules/cell. There was no correlation between levels of expression of ras genes and the type of ras gene activated in different tumor types.

Radioautographic comparison of RNA synthesis patterns in the epithelial cells of mouse pyloric antrum following 3H-uridine and 3H-orotic acid injections

RNA synthesis was examined in the epithelial cells of the mouse pyloric antrum using radioautography 20 min after injection of either 3H-uridine or 3H-orotic acid. The epithelium of the mouse antrum was known to invaginate into blind tubular units composed of mucous cells arranged from base to top into a gland, an isthmus, and a pit. These were subdivided into segments and, after radioautography, silver grains were counted over cell nuclei in each segment. Following 3H-uridine injection, silver grains were present over all nuclei but were more abundant over those of the isthmus than of the gland or the pit. When nuclei were examined in the electron microscope, nucleoplasmic as well as nucleolar silver grains were more numerous in the isthmus than in the pit or gland. Following 3H-orotic acid injection, silver grains were again present over all nuclei; but maximal incorporation appeared to be in pit cell nuclei where, by electron microscopy, it was mainly assigned to the nucleoplasm. When the incorporation was calculated per whole nucleus, however, it was less in pit cell than in isthmal cell nuclei. Even so, the proportion of label in pit cell nuclei was much greater than after 3H-uridine injection. The interpretation of these findings is based on the fact that isthmal cells are immature, whereas cells migrating from the isthmus to become gland or pit cells show increasing differentiation. The immature cells of the isthmus incorporate both uridine and orotic acid more effectively than do the differentiated cells of pit and gland. Since silver grain counts over nuclei provide an index of the rate of RNA synthesis, this synthesis proceeds more actively in the isthmus than in the pit or gland. This is true of ribosomal RNA synthesis, as shown by nucleolar grain counts, and of other RNA's synthesis, as shown by nucleoplasmic grain counts. It seems, however, that while uridine is involved in the synthesis of all types of RNA, orotic acid is mainly implicated in the synthesis of the heterogeneous RNA from which the messenger RNA arises.

rDNA transcription and pre-rRNA processing during the differentiation of a mouse myoblast cell line

The rates of formation and processing of rRNA and transcription of rDNA were examined during the differentiation of MM14DZ mouse myoblasts into muscle fibers. Analyses of the incorporation of [3H]uridine into 18 and 28 S rRNAs and the UTP precursor pool indicate that the rate of rRNA formation is 2.3-fold higher in myoblasts as compared to muscle fibers. To determine if the rate of rRNA formation is regulated at the level of pre-rRNA processing, the labeling kinetics and steady state levels of pre-rRNAs were measured in myoblasts and fibers. These experiments suggest that the time required for and the efficiency of pre-rRNA processing are the same in myoblasts and fibers, but that the steady state levels of all pre-rRNAs detected (32, 34, 37, 41, and three 45 S subspecies) are reduced 2.5- to 3.0-fold in fibers. This suggests that the reduced rate of rRNA formation in fibers is not regulated at the level of pre-rRNA processing but is due to a decrease in the rate of rDNA transcription. The transcriptional rates for rRNA in myoblasts and fibers were calculated from measurements of the total rate of transcription and from hybridization analyses of radioactive rRNA formed in isolated nuclei or in short pulses of cultured cells. These experiments indicate that the rates of 18 and 28 S rDNA and 5 S rDNA transcription are reduced 2.5 to 3.0-fold in fibers. Thus, a coordinate change in the rate of rDNA transcription is the primary mechanism regulating the formation of rRNA during the differentiation of this myoblast line. This decreased transcription in fibers appears to be due to modulation of the activity of the known mouse rDNA promoter, as S1 nuclease mapping experiments indicate that rDNA transcription initiates at the same location in both myoblasts and fibers.

The measurement of the production of tRNAMet1 in the Friend erythroleukemia cell

We have used the gene for tRNAMet1 as a hybridization probe to measure the production of tRNAMet1 in the Friend erythroleukemia cell. In this cell, the relative concentration of tRNAMet1 (i.e., the percentage of total steady-state tRNA representing tRNAMet1) is 1.60 +/- 0.18. To study the relative synthesis of tRNAMet1, cells were labeled in vivo with [3H]uridine for periods ranging from 4 to 24 h, and the tRNA was isolated. The fraction of newly-synthesized tRNA representing tRNAMet1 (1.72% +/- 0.11) does not change when different in vivo labeling times are used. This value is similar to the relative concentration of tRNAMet1 in the older steady-state tRNA (1.61% +/- 0.18). The similar relative synthesis values using different labeling times, plus evidence presented that the total tRNA population decays homogeneously (t 1/2 = 110 h) indicate that tRNAMet1 has a cytoplasmic stability similar to the general tRNA population, and that its concentration relative to the tRNA population is established within the nucleus or soon after exiting the nucleus. Measurements of the synthesis of tRNAMet1 in isolated nuclei, relative to the synthesis of total RNA polymerase III transcripts, showed that this relative synthesis (0.291% +/- 0.017) is only 17% of the relative concentration of tRNAMet1 in the cytoplasm, which may reflect the presence of sequences other than tRNA in total nuclear polymerase III transcripts.

Small nuclear ribonucleoprotein antigens are absent from 10S translation inhibitory ribonucleoprotein but present in cytoplasmic messenger ribonucleoprotein and polysomes

A cytoplasmic 10S ribonucleoprotein particle (iRNP), which is isolated from chick embryonic muscle, is a potent inhibitor of mRNA translation in vitro and contains a 4S translation inhibitory RNA species (iRNA). The iRNP particle shows similarity in size to the small nuclear ribonucleoprotein (snRNP) particles. Certain autoimmune disease patients contain antibodies directed against snRNP antigenic determinants. The possibility that iRNP may be related to the small nuclear particles was tested by immunoreactivity with monospecific autoimmune antibodies to six antigenic determinants (Sm, RNP, PM-1, SS-A (Ro), SS-B (La), and Scl-70). By Ouchterlony immunodiffusion assays, the cytoplasmic 10S iRNP did not show any immunoreactivity. Also, a more sensitive hemagglutination inhibition assay for detecting Sm and RNP antigens failed to show reactivity with the 10S iRNP. Thus, the 10S iRNP particles are distinct from the similarly sized snRNP. However, free and polysomal messenger ribonucleoprotein (mRNP) particles and polysomes also isolated from chick embryonic muscle and analyzed by Ouchterlony immunodiffusion and hemagglutination inhibition for the presence of the antigenic determinants showed reactivity to Sm and RNP autoantibodies, but were not antigenic for the other four antibodies. Some of the Sm antigenic peptides of mRNP particles and polysomes were identical to those purified from calf thymus nuclear extract, as judged by Western blot analysis. The association of Sm with free and polysomal mRNP and polysomes suggests that Sm may be involved in some cytoplasmic aspects of mRNA metabolism, in addition to a nuclear function in mRNA processing.

Regulation of RNA metabolism in relation to insulin production and oxidative metabolism in mouse pancreatic islets in vitro

This study was undertaken to investigate the long-term effects of different substrates, in particular glucose, on the regulation of islet RNA metabolism and the relationship of this regulation to the metabolism and insulin production of the islet B-cell. For this purpose collagenase-isolated mouse islets were used either in the fresh state or after culture for 2 or 5 days in RPMI 1640 plus 10% calf serum supplemented with various test compounds. Islets cultured with 16.7 mM glucose contained more RNA than those cultured with 3.3 mM glucose. Culture of islets in glucose at low concentrations inhibited glucose-stimulated RNA synthesis and this inhibitory effect was reversed by prolonged exposure to high glucose concentrations. Culture with 10 mM leucine and 3.3 mM glucose or with 10 mM 2-ketoisocaproate and 3.3 mM glucose increased the total RNA content of islets as compared to that of islets cultured with 3.3 mM glucose alone. Islets cultured with 5 mM theophylline maintained a high RNA content in the presence of 3.3 mM glucose. Theophylline also increased the islet RNA content when added together with 16.7 mM glucose, as compared to 16.7 mM glucose alone. Theophylline probably exerted this effect by decreasing the rate of RNA degradation. Changes in islet RNA metabolism showed a close correlation to changes in islet total protein biosynthesis, whereas islet (pro)insulin biosynthesis and insulin release exhibited different glucose-dependency patterns. The response of islet oxygen uptake to glucose was similar to that of islet RNA and protein biosynthesis. It is concluded that the RNA content of the pancreatic islets is controlled at the levels of both synthesis and degradation. Glucose stimulates the RNA synthesis and inhibits its degradation. Moreover, the results suggest that regulation of RNA synthesis may be mediated through islet metabolic fluxes and the cAMP system.

Nuclease digestion of DNA and RNA in nuclei from young adult and senescent Caenorhabditis elegans (Nematoda)

Nuclei prepared from young adult and senescent Caenorhabditis elegans (Nematoda) were subjected to digestion by micrococcal nuclease and DNaseI. The kinetics of digestion of nuclei by micrococcal nuclease showed no change with age. There was, however, an age-related increase of acid-soluble deoxyribonucleotides released by DNaseI, suggesting that subtle alterations of chromatin conformation occur in aged nematodes. The ratio of nuclear RNA to DNA decreased and the nuclear RNA became more susceptible to enzymatic degradation as the worms grew old. These findings appear to indicate that nuclear RNA is less protected by protein in old nematodes. The decline of the nuclear RNA/DNA ratio with age is in good agreement with the generally accepted idea that there is a reduced level of RNA and protein synthesis in old animals.

Gene expression during oogenesis and oocyte development in mammals

Mouse oocytes progress through early meiotic prophase during fetal life and reach the diplotene stage by birth. During prepubertal and reproductive life, oocytes are continuously selected to grow from the pool of small primordial oocytes. Growing oocytes reach full size in 2 weeks, and full-grown oocytes are present in rapidly enlarging follicles for about 5 days before meiotic maturation and ovulation. RNA synthesis during early meiotic prophase, as estimated from [3H]uridine incorporation followed by autoradiography and from electron microscopic analysis of nuclear components, proceeds at a moderate rate throughout except for a brief period in early pachytene when synthesis is low or absent. RNA synthesis continues in primordial oocytes at a moderate rate. Incorporation studies, electron microscopic analyses, and particularly measurements of ongoing RNA polymerase activity (completion of initiated chains as analysed in tissue sections) indicate a distinctly increased rate of synthesis during oocyte growth over that of primordial oocytes, followed by a decline in full-grown oocytes. During growth, this rate increases severalfold. The absolute rate of synthesis of heterogeneous nuclear RNA (using rRNA as a standard) during mid-growth is very rapid, but nevertheless still much lower than that in typical lampbrush chromosomes. Most of the hnRNA turns over with a half-life of about 20 min, as is typical in somatic cells. Newly synthesized mRNA-like RNA enters the cytoplasm at about one-half the rate of rRNA, and about one-third of the ribosomes and one-fourth of the mRNA appear in polysomes. In full-grown oocytes, the rate of synthesis falls distinctly, but a significant level of synthesis continues until it essentially ceases at breakdown of the germinal vesicle. During meiotic prophase, chromosomes are most compact at pachytene and unfold lateral projections as RNA synthesis increases in late pachytene-early diplotene. In primordial oocytes, the diplotene state of chromosomes is obvious in most mammals, but in rodents the chromosomes are more evenly dispersed and are said to be in a dictyate state, although they are still presumably in a diplotene configuration. The chromosome core, which is present in leptotene through early diplotene stages, apparently disappears in the dictyate stage.(ABSTRACT TRUNCATED AT 400 WORDS)

Demonstration of T antigens on the surface of cells transformed with primate polyoma viruses

Primate polyoma virus-transformed hamster, mouse, and rat cell lines were examined by indirect immunofluorescence staining for cell surface-associated T antigens, by using a rabbit antiserum prepared against sodium dodecyl sulfate-denatured large T antigen of simian virus 40 (anti-SV40-SDS-T serum). Positive surface staining was shown not only on SV40-transformed cells, but also on BK and JC virus-transformed cells. In contrast, normal cells and cells transformed with mouse polyoma-, human adeno-, and murine sarcoma viruses were negative. The data on SV40-transformed cells confirmed the reports of others demonstrating the cell surface location of SV40 large T antigen, and the data on BK and JC virus-transformed cells proved that these cells have cell-surface T antigens that cross-react with anti-SV40-SDS-T serum.

A mathematical model that applies to protein degradation and post-translational processing of proteins and to analogous processes for other molecules in non-growing and exponentially growing cells

A mathematical model is presented that describes first order degradation and post-translational processing of proteins in non-growing and exponentially growing cells. The model applies to proteins that are substrates or products of processing. General equations are presented that can be applied to many different experimental protocols. Application of the model to pulse-chase and continuous labeling experiments is illustrated. The mathematical expressions apply to any cellular component that is synthesized in proportion to cellular mass and is degraded or processed by reactions that follow first order kinetics. However, in this paper, the model is discussed solely as it applies to protein metabolism.

rRNA accumulation and protein synthetic patterns in growing mouse oocytes

The rRNA contents of mouse primordial oocytes, three stages of growing oocytes, full-grown oocytes, and ovulated ova have been measured by hybridization of RNA samples to excess 3H-DNA complementary to rRNA. Since it was known from previous work that rRNA is stable, the results when plotted against days of oocyte growth indicated that rRNA was synthesized at a constant rate over the first 9 days of growth and about 1.5 times faster in the last 5 days. The maximum value of 0.3 ng per oocyte was attained by about 14 days of growth in oocytes 59 micrometers in diameter, well below the maximum diameter of 77 micrometers for full-grown oocytes. The stability of proteins synthesized in mid-growth phase oocytes was measured by labeling for 5 h with 35S-methionine and then following the decline of incorporated label during a 48h chase; 40% of the label decayed with a half-life of 11 h. and 60% was apparently stable. The two-dimensional electrophoretic patterns of labeled proteins synthesized by growing and full-grown oocytes were compared. The principal change was the appearance or great increase in intensity of several spots in full-grown oocytes as compared to growing oocytes. Egg proteins separated on a two-dimensional gel were visualized by silver staining. The cytoskeletal proteins actin, tubulin, and putative intermediate filament protein, as well as putative lactate dehydrogenase, were synthesized in growing and full-grown oocytes, and accumulated to form a significant portion of bulk egg protein.