The molecular cytology of gene expression: fluorescent RNA as both a stain and tracer in vivo.

For more than 60 years, RNA has been detectable in fixed cells and tissues by relatively specific staining methods. More recently, it has become possible to study RNA in unfixed, live cells. This review article describes how the intracellular dynamics and localization of RNA in vivo can be studied by microinjection of fluorescent RNA into cells- an approach we have termed Fluorescent RNA Cytochemistry. Depending on the particular RNA species under investigation, Fluorescent RNA Cytochemistry can operate as a "stain" to reveal intracellular sites at which a given RNA resides, or as a "tracer" to allow movements of a dynamically translocating RNA to be followed in the living cell. Several examples of Fluorescent RNA Cytochemistry are presented, collectively illustrating the range of applicability this approach offers in the toolbox of gene expression, studied as in vivo cell biology.

Human cell lines expressing hormone regulated T7 RNA polymerase localized at distinct intranuclear sites.

Although several systems are now available for the controlled expression of eukaryotic genes transcribed by RNA polymerase II, regulated expression has been more difficult to achieve in the case of genes transcribed by RNA polymerase III. In the present study the gene for bacteriophage T7 RNA polymerase, implanted with a eukaryotic nuclear localization signal, was linked to a 5'-flanking ecdysone-responsive promoter and stably transformed human cell lines were constructed in which the ecdysone promoter-T7 RNA polymerase gene had been integrated intact, as demonstrated by a polymerase chain reaction assay. Exposure of these cells to the ecdysone analog ponasterone A resulted in the appearance of a single protein having the expected size of T7 RNA polymerase in immunoblots of cell extracts probed with an affinity purified antibody raised against the C-terminus of T7 RNA polymerase. The induced T7 RNA polymerase was exclusively localized in the nucleus of induced cells and was undetectable in uninduced cells either by immunoblotting or immunofluorescence. The induced T7 RNA polymerase was present at numerous punctate foci dispersed throughout the nucleoplasmic regions of the nucleus and was also present in the nucleoli. Both of these observed intranuclear localizations have relevance to the potential applications of this system.

Fluorescent RNA cytochemistry: tracking gene transcripts in living cells.

The advent of jellyfish green fluorescent protein and its spectral variants, together with promising new fluorescent proteins from other classes of the Cnidarian phylum (coral and anemones), has greatly enhanced and promises to further boost the detection and localization of proteins in cell biology. It has been less widely appreciated that highly sensitive methods have also recently been developed for detecting the movement and localization in living cells of the very molecules that precede proteins in the gene expression pathway, i.e. RNAs. These approaches include the microinjection of fluorescent RNAs into living cells, the in vivo hybridization of fluorescent oligonucleotides to endogenous RNAs and the expression in cells of fluorescent RNA-binding proteins. This new field of 'fluorescent RNA cytochemistry' is summarized in this article, with emphasis on the biological insights it has already provided. These new techniques are likely to soon collaborate with other emerging approaches to advance the investigation of RNA birth, RNA-protein assembly and ribonucleoprotein particle transport in systems such as oocytes, embryos, neurons and other somatic cells, and may even permit the observation of viral replication and transcription pathways as they proceed in living cells, ushering in a new era of nucleic acids research in vivo.

Serine/threonine phosphorylation of IRS-1 triggers its degradation: possible regulation by tyrosine phosphorylation.

Insulin receptor substrate (IRS)-1 protein expression is markedly reduced in many insulin-resistant states, although the mechanism for this downregulation is unclear. In this study, we have investigated the early events in the insulin pathway that trigger the degradation of IRS-1. Incubation of the adipocytes with insulin induced a fast electrophoretic mobility shift of IRS-1 and a subsequent degradation of the protein. Wortmannin and rapamycin blocked this mobility shift of IRS-1, maintained the insulin-induced tyrosine phosphorylation of IRS-1, and blocked its degradation. In contrast, a glycogen synthase kinase 3 inhibitor, a mitogen-activated protein kinase/extracellular-regulated kinase inhibitor, and various protein kinase C inhibitors had no effect. Incubation with okadaic acid increased the serine/threonine phosphorylation of IRS-1 and its degradation, mimicking insulin, and its effect was prevented by the proteasome inhibitor lactacystin, as well as by rapamycin. Treatment of the cells with the tyrosine phosphatase inhibitor orthovanadate in the presence of insulin or okadaic acid partially inhibited the degradation of IRS-1. We propose that a rapamycin-dependent pathway participates as a negative regulator of IRS-1, increasing its serine/threonine phosphorylation, which triggers degradation. Thus, regulation of serine/threonine versus tyrosine phosphorylation may modulate IRS-1 degradation, affecting insulin sensitivity.

Regulation of proteins involved in insulin signaling pathways in differentiating human adipocytes.

In the present study we have examined the proteins involved in the insulin signaling cascade during and after differentiation of human adipocyte precursor cells and their correlation with glucose uptake. The differentiation of human adipocytes was characterized by a two- to threefold stimulation of glucose transport in response to insulin and a marked increase protein expression for the insulin receptor, IRS-1, GLUT-4, PI 3-kinase, and PKB, with respect to undifferentiated cells. In contrast, there were small changes in the protein expression of IRS-2, and no changes in PKC zeta and MAP kinases, although basal MAP kinase activity and GLUT-1 protein were reduced during differentiation. In conclusion, there are quantitative differences in the regulation of IRS-1 and other proteins during differentiation which may contribute to more efficient insulin signaling leading to glucose uptake in mature fat cells. Alterations in this pattern may reflect or contribute to an insulin-resistant state.

Review: movement of mRNA from transcription site to nuclear pores.

Pre-mRNA is transcribed primarily from genes located at the interface between chromatin domains and the interchromatin space. After partial or complete processing and complexing with nuclear proteins, the transcripts leave their site of synthesis and travel through the interchromatin space to the nuclear pores for export to the cytoplasm. It is unclear whether transcripts are tethered within the interchromatin space and move toward the nuclear pores using a metabolic energy-requiring, directed mechanism or, alternatively, move randomly by a diffusion-based process. We discuss here recent progress in understanding this step of gene expression, including our experiments tracking the movement of intranuclear poly(A) RNA in living cells. Our results and those of others are most consistent with a model in which newly synthesized mRNAs diffuse throughout the interchromatin space until they randomly encounter and are captured by the export machinery. Because the export machinery appears to preferentially bind transport-competent mRNAs (complexed with the correct complement of nuclear proteins), this diffusion-based model for intranuclear RNA movement potentially allows for a significant level of posttranscriptional control of gene expression.

Half a century of "the nuclear matrix".

A cell fraction that would today be termed "the nuclear matrix" was first described and patented in 1948 by Russian investigators. In 1974 this fraction was rediscovered and promoted as a fundamental organizing principle of eukaryotic gene expression. Yet, convincing evidence for this functional role of the nuclear matrix has been elusive and has recently been further challenged. What do we really know about the nonchromatin elements (if any) of internal nuclear structure? Are there objective reasons (as opposed to thinly veiled disdain) to question experiments that use harsh nuclear extraction steps and precipitation-prone conditions? Are the known biophysical properties of the nucleoplasm in vivo consistent with the existence of an extensive network of anastomosing filaments coursing dendritically throughout the interchromatin space? To what extent may the genome itself contribute information for its own quarternary structure in the interphase nucleus? These questions and recent work that bears on the mystique of the nuclear matrix are addressed in this essay. The degree to which gene expression literally depends on nonchromatin nuclear structure as a facilitating organizational format remains an intriguing but unsolved issue in eukaryotic cell biology, and considerable skepticism continues to surround the nuclear matrix fraction as an accurate representation of the in vivo situation.

Signal recognition particle components in the nucleolus.

The signal recognition particle (SRP) is a ribonucleoprotein composed of an Alu domain and an S domain. The S domain contains unique sequence SRP RNA and four SRP proteins: SRP19, SRP54, SRP68, and SRP72. SRP interacts with ribosomes to bring translating membrane and secreted proteins to the endoplasmic reticulum (ER) for proper processing. Additionally, SRP RNA is a member of a family of small nonribosomal RNAs found recently in the nucleolus, suggesting that the nucleolus is more plurifunctional than previously realized. It was therefore of interest to determine whether other SRP components localize to this intranuclear site. In transfected rat fibroblasts, green fluorescent protein fusions of SRP19, SRP68, and SRP72 localized to the nucleolus, as well as to the cytoplasm, as expected. SRP68 also accumulated in the ER, consistent with its affinity for the ER-bound SRP receptor. SRP54 was detected in the cytoplasm as a green fluorescent protein fusion and in immunofluorescence studies, but was not detected in the nucleolus. In situ hybridization experiments also revealed endogenous SRP RNA in the nucleolus. These results demonstrate that SRP RNA and three SRP proteins visit the nucleolus, suggesting that partial SRP assembly, or another unidentified activity of the SRP components, occurs at the nucleolus. SRP54 apparently interacts with nascent SRP beyond the nucleolus, consistent with in vitro reconstitution experiments showing that SRP19 must bind to SRP RNA before SRP54 binds. Our findings support the notion that the nucleolus is the site of assembly and/or interaction between the family of ribonucleoproteins involved in protein synthesis, in addition to ribosomes themselves.

Movement of nuclear poly(A) RNA throughout the interchromatin space in living cells.

BACKGROUND: Messenger RNA (mRNA) is transcribed and processed in the nucleus of eucaryotic cells and then exported to the cytoplasm through nuclear pores. It is not known whether the movement of mRNA from its site of synthesis to the nuclear pore is directed or random. Directed movement would suggest that there is an energy-requiring step in addition to the step required for active transport through the pore, whereas random movement would indicate that mRNAs can make their way to the nuclear envelope by diffusion. RESULTS: We devised a method to visualize movement of endogenous polymerase II transcripts in the nuclei of living cells. Oligo(dT) labeled with chemically masked (caged) fluorescein was allowed to penetrate cells and hybridize to nuclear poly(A) RNA. Laser spot photolysis then uncaged the oligo(dT) at a given intranuclear site and the resultant fluorescent, hybridized oligo(dT) was tracked using high-speed imaging microscopy. Poly(A) RNA moved away from the uncaging spot in all directions with a mean square displacement that varied linearly with time, and the same apparent diffusion coefficient was measured for the movement at both 37 degrees C and 23 degrees C. These properties are characteristic of a random diffusive process. High resolution three-dimensional imaging of live cells containing both Hoechst-labeled chromosomes and uncaged oligo(dT) showed that, excluding nucleoli, the poly(A) RNA could access most, if not all, of the non-chromosomal space in the nucleus. CONCLUSIONS: Poly(A) RNA can move freely throughout the interchromatin space of the nucleus with properties characteristic of diffusion.

A human U2 RNA mutant stalled in 3' end processing is impaired in nuclear import.

The biosynthesis of U1, U2, U4 and U5 spliceosomal small nuclear RNAs (snRNAs) involves the nuclear export of precursor molecules extended at their 3' ends, followed by a cytoplasmic phase during which the pre-snRNAs assemble into ribonucleoprotein particles and undergo hypermethylation of their 5' caps and 3' end processing prior to nuclear import. Previous studies have demonstrated that the assembly of pre-snRNAs into ribonucleoprotein particles containing the Sm core proteins is essential for nuclear import in mammalian cells but that 5' cap hypermethylation is not. In the present investigation we have asked whether or not 3' end processing is required for nuclear import of U2 RNA. We designed human pre-U2 RNAs that carried modified 3' tails, and identified one that was stalled (or greatly slowed) in 3' end processing, leading to its accumulation in the cytoplasm of human cells. Nonetheless, this 3' processing arrested pre-U2 RNA molecule was found to undergo cytoplasmic assembly into Sm protein-containing complexes to the same extent as normal pre-U2 RNA. The Sm protein-associated, unprocessed mutant pre-U2 RNA was not observed in the nuclear fraction. Using an assay based on suppression of a genetically blocked SV40 pre-mRNA splicing pathway, we found that the 3' processing deficient U2 RNA was significantly reduced in its ability to rescue splicing, consistent with its impaired nuclear import.

Movement and localization of RNA in the cell nucleus.

The movement of various RNAs from their sites of chromosomal synthesis to their functional locations in the cell is an important step in eukaryotic gene readout, though one less well understood than the transcription, RNA processing, and various functions of RNA. The segregation of the many classes of RNA out into to their appropriate sites in the cell is, from a physical chemical point of view, a remarkable phenomenon. This paper summarizes investigations my colleagues and I have undertaken over the past 7 years to describe the intracellular traffic and localization of RNA in living cells. One approach we have developed is to glass-needle microinject approximately 0.01 pl of fluorescent RNA solutions into the nucleus or cytoplasm of cultured mammalian cells. This 'fluorescent RNA cytochemistry' approach has resolved intranuclear sites ('speCkles') for which premessenger RNAs (pre-mRNA) have high affinity and has revealed very rapid movements of certain other RNAs from their nucleoplasmic injection sites to the nucleoli. One of these rapidly trafficking nucleolar RNAs is the signal recognition particle (SRP) RNA, and further results indicate that the nucleolus is a site of SRP RNA processing or ribonucleoprotein assembly prior to export to the cytoplasm. In these fluorescent RNA microinjection studies, we have also used mutant RNA molecules to identify specific nucleotide sequences that function as targeting elements for the localization of RNAs at their respective intranuclear sites. In a second approach, we have used fluorescent correlation spectroscopy (FCS), a classical biophysical method for measuring molecular motion in vitro, coupled with confocal fluorescence microscopy to measure the movement of poly(A) RNA in the nucleus, with the interesting finding that these RNAs appear to move about inside the nucleus at rates comparable to diffusion in aqueous solution. Parallel experiments using the method of fluorescence recovery after photobleaching (FRAP) revealed a diffusion coefficient for intranuclear poly(A) RNA close to that measured by FCS. These results bear on the structure of the nucleoplasmic ground substance-an extremely controversial and unsolved problem in cell biology (29). The methods we have developed and these initial results represent the first major step toward a comprehensive understanding of RNA traffic in the cell nucleus.

Chronic evaluation of orthotopically implanted bileaflet mechanical aortic valves in adult domestic sheep.

This study was intended to develop a technically feasible and reproducible model for chronic hemodynamic and mechanical evaluation of orthotopically implanted bileaflet mechanical aortic valves in adult domestic sheep. Three adult sheep (mean age 22 weeks, mean weight 76 kg) underwent aortic valve replacement using 19-mm bileaflet aortic valves. Standard cardiopulmonary bypass techniques were followed, including mild hemodilution, systemic hypothermia, and cardioplegic arrest. After performing a left fourth intercostal thoracotomy, the valves were placed using interrupted 3-0 Ticron (Davis + Geck) inverted mattress sutures through a transverse aortotomy. The average cardiopulmonary bypass time was 58+/-1 min. No chronic anticoagulation was used. There were no surgical complications. All three animals (100%) remained clinically well until elective sacrifice after postoperative day 150. The average cardiac output for the animals at sacrifice was 3.8+/-1.0 L/min. The mean aortic ejection velocity was 304.7+/-47.3 cm/s and the mean pressure gradient was 24.6+/-6.7 mm Hg. There was no clinically significant thrombus formation or paravalvular leaks. Thus, we have demonstrated that it is technically feasible to orthotopically implant mechanical aortic valves in sheep. There are several features that contribute to the success of this model, including use of a transverse aortotomy, adequate de-airing, and the use of mild hemodilution during bypass. We believe that this model is reproducible and can be used to study other valve designs. In addition, this model allows for site-specific preclinical assessment of new or modified mechanical heart valves.

Long-term evaluation of orthotopically implanted stentless bioprosthetic aortic valves in juvenile sheep.

The aim of this study was to develop a technically feasible and reproducible model for chronic evaluation of stentless bioprosthetic aortic valves implanted orthotopically using juvenile domestic sheep. This report summarizes the results of a study conducted to assess orthotopically placed 19-mm stentless aortic bioprosthetic valves. Twenty-seven juvenile sheep underwent aortic valve replacement. Standard cardiopulmonary bypass techniques were followed. The average cardiopulmonary bypass time was 73 min. No chronic anticoagulation was used. There were two deaths (7%) due to surgical complications. In the remaining 25 experiments, 11 animals (41%) died prior to the scheduled sacrifice on postoperative day 150. One early death occurred due to coccidiomycosis infection, one due to technical error, one due to pulmonary embolus, four due to prosthetic annular size disproportion, and four due to thrombi. The remaining 14 animals (52%) underwent left and right heart catheterization, angiography, echocardiography, and sacrifice after postoperative day 150. The average weight of the sheep at elective sacrifice was 60 kg (mean weight gain 12.5 kg). The average cardiac output for the sacrificed animals was 5.1 L/min. The mean velocity of blood across the aortic valve for the sacrificed animals was 317 cm/s and the mean pressure gradient was 26.2 mm Hg. Two features suggest that this model may have broad application. First, we have demonstrated that it is technically feasible to evaluate orthotopically placed stentless bioprosthetic aortic valves in growing sheep. Second, the aortic root size of the juvenile sheep allows for implantation and evaluation of a human size aortic valve (19 mm). We believe that this model is reproducible and can be used to study stentless valve designs.