Radioactive RNA Research Articles

Similar poly(C)-sensitive RNA-binding complexes regulate the stability of the heavy and light neurofilament mRNAs

The potential role of RNA processing in regulating neurofilament (NF) subunit expression and in mediating the neuropathic effects of NF transgenes was explored by determining whether similar regulatory elements and cognate binding factors are present in NF mRNAs. Gel-shift studies were used to compare RNA-binding complexes that assemble on the 3′UTR of the heavy (NF-H), mid-sized (NF-M) and light (NF-L) NF mRNAs when radioactive RNA probes are incubated with high-speed supernatants (S100) of rat brain homogenates. RNA-binding complexes were characterized by their rate of migration in non-denaturing gels and by their ability to be competed with specific homoribopolymers. Similar RNA-binding complexes formed on probes to the 3′UTRs of NF-L and NF-H mRNAs. The complexes were competed with poly(C) and are referred to as poly(C)-sensitive complexes. Their binding sites were localized to a 36 nt sequence in the mid-distal region of the NF-H 3′UTR and to a 45 nt sequence at the proximal edge of the 3′UTR of the NF-L transcript. Although the binding sites showed limited sequence homology, the complexes were cross-competed with unlabeled probes and radioactivity in either probe was cross-linked to a 43 kDa protein. The 43 kDa protein also bound directly to NF-L and NF-H probes in Northwestern blots. Functional studies showed that deletion of the binding sites markedly increased expression of a luciferase reporter gene containing the 3′UTR of NF-L or NF-H by stabilizing the fusion transcripts. Point mutations in the NF-H binding site which prevented formation of the poly(C)-sensitive complex also stabilized the fusion mRNA. The findings reveal a common destabilizing element in the 3′UTR of NF-L and NF-H mRNAs that may be important in coordinating NF subunit expression and in mediating the neuropathic effects of the NF-L and NF-H transgenes in transgenic mice.

Effects of rho-independent terminators on the expression of the prokaryoticβ-glucuronidase gene in tobacco

The threonine (thr) attenuator with a dyad symmetrical structure is from the regulatory region of the thr operon of Escherichia coli, and encodes RNA with a stem-and-loop structure followed by a stretch of uridine residues. The thr attenuator and its variants were subcloned into the region between the 35S promoter and β-glucuronidase (GUS) coding region, and the transient expression of GUS gene in tobacco protoplast was treated as a reporter for gene regulation in plants. Results from the 14 variants in the stem region of the thr attenuator indicated that both base pairing and sequence specificity in the G+C-rich region of the stem were important for the GUS expression, but 1 base mismatch in the A+U-rich region of stem did not affect the GUS expression in plants. Seven variants with nested deletion in the stretch of uridine residues were also analyzed, and the results suggested that the variants with the shorter uridine stretch produced more GUS protein than those with the longer stretch. Transgenic tobacco plants with the thr attenuator and its variants located between the 35S promoter and GUS coding region were also generated, and their steady state RNAs were hybridized with 2 radioactive antisense RNA probes which bound 5′ and 3′ of the thr hairpin, respectively. After the digestion of S1 nuclease, the amount of the nuclease-resistant transcript from the protection of the 5′ antisense RNA probe was much more than that from the protection of the 3′ probe in all tested variants. This result suggests that these dyad symmetries may affect transcription of plant RNA polymerase II.

Cloning, gene expression, and characterization of CP27, a novel gene in mouse embryogenesis.

We report the full-length sequencing, tissue-specific expression, and immunolocalization of cp27, a novel gene in mouse embryogenesis. The cp27 gene was isolated and cloned from a mouse E11 lambdagt11 library using a peptide antibody that recognized a distinct expression pattern in mouse craniofacial development. The cp27 gene contains an open reading frame of 295 amino acids corresponding to a predicted molecular mass of 33kDa. On Western blots, a polyclonal antibody against CP27 detected a single epitope at 27kDa. The putative CP27 protein has an isoelectric point of 4.75 and features a distinct helix-loop-helix structure according to prediction algorithms. We have cloned the human cp27 gene and mapped it to a locus on the human chromosome 16 which is in proximity to several loci associated with inherited craniofacial diseases such as fanconi anemia type A. Northern blot analysis of RNA from multiple mouse tissues demonstrated high levels of expression in developing mouse teeth, heart, lung, and liver of a single transcript of approx. 1. 8kbp. In situ hybridization using a radioactive RNA probe resulted in distinct signals in the developing neuroepithelium, cerebellum, heart, lung, liver, teeth, salivary glands, and periosteum of developing bones. Immunohistochemical staining of developing mouse tissues detected epitopes specific for CP27 in the mesenchyme surrounding the primary brain vesicles, in basement membranes, in the periosteum, in salivary glands, and in the stellate reticulum of teeth. Thus, CP27 represents a unique gene product involved in mouse embryogenesis.

Lack of a role for the D 3 receptor in clozapine induction of c-fos demonstrated in D 3 dopamine receptor-deficient mice

The role of the D 3 dopamine receptor in mediating the effects of clozapine was analysed using in situ hybridization histochemistry to measure the induction of the immediate early gene c-fos in different brain areas of mice lacking a functional D 3 dopamine receptor compared to wild type mice. Clozapine treatment (15 and 30 mg/kg, s.c.) resulted in a dose-dependent pattern of induction of c-fos messenger RNA in the striatum, accumbens and septal area, with a non-significant increase in the prefrontal cortex. There was no difference detected in any of these areas in the level of induction between mice lacking the D 3 receptor (D 3−/−) and wild type (D 3+/+). To determine which types of neurons in the striatum and accumbens displayed clozapine (30 mg/kg) induction of c-fos messenger RNA, a double-labeling experiment was performed using a radioactive c-fos messenger RNA probe and a digoxigenin-labeled enkephalin messenger RNA probe, the latter used as a marker of D 2-containing neurons. Clozapine-induced c-fos was detected in 20% of enkephalin-positive striatal neurons and 15% of enkephalin-positive accumbens neurons, and in both areas in about 10% of enkephalin-negative, putative D 1 neurons, in both D 3+/+ and D 3−/− mice. These results demonstrate that clozapine induction of c-fos messenger RNA is not dependent on the D 3 dopamine receptor subtype in the striatum or nucleus accumbens.

Laminar and cellular distribution of AMPA, kainate, and NMDA receptor subunits in monkey sensory-motor cortex.

In situ hybridization histochemistry and immunocytochemistry were used to examine lamina- and cell-specific expression of glutamate receptor (GluR) mRNAs and polypeptide subunits in motor and somatosensory cortex of macaque monkeys. Radioactive complementary RNA (cRNA) probes were prepared from cDNAs specific for alpha-amino-3-hydroxy-5-methylisoxozolepropionate (AMPA)/kainate (GluR1-GluR4), kainate (GluR5-GluR7), and N-methyl-D-aspartate (NMDA; NR1, NR2A-NR2D) receptor subunits. AMPA/kainate and NR1, NR2A, and NR2B receptor transcripts show higher expression than other transcripts. All transcripts show lamina-specific patterns of distribution. GluR2 and GluR4 mRNAs show higher expression than do GluR1 and GluR3 mRNAs. GluR6 transcript expression is higher than that of GluR5 and GluR7. NR1 mRNA expression is much higher than that of NR2 mRNAs. NR2C subunit expression is very low except for a very distinct band of high expression in layer IV of area 3b. Immunocytochemistry, using subunit-specific antisera and double labeling for calbindin, parvalbumin, or alpha type II Ca2+/calmodulin-dependent protein kinase (CaMKII-alpha), allowed identification of cell types expressing different subunit genes. GluR1 and GluR5/6/7 immunoreactivity is found in both pyramidal cells and gamma-amino butyric acid (GABA) cells; GluR2/3 immunoreactivity is preferentially found in pyramidal cells, whereas GluR4 immunoreactivity is largely restricted to GABA cells; NMDA receptor subunit immunoreactivity is far greater in excitatory cells than in GABA cells. The density of expression of AMPA/kainate, kainate, and NMDA receptor subunit mRNAs differed within and across the architectonic fields of sensory-motor cortex. This finding and the lamina- and cell-specific patterns of expression suggest assembly of functional receptors from different arrangements of available subunits in specific neuronal populations.

Human papillomavirus and Epstein-Barr virus in sinonasal Schneiderian papillomas. An in situ hybridization and polymerase chain reaction study.

Using the polymerase chain reaction (PCR), it has been recently reported that the Epstein-Barr virus (EBV) is present in the majority of Schneiderian sinonasal papillomas (SNP) of the inverted type and may play a role in the pathogenesis of these lesions. The reported prevalence rates of human papillomavirus (HPV) in different types of SNP is also controversial and in need of clarification. Twenty-eight SNP from 27 patients were histologically classified and evaluated for evidence of EBV using PCR and 2 different sensitive and specific in situ hybridization (ISH) procedures for EBER1. Similarly, two methods of ISH were also used for the detection of HPV, using biotinylated DNA probes sensitive for 14 different HPV types as well as more sensitive and specific radioactive RNA probes for HPV types 6, 11, and 16. Polymerase chain reaction was successful in 19 papillomas, including 12 of 19 inverted SNP, 1 of 1 inverted SNP with squamous cell carcinoma, 4 of 5 fungiform SNP, and 2 of 3 oncocytic lesions. Southern blot hybridization of PCR products showed the presence of EBV DNA in two lesions, including one inverted SNP and the single inverted SNP with squamous cell carcinoma. By both DNA- and RNA-mRNA ISH, positivity for EBER was detected in rare stomal lymphocytes but not the overlying epithelium in the inverted SNP with SCC. The remaining cases, including the other inverted SNP positive for EBV by PCR, were completely negative by both ISH techniques. Human papillomavirus was detected by ISH in 1 of 19 (5%) inverted, 1 of 1 (100%) inverted with squamous cancer, 5 of 5 (100%) fungiform, and 0 of 3 (0%) oncocytic SNP. Three SNP contained HPV 6 (all fungiform), three SNP labeled for HPV 11 (two fungiform and the inverted SNP with squamous cancer), and one inverted SNP contained HPV 16. Of the five fungiform SNP, four showed foci of koilocytosis. The results indicate that EBV is not present in sinonasal papillomas. The presence of EBV positive stromal lymphocytes in these lesions may account for a proportion of PCR-positive cases. Oncocytic SNP are unassociated with HPV, whereas inverted SNP contain HPV in a minority of cases. In contrast, fungiform SNP are consistently associated with HPV types 6 and 11 and usually show histologic evidence of viral infection.

PIPPin, a Putative RNA-Binding Protein Specifically Expressed in the Rat Brain

In looking for genes encoding RNA-binding factors, we prepared an expression library in λgt11, by cloning cDNAs corresponding to the polyadenylated fraction of RNA from rat brain at the embryonal day 18. The library was then screened by binding to a radioactive RNA, transcribed in vitro from a cDNA encoding the rat histone variant H3.3. Here we report some findings concerning a cDNA for a protein which contains two putative double stranded RNA-binding domains (dsBD). The corresponding message is specifically expressed in the brain. Moreover, Southern blot analysis showed that the gene is highly conserved from Drosophila melanogaster to man.

Laminar patterns of expression of GABA-A receptor subunit mRNAs in monkey sensory motor cortex.

Radioactive complementary RNA probes, made from monkey-specific cDNAs specific for the alpha 1, alpha 2, alpha 4, alpha 5, beta 1, beta 2, and gamma 2 subunits of the gamma-aminobutyric acid A (GABAA) receptor were used for in situ hybridization histochemistry of the primary motor, somatosensory, and anterior parietal areas of the cerebral cortex in macaque monkeys. mRNAs for the alpha 1, beta 2, and gamma 2 subunit polypeptides, which form receptors with the full range of classical properties, are expressed at much higher levels in all areas and show laminar- and sublaminar-specific concentrations. alpha 2, alpha 4, alpha 5, and beta 1 subunit transcripts are expressed at much lower levels but also display individual, laminar-specific concentrations; alpha 5 expression, in particular, is highly expressed in layer IV in the somatosensory and parietal areas and in a layer IV-like band in the motor cortex. In layers in which expression of a particular transcript is high, all neurons may express the gene, but in layers in which expression is moderate, it is possible to detect differences in the degree of labeling of individual neurons for a particular mRNA, and some neurons may not express certain subunit transcripts in detectable amounts. These findings indicate the variability in expression of different GABAA receptor subunits in the cerebral cortex. Laminar differences may indicate the assembly of functional receptors from different arrangements of available subunits in different classes of cells.

The rat intrinsic factor gene: its 5'-upstream region and chief cell-specific transcription.

A DNA segment containing the 5'-upstream region and amino terminal reading frame of the gastric intrinsic factor gene was cloned from rat and its nucleotide sequence was determined. S1 mapping demonstrated that the transcription initiation site is located downstream of the second TATA-box sequence. Similar sequence motifs to those in the pepsinogen genes transcribed in gastric chief cells were found in the deduced sequence, suggesting that the rat intrinsic factor gene is transcribed in these cells. The genes for the intrinsic factor and its homologous protein transcobalamin I were apparently derived from a common ancestoral gene, since the positions of their intron insertions as well as the amino acid residues are conserved. Northern blot hybridization showed that the gene for the intrinsic factor is transcribed in the stomach but not detectably in the intestine, kidney, testis, brain, heart, liver, lung, or spleen. In situ hybridization using radioactive complementary RNA clearly indicated that the major transcription site in gastric glands is chief cells. Different locations of expression of intrinsic factor proteins in various mammals were observed previously using antibodies: in rat parietal cells and chief cells, in mouse chief cells, and in human parietal cells. The present results clearly demonstrated the intrinsic factor mRNA mainly in chief cells of adult rats, as in mice, suggesting that transcriptional regulation of the intrinsic factor gene is essentially the same in rodents.

Changes in gene expression following short coronary occlusions studied in porcine hearts with run-on assays

Brief coronary occlusions cause upregulation of expression in a wide variety of genes. These changes in tissue mRNA concentration could have been produced by transcriptional or post-transcriptional events. The aim of this study was to discriminate between increased transcription and changes in mRNA stability using run-on assays with isolated myocyte nuclei. Myocyte nuclei isolated from ischaemic/reperfused and normal myocardium were incubated with labelled ribonucleotides. The radioactive RNA was then hybridised with specific cDNA probes and slot blots were autoradiographed. There was increased transcriptional activity for the proto-oncogenes c-myc, c-jun, jun-B, and jun-D. There were marked increases in transcriptional activity for sarcoplasmic Ca(2+)-ATPase, calmodulin, phospholamban, and calsequestrin. Strong transcriptional activity was found for the ubiquitin and heat shock protein (hsp27, hsp70) genes, and for PAI-1 and GAPDH. The transcription for the beta myosin heavy chain gene was not altered. Changes in the tissue concentration of mRNA species following brief coronary occlusion and reperfusion are most often the result of altered transcriptional activity. Increased c-fos mRNA concentrations observed in earlier studies cannot be explained by transcriptional activity of myocytes during reperfusion. Calmodulin is strongly transcribed but tissue concentration stays constant. The overall pattern of gene expression is indicative of damage at the molecular level, and calcium binding proteins (among perhaps many others) are in need of repair.

Partial characterization of a cDNA for human stearoyl-CoA desaturase and changes in its mRNA expression in some normal and malignant tissues.

A segment of 712 bases coding for part of the human stearoyl-CoA desaturase gene was made by polymerase chain reaction (PCR) using primers based on published rat cDNA sequences. The human PCR product was confirmed by DNA sequencing. It was next cloned into a vector from which anti-sense, highly radioactive RNA transcripts were made in vitro using T7 polymerase. The transcripts were used to probe desaturase mRNA in a number of human tumour and control tissues, using a very sensitive solution hybridization/RNase protection assay. Increased desaturase mRNA levels were found in colonic and oesophageal carcinomas and in hepatocellular adenoma; however, no consistent trend was seen in hepatocellular carcinoma. It is suggested that certain classes of tumour may exhibit increased levels of desaturase mRNA.

In Situ Hybridization for Detection of HIVRNA

In HIV studies, in situ hybridization can be used for identifying virion RNA, mRNA being produced for virion packaging, and proviral DNA in the cytoplasm or integrated in the nucleus. This unit focuses primarily on identifying virion RNA, because this is the most sensitive means by which in situ hybridization can be employed to detect HIV expression. In situ hybridization, as developed for HIV RNA detection, involves several protocols: (1) preparation of a radioactive or nonradioactive RNA probe; (2) in situ hybridization of probe to cells and paraffin sections of tissue; (3) detection of radiolabeled probe by emulsion autoradiography; (4) development, staining, and mounting of slides; and finally (5) examination of slides by bright-field, dark-field, specular reflectance, or laser-scanning confocal microscopy. The protocols presented in this unit describe a setup involving up to 150 slides.

Antibodies specific to histone H1 inhibit in vitro transcription in isolated mammalian nuclei.

The issue of whether histone H1 is present in transcriptionally active chromatin has been approached by studying the effect specific anti-H1 antibodies have on in vitro transcription in isolated nuclei. To that end, the incorporation of radioactive RNA precursors into trichloroacetic acid-precipitable material was compared for control nuclei and nuclei that had been preincubated with specific anti-H1 antibody populations (whole sera, affinity-purified immunoglobulins and monovalent Fab fragments). The anti-H1 antibodies significantly and reproducibly inhibited the transcriptional activity in isolated nuclei. Experiments were also performed to exclude the possibility that the inhibition observed was due to some long-distance effect of the binding of the antibodies to chromatin. The results are interpreted as indicating that active gene chromatin does contain histone H1.

A regulatory cis element and a specific binding factor involved in the mitogenic control of murine ribosomal protein L32 translation.

The mRNA encoding ribosomal protein L32 redistributes from untranslated subribosomal particles into polysomes after mitogenic activation of quiescent T-lymphocytes and fibroblasts. To identify the regions of the L32 mRNA which are important in regulating its cytoplasmic location we constructed a plasmid containing the murine L32 cDNA under the control of the Rous sarcoma virus (RSV) long terminal repeat promoter and introduced this construct into murine 3T3 fibroblasts. The mRNA transcribed from the RSV-L32 construct redistributed from subribosomal particles into polysomes in response to mitogenic activation in a manner similar to endogenous L32 mRNA. A conserved polypyrimidine region present at the 5' terminus of all ribosomal protein mRNAs is required for translational regulation of L32 mRNA since deletion of this sequence resulted in a mRNA that was not sequestered in subribosomal particles in quiescent cells. A radioactive RNA probe containing the first 34 nucleotides of the L32 5'-untranslated region, including the polypyrimidine region, specifically interacted with a protein of about 56 kDa. This protein did not bind detectably to RNA probes lacking the polypyrimidine sequence. Binding activity was similar in protein extracts made from resting and activated cells, suggesting that binding of the 56-kDa protein as measured in this assay is not regulated. This protein is a member of what may be an emerging family of polyribopyrimidine-binding proteins with diverse biochemical functions.

Acceleration of adenovirus replication and increased virion production by treatment with the steroid hormone 17 beta-estradiol.

We report here that concentration of an estrogen known to promote enhanced transformation and to increase oncogenicity of rat embryo cells, accelerate the production and increase the yield of progeny virions in adenovirus type 12 (Ad 12)-infected HEp-2 cells. Further, measurement of the incorporation of radioactive RNA and DNA precursors indicated that macromolecular synthesis in the estrogen-treated, infected cells was accelerated. Possible explanations for this observation are discussed.

Detection of BMYV and BWYV isolates using monoclonal antibodies and radioactive RNA probes, and relationships among luteoviruses

SummaryIn order to discriminate between sugar beet infecting beet mild yellowing virus (BMYV) and other isolates of beet western yellows virus (BWYV), monoclonal antibodies (MAbs) and radioactive riboprobes were used. With MAbs prepared against BMYV or potato leafroll virus (PLRV) no distinction could be established between BMYV and BWYV. Seven probes were synthesised from a lettuce infecting BWYV isolate; their localisation in the genome is known and they cover almost its entire length. Probes from the ′3 part of the genome hybridised with all BMYV and BWYV isolates whereas those from the ′5 part did not recognise BMYV isolates, showing that a divergent ′5 region exists in the genomes of BMYV and BWYV. Probes also readily detected the virus in single aphids. The relevance of this finding for epidemiological studies is discussed.MAbs and riboprobes were also tested against other luteoviruses (PLRV; barley yellow dwarf virus (BYDV) MAV, PAV and RPV strains). The serological relationship between BMYV and PLRV was confirmed and an epitope common to PLRV and BYDV‐RPV was found. Using probes, PLRV and BYDV‐RPV were found to share domains of homology with BWYV. BYDV‐PAV showed weak homology with BWYV, while BYDV‐MAV showed none.

RNA-binding properties of the matrix protein (p19gag) of avian sarcoma and leukemia viruses

We have reinvestigated the ability of the matrix protein (MA) (p19gag) of avian sarcoma and leukemia viruses to interact with RNA. Previous reports claimed on the one hand that MA can bind tightly and with a high degree of specificity to avian sarcoma and leukemia virus RNA in vitro and on the other that it cannot bind to RNA at all. We found that MA purified by any of several methods does bind to RNA, as measured by its ability to cause retention of radioactive RNA on nitrocellulose membranes in a filtration assay. However, this interaction is weak and lacks specificity. The interaction of MA with RNA was barely detectable by classical sedimentation analysis, and from this observation we estimate that the intrinsic MA-RNA association constant is ca. 10(3) M-1, at least 3 orders of magnitude smaller than the constant describing the interaction of the viral nucleocapsid protein (NC) (p12gag) with RNA, ca. 10(6) M-1. Separately purified phosphorylated and nonphosphorylated MA species bound RNA equally. We also found that MA can bind to DNA with an affinity similar to that for RNA. The large quantitative discrepancy between our results and earlier published reports can be traced in part to methods of data analysis.

Transcripts of individual Drosophila actin genes are differentially distributed during embryogenesis

The temporal and spatial patterns of accumulation of transcripts from individual actin genes during Drosophila embryogenesis have been determined by in situ hybridization. We describe the subcloning into transcription vectors of unique DNA fragments derived from the 3' transcribed, but nontranslated region of each actin gene. These fragments then served as templates for the synthesis in vitro of single-stranded, radio-active gene-specific RNA probes. Probe characterization and hybridization to developmental RNA blots are presented, demonstrated the independent developmental accumulation of actin transcripts from each gene. Each gene-specific probe has been hybridized in situ to the transcripts present in embryonic frozen sections. The results of these experiments have demonstrated that transcripts from each actin gene accumulate differentially in developing Drosophila tissues. The 5C and 42A actin genes are cytoplasmic actin genes, with transcripts distributed in all cells and tissues of the developing embryo. Therefore these genes presumably encode the cytoplasmic actins used for functions common to all cells. Transcripts from both cytoplasmic actin genes are evenly distributed in preblastoderm embryos, becoming localized to the periphery at blastoderm formation [5C: Burn et al.: Dev Biol 131:345-355, 1989]. Later in development, levels of these cytoplasmic transcripts vary in specific tissues. While the patterns of localization of 5C actin transcripts have been published [Burn et al.: Dev Biol 131:345-355, 1989], differential neurological localization is presented here; 42A transcripts are localized at higher concentrations in the midgut, the brain, nerve cord, and gonad. Both 87E and 57B transcripts accumulated in the developing larval body wall musculature, but at differing levels and in differing patterns. Transcripts of the 79B and the 88F actin genes were undetectable in embryos. The results of these experiments suggest dedicated contributions of individual actin genes to complex developmental processes.

Action of Aldosterone on Cultured Renal Collecting Duct Cells during the Latent Period

The effects of aldosterone on protein synthesis in the latent period were investigated on cultured renal collecting duct cells from neonatal rabbit kidneys. Tissue was incubated with radioactively labelled uridine and amino acids and then precipitated with trichloroacetic acid in order to determine the intracellular precursor pool and identify new synthesis of RNA and protein. During the latent period, aldosterone increased the intracellular radioactive uridine pool and total radioactive RNA content already 20 and 60 min after its application; conversely 40 min after aldosterone introduction, no stimulation was found. Further experiments revealed that the intracellular radioactive amino acid pool was generally increased by aldosterone after 20, 40 and 60 min, while a distinct increased radioactive protein content was found to be induced by aldosterone only after 40 min. This indicates that aldosterone increases the uptake of RNA and protein precursors and the new synthesis of RNA and proteins. These events seem to to be regulated not continuously but intermittently. The induced proteins possibly take part in the mediation of the early hormone response. Experiments with the aldosterone antagonist, spironolactone, provide evidence for the specificity of the described hormone effects. The results after application of the Na+ channel blocker, amiloride, and the Na+/K(+)-ATPase inhibitor, G-strophanthin, indicate that the aldosterone effects are controlled by Na+ channels and Na+ pumps and therefore by the intracellular Na+ content. The inhibitory effect of cycloheximide on the aldosterone-induced protein synthesis indicates the role of these proteins on the hormone-stimulated Na+ transport.

Mapping introns by exon excision

A direct method for mapping introns has been devised. The technique makes use of a radioactive synthetic RNA transcript of the gene and a complementary, single-stranded DNA copy of mRNA-derived sequences. Upon hybridization of the cDNA to RNA and cleavage with ribonuclease H, only exonic RNA sequences are degraded. The surviving RNA fragments are the introns. Electrophoretic analysis in denaturing agarose gels reveals the number and size of the introns. The order of the introns is determined separately using unlabeled RNA transcripts; surviving RNA fragments are transferred to a solid support and the blot is probed sequentially with a nested set of genomic RNA transcripts of the opposite strand. Using the human prothymosin α gene as an example, four introns were identified which from 5′ to 3′ were 2.6, 0.47, 0.47, and 0.28 kb in size. From mapping and sequencing experiments the sizes are 2.6, 0.465, 0.459, and 0.295 kb, respectively. Similarly, the presence of two 300-bp insertions in a human prothymosin α pseudogene was established; the inserts were later identified as 295-bp Alu repetitive elements.