Intron-containing Transcripts Research Articles

Intron-containing beta-tubulin transcripts in Cryptosporidium parvum cultured in vitro.

The genome of Cryptosporidium parvum contains a relatively small number of introns, which includes the beta-tubulin gene with only a single intron. Recently, it was observed that the intron was not removed from some of the beta-tubulin transcripts in the late life cycle stages cultured in vitro. Although normally spliced beta-tubulin mRNA was detected in all parasite intracellular stages by RT-PCR (e.g. HCT-8 or Caco-2 cells infected with C. parvum for 12-72 h), at 48-72 h post-infection unprocessed beta-tubulin transcripts containing intact introns started to appear in parasite mRNA within infected host cells. The intron-containing transcripts could be detected by fluorescence in situ hybridization (FISH) using an intron-specific probe. The intron-containing beta-tubulin transcripts appeared unique to the in vitro-cultured C. parvum, since they were not detected in parasite-infected calves at 72 h. As yet, it is unclear whether the late life cycle stages of C. parvum are partially deficient in intron-splicing or the intron-splicing processes have merely slowed, both of which would allow the detection of intron-containing transcripts. Another possible explanation is that the decay in transcript processing might simply be due to the onset of parasite death. Nonetheless, the appearance of intron-containing transcripts coincides with the arrest of C. parvum development in vitro. This unusual observation prompts speculation that the abnormal intron-splicing of beta-tubulin transcripts may be one of the factors preventing complete development of this parasite in vitro. Furthermore, the presence of both processed and unprocessed introns in beta-tubulin transcripts in vitro may provide a venue for studying overall mechanisms for intron-splicing in this parasite.

Differential Amplification of Intron-containing Transcripts Reveals Long Term Potentiation-associated Up-regulation of Specific Pde10A Phosphodiesterase Splice Variants

We employed differential display of expressed mRNAs (Liang, P., and Pardee, A. B. (1992) Science 257, 967-971) to identify genes up-regulated after long term potentiation (LTP) induction in the hippocampus of awake adult rats. In situ hybridization confirmed the differential expression of five independently amplified clones representing two distinct transcripts, cl13/19/90 and cl95/96. Neither cl13/19/90 nor cl95/96 showed significant sequence homology to known transcripts (mRNA or expressed sequence tag) or to the mouse or human genome. However, comparison with the rat genome revealed that they are localized to a predicted intron of the phosphodiesterase Pde10A gene. cl13/19/90 and cl95/96 are likely to be part of the Pde10A primary transcript as, using reverse transcriptase-PCR, we could specifically amplify distinct introns of the Pde10A primary transcript, and in situ hybridization demonstrated that a subset of Pde10A splice variants are also up-regulated after LTP induction. These results indicate that amplification of a primary transcript can faithfully report gene activity and that differential display can be used to identify differential expression of RNA species other than mRNA. In transiently transfected Cos7 cells, Pde10A3 reduces the atrial natriuretic peptide-induced elevation in cGMP levels without affecting basal cGMP levels. This cellular function of LTP-associated Pde10A transcripts argues for a role of the cGMP/cGMP-dependent kinase pathway in long term synaptic plasticity.

Functional analysis of Epstein-Barr virus SM protein: identification of amino acids essential for structure, transactivation, splicing inhibition, and virion production.

The Epstein-Barr virus (EBV) SM protein is a posttranscriptional regulator of cellular and viral gene expression that binds and stabilizes target mRNAs and shuttles from nucleus to cytoplasm. SM enhances expression of several EBV genes required for lytic replication and is essential for virion production. SM increases accumulation of specific mRNAs but also inhibits expression of several intron-containing transcripts. The mechanism by which SM inhibits gene expression is poorly understood. The experiments described here had several aims: to determine whether specific domains of SM were responsible for activation or inhibition function; whether these functions could be separated; and whether one or more of these functions were essential for virion production. A mutational analysis of SM was performed, focusing on amino acids in SM that are evolutionarily conserved among SM homologs in other herpesviruses. Mutation of the carboxy-terminal region of SM revealed a region that is likely to be structurally important for SM protein conformation. In addition, several amino acids were identified that are critical for activation and inhibition function. A specific mutation of a highly conserved cysteine residue revealed that it was essential for gene inhibition but not for transactivation, indicating that these two functions operate through independent mechanisms. Furthermore, the ability of wild-type SM and the inability of the mutant to inhibit gene expression were shown to correlate with the ability to inhibit splicing of a human target gene and thereby prevent accumulation of its processed mRNA. Surprisingly, some mutations which preserved both activation and inhibition functions in vitro nevertheless abolished virion production, suggesting that other SM functions or protein-protein interactions are also required for lytic replication.

The SUV3 gene from Saccharomyces douglasii is a functional equivalent of its Saccharomyces cerevisiae orthologue and is essential for respiratory growth.

In the yeast Saccharomyces cerevisiae the product of the nuclear gene SUV3 has been shown to be involved in a variety of mitochondrial post-transcriptional processes. We have cloned and sequenced the SUV3 gene from Saccharomyces douglasii, a close relative of S. cerevisiae which has important changes in the organization of its mitochondrial genome and concomitant changes in nucleo-mitochondrial interactions. We show that the S. douglasii SUV3 gene shares considerable structural homology (92% amino acid sequence identity) with its S. cerevisiae counterpart and that their nucleotide sequences display evidence of recent divergence. To determine the function of the S. douglasii SUV3 gene we have constructed a strain carrying an inactive SUV3 gene and analyzed the effect of this inactivation on the integrity of the mitochondrial genome and on the stability of mitochondrial transcripts. We have demonstrated that the S. douglasii SUV3 gene, like the S. cerevisiae gene, is essential for respiratory growth and for stability of the intron-containing mitochondrial transcripts, thus the two genes are functionally equivalent. Also the S. douglasii and S. cerevisiae SUV3 genes are completely interchangeable, despite the differences in the structure of the mitochondrial chromosome in the two yeasts.

Splicing goes global

Transcriptomics, the analysis of the complement of mRNAs transcribed from a cell's genome, currently focuses mainly on mature, processed mRNAs. However, posttranscriptional processing of primary transcripts can significantly affect both the quantity and the structure of the mature mRNAs and therefore of the protein products. Recently, the development of an intron-specific microarray has permitted a preliminary analysis of the splicing of all intron-containing transcripts in Saccharomyces cerevisiae. Here, we discuss the findings and what might be learned from this kind of approach.

Overexpression of the clpP 5'-untranslated region in a chimeric context causes a mutant phenotype, suggesting competition for a clpP-specific RNA maturation factor in tobacco chloroplasts.

The plastid ribosomal RNA (rrn) operon promoter was fused with DNA segments encoding the leader sequence (5'-untranslated region [UTR]) of plastid mRNAs to compare their efficiency in mediating translation of a bacterial protein neomycin phosphotransferase (NPTII) in tobacco (Nicotiana tabacum) chloroplasts. In young leaves, NPTII accumulated at 0.26% and 0.8% of the total soluble leaf protein from genes with the clpP and atpB 5'-UTR, respectively. Interestingly, expression of NPTII from the promoter with the clpP 5'-UTR (0.26% NPTII) caused a mutant (chlorotic) phenotype, whereas plants accumulating approximately 0.8% NPTII from the atpB 5'-UTR were normal green, indicating that the mutant phenotype was independent of NPTII accumulation. Low levels of monocistronic clpP mRNA and accumulation of intron-containing clpP transcripts in the chlorotic leaves suggest competition between the clpP 5'-UTR in the chimeric transcript and the native clpP pre-mRNA (ratio 16:1) for an mRNA maturation factor. Because maturation of 11 other intron-containing mRNAs was unaffected in the chlorotic leaves, it appears that the factor is clpP specific. The mutant phenotype is correlated with reduced levels (approximately 2 times) of the ClpP1 protease subunit, supporting an important role for ClpP1 in chloroplast development.

Nuclear interactions are necessary for translational enhancement by spleen necrosis virus RU5.

The 5' long terminal repeat of spleen necrosis virus (SNV) facilitates Rev/Rev-responsive element (RRE)-independent expression of intron-containing human immunodeficiency virus type 1 (HIV-1) gag. The SNV RU5 region, which corresponds to the 165-nucleotide 5' RNA terminus, functions in a position- and orientation-dependent manner to enhance polysome association of intron-containing HIV-1 gag RNA and also nonviral luc RNA. Evidence is mounting that association with nuclear factors during intron removal licenses mRNAs for nuclear export, efficient translation, and nonsense-mediated decay. This project addressed the relationship between the nuclear export pathway of SNV RU5-reporter RNA and translational enhancement. Results of RNA transfection experiments suggest that cytoplasmic proteins are insufficient for SNV RU5 translational enhancement of gag or luc RNA. Reporter gene assays, leptomycin B (LMB) sensitivity experiments, and RNase protection assays indicate that RU5 gag RNA accesses a nuclear export pathway that is distinct from the LMB-inhibited leucine-rich nuclear export sequence-dependent CRM1 pathway, which is used by the HIV-1 RRE. As a unique tool with which to investigate the relationship between different RNA trafficking routes and translational enhancement, SNV RU5 and Rev/RRE were combined on a single gag RNA. We observed a less-than-synergistic effect on cytoplasmic mRNA utilization. Instead, Rev/RRE diverts RU5 gag RNA to the CRM1-dependent, LMB-inhibited pathway and abrogates translational enhancement by SNV RU5. Our study is the first to show that a nuclear factor(s) directs SNV RU5-containing RNAs to a distinct export pathway that is not inhibited by LMB and programs the intron-containing transcript for translational enhancement.

Regulation of interleukin 1 beta RNA expression in the common carp, Cyprinus carpio L.

The intron-exon organisation of the carp IL-1β gene consists of 2455 bp and comprises seven exons. Three IL-1β RNA transcripts have been found in carp: (1) a fully spliced product; (2) exon 1–7 with introns 5 and 6; and (3) exon 1–7 with intron 5 only. The intron-containing products probably represent partially spliced transcripts. IL-1β mRNA expression in carp was semi-quantitatively analysed by RT-PCR in multiple organs, including brain and pituitary. Constitutive expression of the IL-1β mRNA was found in these organs with a predominant expression in the immune organs head kidney and spleen. Furthermore, a scattered distribution of IL-1β producing cells was shown by in situ hybridisations of head kidney tissue. Administration of phorbol-myristate-acetate (PMA), lipopolysaccharide (LPS) or retinoic acid (RA), to phagocytes isolated from the head kidney, resulted in expression of IL-1β intron-containing transcripts. Of these, only PMA and LPS were stimulators that induced the fully spliced transcript. A role for the nuclear factor (NF)-κB pathway in carp IL-1β expression was shown with suppression of the LPS-induced IL-1β expression by NF-κB inhibitor pyrrolidine dithiocarbamate (PDTC). Cortisol was able to inhibit in vitro constitutive expression of IL-1β transcripts. Addition of cortisol simultaneously with LPS could not substantially inhibit transcription.

Processing of alpha-globin and ICP0 mRNA in cells infected with herpes simplex virus type 1 ICP27 mutants.

Herpes simplex virus (HSV) ICP27 is an essential and multifunctional regulator of viral gene expression that modulates RNA splicing, polyadenylation, and nuclear export. We have previously reported that ICP27 causes the cytoplasmic accumulation of unspliced alpha-globin pre-mRNA. Here we examined the effects of a series of ICP27 mutations that alter important functional regions of the protein on the processing and nuclear transport of alpha-globin and HSV ICP0 RNA. The results demonstrate that ICP27 mutants that are impaired for growth in noncomplementing cells, including mutants in the N- and C-terminal regions, are defective in the accumulation of alpha-globin pre-mRNA. Unexpectedly, several mutants that are competent to repress the expression of reporter genes in transient transfection assays failed to accumulate unspliced RNA, implying that different mechanisms are responsible for transrepression and pre-mRNA accumulation. Several mutants caused a marked increase in the length and heterogeneity of the alpha-globin mRNA poly(A) tail, suggesting that ICP27 may directly or indirectly affect the regulation of poly(A) polymerase. ICP27 was also required for the accumulation of multiple ICP0 intron-bearing transcripts, but this effect displayed a mutational sensitivity profile different from that of accumulation of unspliced alpha-globin RNA. Moreover, unlike spliced and unspliced alpha-globin RNAs, which were efficiently exported to the cytoplasm, spliced and intron-containing ICP0 transcripts were predominantly nuclear in localization, and ICP27 was not required for nuclear retention of the spliced message. We propose that these transcript- and ICP27 allele-specific differences may be explained by the presence of a strong cis-acting ICP27 response element in the alpha-globin transcript.

Sam68, RNA helicase A and Tap cooperate in the post-transcriptional regulation of human immunodeficiency virus and type D retroviral mRNA.

Unlike cellular mRNA, retroviral mRNA bypasses the tight coupling of the splicing and nuclear export steps to allow the export of intron-containing viral RNA transcripts to the cytoplasm. Two distinct nuclear export pathways for retroviral mRNA have been described: a CRM-1 dependent pathway mediated by the HIV-1 Rev protein and the Rev Response Element (RRE), and a CRM-1 independent pathway mediated by the Constitutive Transport Element (CTE) of type D retroviruses. Two CTE-binding proteins, RNA helicase A (RHA) and Tap, have been implicated in the nuclear export of CTE-containing RNA. Recently, we reported that expression of RRE-containing RNA could also be mediated by a cellular protein, Sam68, independently of Rev. Here we report evidence that Sam68, RHA and Tap cooperate in the nuclear export of both CTE- and RRE-containing RNA. RHA binds to Sam68 and to Tap both in vivo and in vitro. Over-expression of Sam68 activates both RRE- and CTE-regulated reporter gene expression in human cells and in quail cells in the presence of human Tap. This activation was competitively inhibited by the nuclear transport domain (NTD) of RHA and a transdominant negative mutant of Tap. Conversely, the activation of CTE by Tap in quail cells was inhibited by a transdominant mutant of Sam68 and NTD. We propose that both HIV and type D retroviruses may access the same constitutive RNA nuclear export pathway involving RHA, Tap and Sam68, even though HIV also utilizes the Rev protein for more efficient nuclear export. it is likely that this constitutive export pathway is also used by cellular mRNA, but at a different interface with the splicing process.

The formation of respiratory chain complexes in mitochondria is under the proteolytic control of the m-AAA protease.

Yta10p (Afg3p) and Yta12p (Rcal1p), members of the conserved AAA family of ATPases, are subunits of the mitochondrial m-AAA protease, an inner membrane ATP-dependent metallopeptidase. Deletion of YTA10 or YTA12 impairs degradation of non-assembled inner membrane proteins and assembly of respiratory chain complexes. Mutations of the proteolytic sites in either YTA10 or YTA12 have been shown to inhibit proteolysis of membrane-integrated polypeptides but not the respiratory competence of the cells, suggesting additional activities of Yta10p and Yta12p. Here we demonstrate essential proteolytic functions of the m-AAA protease in the biogenesis of the respiratory chain. Cells harbouring proteolytically inactive forms of both Yta10p and Yta12p are respiratory deficient and exhibit a pleiotropic phenotype similar to Deltayta10 and Deltayta12 cells. They show deficiencies in expression of the intron-containing mitochondrial genes COX1 and COB. Splicing of COX1 and COB transcripts is impaired in mitochondria lacking m-AAA protease, whilst transcription and translation can proceed in the absence of Yta10p or Yta12p. The function of the m-AAA protease appears to be confined to introns encoding mRNA maturases. Our results reveal an overlapping substrate specificity of the subunits of the m-AAA protease and explain the impaired assembly of respiratory chain complexes by defects in expression of intron-containing genes in mitochondria lacking m-AAA protease.

Herpes simplex virus type 1 immediate early protein IE63 shuttles between nuclear compartments and the cytoplasm.

Herpes simplex virus type 1 (HSV-1) immediate early protein IE63, an essential nuclear protein, is pleiotropic in function and, at the post-transcriptional level, inhibits RNA splicing, interacts with cellular splicing small nuclear ribonucleoprotein particles (snRNPs), binds RNA and prevents the nucleocytoplasmic transport of intron-containing mRNAs. Here it is reported that IE63 is a nucleocytoplasmic shuttle protein able to travel from snRNP- and RNA-rich nuclear foci to the cytoplasm, where it accumulates during actinomycin D treatment. This newly identified property suggests that IE63 facilitates nuclear export of HSV-1 transcripts, in addition to retaining intron-containing transcripts in the nucleus. The mechanism by which IE63 controls RNA export has yet to be defined.

Expression and RNA splicing of the maize glutathione S-transferase Bronze2 gene is regulated by cadmium and other stresses.

The Bronze2 (Bz2) gene in maize (Zea mays) encodes a glutathione S-transferase that performs the last genetically defined step in anthocyanin biosynthesis--tagging anthocyanin precursors with glutathione, allowing for recognition and entry of anthocyanins into the vacuole. Here we show that Bz2 gene expression is highly induced by heavy metals such as cadmium. Treatment of maize seedlings with cadmium results in a 20-fold increase in Bz2 message accumulation and a 50-fold increase in the presence of the unspliced, intron-containing transcript. The increase in message levels during cadmium stress appears to result, at least in part, from activation of an alternative mRNA start site approximately 200 nucleotides upstream of the normal start site; this site is not used in unstressed or heat-stressed tissues. The effect of cadmium on the RNA splicing of Bz2 seems to be specific: splicing of other intron-containing maize genes, including a maize actin gene under the control of the cadmium-inducible Bz2 promoter, is unaffected by cadmium stress. Conversely, Bz2 intron splicing is not affected by other stress conditions that induce Bz2 gene expression, such as abscisic acid, auxin, or cold stress. Surprisingly, the increase in Bz2 mRNA during cadmium stress does not result in an increase in Bz2 glutathione S-transferase activity. We propose that an alternative protein may be encoded by Bz2 that has a role during responses to heavy metals.

Rev Protein of Human Immunodeficiency Virus Type 1 Facilitates Translation of rev-dependent Viral Messenger RNAs.

Human immunodeficiency virus type 1 (HIV1) Rev has been reported to act by inducing the nucleocytoplasmic transport of unspliced and singly spliced RNAs that encode viral structural proteins. However, our initial experiments indicated the cytoplasmic expression of intron-containing mRNAs in Rev-cells [12]. To determine whether or not the post-transcriptional induction of gene expression by Rev extends to the level of increasing the efficiency of translation, Rev+ and Rev-cells were morphologically examined by means of in situ hybridization and immunofluorescence assays. Hybridization to an intron-specific probe revealed that the transfection of HeLa cells with a rev-defective HIV-1 expression plasmid caused the export of overexpressed, unspliced gag mRNAs, possibly through a default process of nuclear retention. However, subsequent immunofluorescence assaying demonstrated that mRNA exported by Rev, but not mRNA directed through the default process, was translated into the corresponding protein. The findings were extended to a group of singly spliced viral mRNAs that produce Env in the following biochemical analyses. These findings suggest that Rev is directly or indirectly involved in the translational regulation of HIV-1 structural gene mRNAs. We discuss the possibility that Rev could cause the intron-containing transcripts to follow the appropriate pathway to reach the translational machinery.

Accumulation of immature intron-containing cd44 gene transcripts in breast cancer tissues

Background: Disorderly expression of the CD44 gene is a characteristic feature of many common types of human malignancy. The explanation for the diversity, abundancy, and abnormally large size of the resulting transcripts is under investigation. Methods and Results: This study used reverse transcription-polymerase chain reaction (RT-PCR)/Southern blot hybridization to examine the expression of the CD44 gene in fresh tissue samples from 21 breast cancers and 11 matched non-neoplastic breast tissue specimens from the same patients. Using probes for several exons and for a noncoding region (intron 9) of the gene, it was found that the previously described elevated levels of CD44 transcripts in malignant tumors of this organ include many unusual, alternatively spliced isotypes as well as immature forms that retain this intron and probably several others. All of the exons that were tested were involved in the disorderly overexpression of this gene observed in all of the cancer tissues, and we were able to detect retention of the intron 9 sequence in 14 (67%) of the 21 tumor samples. In contrast, it was possible to detect signals in only 3 (27%) of the 11 samples from nonmalignant breast tissue with this probe, and these were extremely faint. Conclusions: These findings imply that there is a profound disorder in the regulation of production, splicing, and processing of CD44 pre-mRNA in breast cancer tissues comparable to that described in tumors of many other organs. The clinical implication of this information is that analysis of tissue samples containing borderline or suspected premalignant lesions for the presence of these molecular abnormalities, which appear to be characteristic of neoplasia, may in due course help assessment of individual patient prognosis and optimization of treatment. (Mol Diagn 1996 Sep;1(3):175-181)

Herpes simplex virus type 1 protein IE63 affects the nuclear export of virus intron-containing transcripts.

Using in situ hybridization labelling methods, we have determined that the herpes simplex virus type 1 immediate-early protein IE63 (ICP27) affects the cellular localization of virus transcripts. Intronless transcripts from the IE63, UL38, and UL44 genes are rapidly exported to and accumulate in the cytoplasm throughout infection, in either the presence or absence of IE63 expression. The intron-containing transcripts from the IE110 and UL15 genes, while initially cytoplasmic, are increasingly retained in the nucleus in distinct clumps as infection proceeds, and the clumps colocalize with the redistributed small nuclear ribonucleoprotein particles. Infections with the IE63 mutant virus 27-lacZ demonstrated that in the absence of IE63 expression, nuclear retention of intron-containing transcripts was lost. The nuclear retention of UL15 transcripts, which demonstrated both nuclear and cytoplasmic label, was not as pronounced as that of the IE110 transcripts, and we propose that this is due to the late expression of UL15. Infections with the mutant virus 110C1, in which both introns of IE110 have been precisely removed (R.D. Everett, J. Gen. Virol. 72:651-659, 1991), demonstrated IE110 transcripts in both the nucleus and the cytoplasm; thus, exon definition sequences which regulate viral RNA transport are present in the IE110 transcript. By in situ hybridization a stable population of polyadenylated RNAs was found to accumulate in the nucleus in spots, most of which were separate from the small nuclear ribonucleoprotein particle clumps. The IE63 protein has an involvement, either direct or indirect, in the regulation of nucleocytoplasmic transport of viral transcripts, a function which contrasts with the recently proposed role of herpes simplex virus type 1 Us11 in promoting the nuclear export of partially spliced or unspliced transcripts (J.-J. Diaz, M. Duc Dodon, N. Schaerer-Uthurraly, D. Simonin, K. Kindbeiter, L. Gazzolo, and J.-J. Madjar, Nature [London] 379:273-277, 1996), the significance of which is discussed.

Dynamic organization of pre-mRNA splicing factors.

Studies from several laboratories during the past few years have increased our understanding towards the dynamic organization of pre-mRNA splicing factors in the mammalian cell nucleus. Many well characterized splicing factors have been localized in a speckled pattern in the cell nucleus. Upon the activation of RNA polymerase II transcription, splicing factors are recruited to the sites of transcription from sites of reassembly and/or storage. Nascent intron-containing RNA transcripts are spliced at the sites of transcription. The speckled distribution of splicing factors in the nucleus is altered when either transcription or pre-mRNA splicing activities are interrupted suggesting that the organization of the splicing machinery in the interphase nucleus is a direct reflection of the transcriptional activity of the cell.

Identification of Prp40, a Novel Essential Yeast Splicing Factor Associated with the U1 Small Nuclear Ribonucleoprotein Particle

We have used suppressor genetics to identify factors that interact with Saccharomyces cerevisiae U1 small nuclear RNA (snRNA). In this way, we isolated PRP40-1, a suppressor that restores growth at 18 degrees C to a strain bearing a cold-sensitive mutation in U1 RNA. A gene disruption experiment shows that PRP40 is an essential gene. To study the role of PRP40 in splicing, we created a pool of temperature-sensitive prp40 strains. Primer extension analysis of intron-containing transcripts in prp40 temperature-sensitive strains reveals a splicing defect, indicating that Prp40 plays a direct role in pre-mRNA splicing. In addition, U1 RNA coimmunoprecipitates with Pro40, indicating that Prp40 is bound to the U1 small nuclear ribonucleoprotein particle in vivo. Therefore, we conclude that PRP40 encodes a novel, essential splicing component that associates with the yeast U1 small nuclear ribonucleoprotein particle.

The product of the nuclear gene PET309 is required for translation of mature mRNA and stability or production of intron-containing RNAs derived from the mitochondrial COX1 locus of Saccharomyces cerevisiae.

Expression of the Saccharomyces cerevisiae mitochondrial COX1 locus, which contains several introns and is co-transcribed with the downstream genes AAP1, OLI2 and ENS2, is controlled by at least 18 nuclear-encoded proteins. The PET309 gene, encoding one of these proteins, was cloned, sequenced and shown to contain an open reading frame of 965 codons. Isonuclear PET309+ and delta pet309::URA3 strains carrying mitochondrial genomes that differ in the number of COX1 introns, were generated. Analysis of RNA species from these strains demonstrated an inverse relationship between the number of introns present in the precursor RNA and the amount of COX1 and AAP1/OLI2/ENS2 RNAs accumulated in a pet309 mutant. Hence, PET309 plays a role either in transcription of intron-containing primary transcripts from the COX1-AAP1-OLI2-ENS2 transcription unit or in stabilization of primary transcripts. PET309 is also required in translation of COX1 mRNA. A mitochondrial bypass suppressor of the pet309 deletion mutation was isolated, and shown to consist of a DNA rearrangement at the COX1 locus, such that the 5' untranslated leader region (UTR) of the COB gene was fused to COX1 at nucleotide -174 of its 5' UTR. This result suggests that Pet309p acts through the COX1 5' UTR to activate initiation of translation of the COX1 coding region.

Myoblast and myotube nuclei display similar patterns of heterogeneous acetylcholine receptor subunit mRNA expression.

Muscle progenitor cells differentiate to myoblasts, and subsequently myotubes, upon expression of muscle specific genes. We and others have previously shown that myotube nuclei, even in the absence of nerve, express AChR alpha subunit RNA at varying levels, with a small subset (about ten percent) of the nuclei expressing at high levels. These findings raised two important questions: 1) is the observed heterogeneity a unique property of the alpha subunits, and 2) when does the heterogeneity begin? In particular, is it induced only at or after the time of fusion, or does it exist at the myoblast stage? We have, therefore, extended our observations to the gamma and delta subunits and we also have examined the distributions of AChR alpha, gamma, and delta subunit RNAs in both myoblasts and myotubes. We used intron and intron-exon probes to detect prespliced transcripts or mature mRNAs in the cells. Because intron-containing transcripts are not transported out of the nuclei, the distributions of these transcripts can indicate their expression patterns among nuclei in the same myotubes. Our results show that both myotubes and myoblasts have distributions of the AChR alpha, gamma, and delta subunit RNAs which differ sharply from that of the U1 RNA or Myo D. Thus, the heterogeneous expression of AChR genes is not only an intrinsic property of muscle cell nuclei (in the sense that it does not require the presence of nerves), but it also exists prior to fusion. Our results suggest that muscle nuclei attain individualized capacities for AChR subunit mRNA production early in their development. Conceptual models consistent with such individuality imply an additional level of regulation beyond the known diffusible transcriptional factors.