Childhood asthma is associated with mutations and gene expression differences of ORMDL genes that can interact

BACKGROUND

Genomewide association studies identified ORMDL3 as a plausible asthma candidate gene. ORMDL proteins regulate sphingolipid metabolism and ceramide homeostasis and participate in lymphocyte activation and eosinophil recruitment. Strong sequence homology between the three ORMDL genes and ORMDL protein conservation among different species suggest that they may have shared functions. We hypothesized that if single nucleotide polymorphisms (SNPs) in ORMDL3 alter its gene expression and play a role in asthma, variants in ORMDL1 and ORMDL2 might also be associated with asthma.

METHODS

Asthma associations of 44 genotyped SNPs were determined in at least 1303 subjects (651 asthmatics). ORMDL expression was evaluated in peripheral blood mononuclear cells (PBMC) from 55 subjects (eight asthmatics) before and after allergen stimulation, and in blood (n = 60, 5 asthmatics). Allele-specific cis-effects on ORMDL expression were assessed. Interactions between human ORMDL proteins were determined in living cells.

RESULTS

Sixteen SNPs in all three ORMDLs were associated with asthma (14 in ORMDL3). Baseline expression of ORMDL1 (P = 1.7 × 10(-6) ) and ORMDL2 (P = 4.9 × 10(-5) ) was significantly higher in PBMC from asthmatics, while induction of ORMDLs upon stimulation was stronger in nonasthmatics. Disease-associated alleles (rs8079416, rs4795405, rs3902920) alter ORMDL3 expression. ORMDL proteins formed homo- and heterooligomers and displayed similar patterns of interaction with SERCA2 and SPT1.

CONCLUSIONS

Polymorphisms in ORMDL genes are associated with asthma. Asthmatics exhibit increased ORMDL levels, suggesting that ORMDLs contribute to asthma. Formation of heterooligomers and similar interaction patterns with proteins involved in calcium homeostasis and sphingolipid metabolism could indicate shared biological roles of ORMDLs, influencing airway remodeling and hyperresponsiveness.

Fine-mapping of IgE-associated loci 1q23, 5q31, and 12q13 using 1000 Genomes Project data

BACKGROUND

Genome-wide association studies (GWAS) repeatedly identified 1q23 (FCER1A), 5q31 (RAD50-IL13 and IL4), and 12q13 (STAT6) as major susceptibility loci influencing the regulation of total serum IgE levels. As GWAS may be insufficient to capture causal variants, we performed fine-mapping and re-genotyping of the three loci using 1000 Genomes Project datasets.

METHODS

Linkage disequilibrium tagging polymorphisms and polymorphisms of putative functional relevance were genotyped by chip technology (24 polymorphisms) or MALDI-TOF-MS (40 polymorphisms) in at least 1303 German children (651 asthmatics). The effect of polymorphisms on total serum IgE, IgE percentiles, and atopic diseases was assessed, and a risk score model was applied for gene-by-gene interaction analyses. Functional effects of putative causal variants from these three loci were studied in silico.

RESULTS

Associations from GWAS were confirmed and extended. For 1q23 and 5q31, the majority of associations were found with mild to moderately elevated IgE levels, while in the 12q13 locus, single-nucleotide polymorphisms (SNPs) were associated with strongly elevated IgE levels. Gene-by-gene interaction analyses suggested that the presence of mutations in all three loci increases the risk for elevated IgE up to fourfold.

CONCLUSION

This fine-mapping study confirmed previous associations and identified novel associations of SNPs in 1q23, 5q31, and 12q13 with different levels of serum IgE and their concomitant contribution to IgE regulation.

Polymorphisms in the IRF-4 gene, asthma and recurrent bronchitis in children

BACKGROUND

Interferon-regulatory factors (IRFs) play a crucial role in immunity, not only influencing interferon expression but also T cell differentiation. IRF-4 was only recently recognized as a further major player in T cell differentiation.

OBJECTIVE

As IRF-1 polymorphisms were shown to be associated with atopy and allergy, we comprehensively investigated effects of IRF-4 variants on allergy, asthma and related phenotypes in German children.

METHODS

Fifteen tagging single nucleotide polymorphisms (SNPs) in the IRF-4 gene were genotyped by MALDI-TOF MS in the cross-sectional ISAAC phase II study population from Munich and Dresden (age 9-11; N = 3099). Replication was performed in our previously established genome-wide association study (GWAS) data set (N = 1303) consisting of asthma cases from the Multicenter Asthma Genetic in Childhood (MAGIC) study and reference children from the ISAAC II study.

RESULTS

SNPs were not significantly associated with asthma but with bronchial hyperresponsiveness, atopy and, most interestingly, with recurrent bronchitis in the first data set. The IRF-4 variant rs9378805 was associated with recurrent bronchitis in the ISAAC population and replicated in the GWAS data set where further SNPs showed associations with recurrent bronchitis and asthma.

CONCLUSIONS

We found genetic associations in IRF-4 to be associated with recurrent bronchitis in our two study populations. Associated polymorphisms are localized in a putative regulatory element in the 3'UTR region of IRF-4. These findings suggest a putative role of IRF-4 in the development of bronchitis.

A role of FCER1A and FCER2 polymorphisms in IgE regulation

BACKGROUND

Both FCER2 and FCER1A encode subunits of IgE receptors. Variants in FCER1A were previously identified as major determinants of IgE levels in genome-wide association studies.

METHODS

Here we investigated in detail whether FCER2 polymorphisms affect IgE levels alone and/or by interaction with FCER1A polymorphisms. To cover the genetic information of FCER2, 21 single-nucleotide polymorphisms (SNPs) were genotyped by Illumina HumanHap300 BeadChip (5 SNPs) and the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS; 14 SNPs) in at least 1303 Caucasian children (651 asthmatics) (ISAAC II/ MAGICS population); genotypes of two SNPs were imputed.

RESULTS

SNP rs3760687 showed the most consistent effect on total serum IgE levels (b [SE] = -0.38 [0.16]; P = 0.016), while FCER2 polymorphisms in general were predominantly associated with mildly-to-moderately increased IgE levels (50th and 66th percentiles). Gene-by-gene interaction analysis suggests that FCER2 polymorphism rs3760687 influences IgE levels mainly in individuals not homozygous for the risk allele of FCER1A polymorphism rs2427837, which belongs to the major IgE-determining tagging bin in the population.

CONCLUSION

FCER2 polymorphism rs3760687 affects moderately elevated total serum IgE levels, especially in the absence of homozygosity for the risk allele of FCER1A SNP rs2427837.

[Asthma training in children and adolescents]

In Germany, asthma training courses have been available for a number of years now. The efficacy of these courses in terms of quality of life improvement and the economics of such training has been demonstrated unequivocally. In the present study, the development of asthma training in Germany is discussed. In recent years, in particular, it has been shown that the involvement of the patient's family is of considerable importance. In addition, in the practical work of the asthma trainer, instruments for quality testing and quality control of presently established concepts have been developed, which guarantee a high standard of most pediatric training programs. The interdisciplinary aspect has an eminently important role to play: the cooperation on equal footing of various occupational groups enables the team to adopt a number of different options with regard to their pupils and their families. A model providing a description of coping with the disease on a number of different levels has been worked out (8-level model). In the concept developed by the pediatric hospital in Osnabrück, the social aspect in relation to the child takes pride of place.

Estrogen suppresses hepatitis B virus expression in male athymic mice transplanted with HBV transfected Hep G-2 cells

Hormones are known to regulate both viral and cellular genes. It has been shown previously that estrogen has an effect on liver gene transcription and mRNA stability. Sex hormones might have a role in the chronic persistence of hepatitis B virus (HBV) infection. In fact, there is a male preponderance in the incidence of chronic HBV infection, and HBsAg expression was reported to be much higher in male transgenic mice than in the females. We investigated the effect of estrogen on HBV gene expression and regulation in athymic mice bearing 2.2.15 cells, a human hepatoblastoma cell line derived from Hep G-2 transfected with HBV sequences. Both male and female mice were treated with estradiol after tumors could be observed. Episomal DNA was extracted from the tumors and hybridized with 32P-labelled HBV DNA. Southern blot and slot blot analyses demonstrated that male mice had higher expression of HBV DNA. Estrogen treatment suppressed HBV DNA expression in males, but had only a minor effect on females. HBeAg production in male mice was also inhibited by estrogen treatment. HBV RNA extracted from 2.2.15 cells showed 2-3-fold reduction following beta-estradiol treatment. Moreover, inhibition of HBV transcription by estrogen was demonstrated by an RNA pulse-labelling experiment. These data indicate that estrogen inhibits HBV expression in the in vivo model presented in this study. These results might contribute to a better understanding of the effect of sex hormones on the pathogenesis of HBV-induced liver disease.

In vitro regulation of human hepatitis B virus core gene transcription

In the present study we used a HeLa whole cell extract transcription system to map the transcription start sites and the minimal promoter of the hepatitis B virus core gene. Two initiation sites located at residues 1792 +/- 5 and 1817 +/- 5 were identified. The minimal upstream region essential and sufficient for transcription was defined to a 105-base pair DNA fragment. These results are identical to the in vivo mapping of the transcription start sites and the minimal core gene promoter. When in vitro transcription elongation was carried out in the presence of the anionic detergent Sarkosyl, known to enhance premature transcription termination (attenuation), two short transcripts (as well as two run-offs) were synthesized. Kinetic studies indicated that the short transcripts resulted from a block to transcription elongation and not from RNA processing. RNA mapping showed that the short attenuated transcripts indeed initiated at the two core gene initiation sites and both prematurely terminated at nucleotide 1966 +/- 5, defined as the attenuation site. This site is located in the attenuator RNA within a uridine-rich sequence preceded by a stable hairpin structure. Attenuation at the same site occurred when transcription of the core gene was directed by the Ad2 major late promoter (MLP) and when the poly(A) signal, which precedes the attenuation site, was mutated from TATAAA to TAGAAA. We suggest that the elongation block at nt 1966 +/- 5 in vivo exerts a dual function: first, it regulates the level of RNA by attenuation during the first cycle of transcription and, second, it acts as a termination site at the end of the primary RNA transcript.

Corticosteroids stimulate hepatitis B virus DNA, mRNA and protein production in a stable expression system

The effect of corticosteroids (Dexamethasone) on hepatitis B virus was investigated in human hepatoblastoma cells stable transfected with recombinant HBV DNA. Dexamethasone was found to cause elevation of HBsAg, HBeAg and viral DNA production. HBV poly(A)+ RNA was significantly increased in cells treated with Dexamethasone. Furthermore, pulse labelled nuclear HBV RNA was also stimulated by Dexamethasone. These findings, suggest that corticosteroids enhance expression of viral gene products by stimulating HBV transcription.

Alpha interferon suppresses hepatitis B virus enhancer activity and reduces viral gene transcription

Interferons inhibit replication of hepatitis B virus (HBV). The mechanism for this inhibition was investigated by analyzing the effect of interferons on transcription of a chloramphenicol acetyltransferase reporter gene under control of HBV regulatory sequences and by determining the steady-state level of viral mRNAs in permanently HBV-transfected HepG2 cells. Low doses (100 U/ml) of alpha interferon (IFN-alpha) but not IFN-gamma inhibited chloramphenicol acetyltransferase expression in cultured cells transfected with plasmids containing the HBV enhancer linked to either HBV or simian virus 40 promoters. IFN-alpha also lowered expression of HBV mRNA in HBV-transfected HepG2 cells actively replicating virus, suggesting that IFN-alpha inhibits HBV replication by reducing transcription of viral genes driven by the HBV enhancer.

Liver-specific expression of hepatitis B virus is determined by the combined action of the core gene promoter and the enhancer

The hepatitis B virus (HBV) enhancer and the core gene promoter regulate the expression of the core and polymerase genes, as well as of the 3.5-kilobase pregenomic RNA. RNA analysis and chloramphenicol acetyltransferase gene expression by plasmids carrying the HBV enhancer linked to the heterologous beta-globin or simian virus 40 early promoter demonstrated that the HBV enhancer is 3- to 20-fold preferentially expressed in human liver cells. Core gene promoter activity was mapped to a 100-base-pair fragment which was shown to be sufficient for accurate initiation of transcription. The partial tissue specificity of this promoter was demonstrated by transient transfection into various cell lines with a plasmid containing the core gene promoter linked to the heterologous simian virus 40 enhancer. When the HBV core gene promoter was examined under the control of the HBV enhancer, there was high tissue specificity in that activity could be observed only in differentiated human liver cells. These results suggest that the strict tissue specificity of HBV gene expression is determined by the combinatorial action of these two elements.

The hepatitis B virus-associated reverse transcriptase is encoded by the viral pol gene

We have used activity gel analysis and immunoblotting to provide evidence linking the hepatitis B virus (HBV) reverse transcriptase with its longest unassigned open reading frame (polymerase [Pol]-ORF). Activity gel analysis demonstrated that infectious HBV particles secreted by the Hep 2.2.15 cell line contain major (approximately 70 kilodaltons [kDa]) and minor (approximately 90 kDa) reverse transcriptase activities. By Western immunoblotting, we detected in both HBV particles and Hep 2.2.15 cell extract a approximately 70-kDa Pol-specific peptide. This approximately 70-kDa peptide reacted with antisera directed against the carboxy terminus of the pol gene product. No such immunoreactivity was observed with antisera against the amino terminus of the Pol peptide. The reverse transcriptase protein which was eluted from the major approximately 70-kDa region detected on an activity gel reacted with Pol-specific antisera. Furthermore, reverse transcriptase activity was immunoprecipitated from dissociated HBV particles by using Pol-specific antisera. On the basis of our results, we suggest that HBV encodes its reverse transcriptase from the Pol-ORF.

Two proteins with reverse transcriptase activities associated with hepatitis B virus-like particles

Recent studies suggest that hepatitis B virus (HBV), despite being a DNA virus, replicates via an RNA intermediate (R. H. Miller, P. L. Marion, and S. W. Robinson, Virology 139:64-72, 1984; J. Summers and W. S. Mason, Cell 29:403-415, 1982). The HBV life cycle is therefore a permuted version of the RNA retroviral life cycle. Sequence homology between retroviral reverse transcriptase and the putative HBV polymerase gene product suggests the presence of an HBV reverse transcriptase (H. Toh, H. Hajashida, and T. Miyata, Nature (London) 305:827-829, 1983). As yet, there has been no direct evidence that reverse transcriptase activity is present in the viral particle. We used activity gel analysis to detect the in situ catalytic activities of DNA polymerases after sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Our studies demonstrated that HBV-like particles secreted by a differentiated human hepatoma cell line transfected with genomic HBV DNA contain two major polymerase activities which migrate as approximately 90- and approximately 70-kilodalton (kDa) proteins. This demonstrated, for the first time, that HBV-like particles contain a novel DNA polymerase-reverse transcriptase activity. Furthermore, we propose that the 70-kDa reverse transcriptase may be produced by proteolytic self-cleavage of the 90-kDa precursor protein.

Identification of a promoter element located upstream from the hepatitis B virus X gene

We have analyzed a series of plasmids in which the sequences located upstream from the hepatitis B virus (HBV) X gene were linked to the chloramphenicol acetyl transferase (CAT) gene. Expression of the marker CAT gene in transfected cells clearly demonstrated that sequences preceding the X gene contain an active promoter. RNA mapping by primer extension indicated that the RNA encoded by the X gene promoter initiates at multiple sites spanning nucleotides 1250 to 1350 on the HBV genome. Deletion within the adjacent HBV enhancer element region significantly reduced the activity of the X gene promoter, suggesting that the X gene promoter requires the enhancer element for maximal activity.

Hepatitis B virus gene function: the precore region targets the core antigen to cellular membranes and causes the secretion of the e antigen

The core gene of the hepatitis B virus genome contains two conserved in-phase initiation codons separated by about 90 nucleotides. This region ("the precore region") encodes largely hydrophobic amino acids. We have expressed the coding sequence of the core gene with or without the precore region by using a simian virus 40-derived vector in heterologous mammalian cells. The results show that the precore region is not required for the expression either of core antigen (cAg) or of a related hepatitis B virus antigen, the e antigen (eAg). However, the precore region causes the cAg to become associated with cytoplasmic membranes, probably the endoplasmic reticulum. Further, the presence of the precore sequence results in the secretion of eAg. Our results suggest that the precore region plays a role in targeting core proteins to the membrane; this may be the direct cause of eAg secretion and also may aid in the interaction of the core and surface antigens in the formation of the viral particle.

A human hepatitis B viral enhancer element

Fragments of the cloned hepatitis B virus (HBV) genome were assayed in vivo for the presence of a transcriptional enhancer element. We demonstrate that sequences positioned approximately 450 bp upstream from the HBcAg gene promoter are required for its efficient activity. These HBV stimulatory sequences activate transcription when inserted upstream to a heterologous SV40 early promoter. Like other known enhancer elements, this HBV sequence acts in an orientation-independent manner. Furthermore, the HBV enhancer element exhibits a preferred activity in a human hepatoma cell line.

Transcription of hepatitis B virus by RNA polymerase II

We employed an in vitro cell-free transcription system to locate RNA polymerase II promoters on the hepatitis B virus genome. The strongest promoter precedes the surface antigen (HBsAg) gene, which is comprised of a long (500 base pairs) presurface region as well as the mature HBsAg coding sequence. The origin of this transcript was localized by using truncated templates and S1 endonuclease mapping. The activity of the promoter was confirmed in transfection experiments in which the complete HBsAg gene was introduced into monkey kidney cells via a simian virus 40 expression vector. A second RNA polymerase II promoter preceding the HBcAg gene was also active in the cell-free system. The presence of multiple promoters in the hepatitis B virus genome suggests that the relative levels of viral-specific proteins detected in liver and serum may reflect differential or regulated promoter efficiency.

Hepatitis B virus encodes an RNA polymerase III transcript

We demonstrated that cloned hepatitis B virus (HBV) DNA directs the synthesis of a 700-base RNA (HBV 700) by RNA polymerase III in a cell-free transcription system. HBV 700 is the only transcript known to originate from the viral short strand and has been mapped to the region between roughly 1,635 and 954 base pairs on the viral map, between the surface and core antigen coding sequences but overlapping and opposing the putative DNA polymerase and B protein genes. The in vitro initiation sites for the HBV 700 and core antigen RNAs are only 50 bases apart, suggesting that these two genes may be coordinately regulated. Moreover, both of these initiation sites appear to lie within the approximately 300-base double-stranded region (the nick region) between the 5' end of the HBV short strand and the nick in the viral long strand. We found two unusual sequence elements in the nick region that are conserved between the human and woodchuck viruses.

Synthesis of hepatitis B surface antigen in mammalian cells: expression of the entire gene and the coding region

We have constructed two simian virus 40 early replacement recombinants that have the coding sequences for hepatitis B virus surface antigen (HBsAg). One construction, LSV-HBsAg, has the coding region for HBsAg but not the portion encoding the putative pre-surface antigen leader. Transformed monkey kidney cells (COS) infected with this recombinant express large quantities of the characteristic partially glycosylated HBsAg molecule, which are assembled into 22-nm particles that appear similar to those produced by human liver cells infected with hepatitis B virus. This result indicates that the pre-surface antigen sequences are not required for the synthesis of HBsAg or its assembly into particulate structures. The second recombinant, LSV-HBpresAg, has the entire surface antigen gene, including the putative promoter and pre-surface antigen region. COS cells infected with this recombinant plasmid produce 40- to 50-fold less HBsAg than those infected with the LSV-HBsAg recombinant plasmid. RNA mapping studies suggest that the transcription of the HBsAg gene is initiated at more than one site, or alternatively, that RNA splicing of transcripts occurs in the pre-surface antigen region.

Expression of the human insulin gene in an alternate mammalian cell and in cell extracts

The functional regions of the human insulin gene have been characterized by in vitro and in vivo experiments. The locations of the insulin promoter and cap site have been predicted from the sequence of the gene, and these assignments are consistent with the results of in vitro transcription experiments using HeLa cell extracts. For studies of intracellular expression, the human insulin gene including its promoter and two intervening sequences was inserted into the late region of the virus, SV40, in a construction that eliminates the major splice junction of the late SV40 region. Permissive CV1 monkey kidney cells were infected with this recombinant and a complementing helper virus. During the course of the infection, insulin gene transcripts accumulate at about one-third the level of SV40 late transcripts originated from the same promoter. Analysis of the RNAs containing insulin sequences showed that the insulin introns are excised with precision. Furthermore, the insulin promoter (cap site) and polyadenylation sites are recognized but are less efficiently employed than the viral late promoter and terminator. The mRNA is translated and immunoreactive human proinsulin is secreted into the extracellular medium.

Expression of the human insulin gene and cDNA in a heterologous mammalian system

The human insulin gene or the corresponding cDNA has been inserted into the early region of a simian virus 40 vector in which all SV40 splice junctions were deleted while the early promoter and polyadenylation regions remained intact. The expression of insulin-coding sequences was tested in permissive monkey COS cells. The insulin cDNA was transcribed from the early promoter to produce a stable polyadenylated RNA which was translated, and immunoreactive human proinsulin accumulated in the medium. Thus RNA splicing is not obligatory for insulin expression in this system. The genomic insulin transcript was also initiated from the SV40 promoter and terminated at the SV40 polyadenylation site. S1 endonuclease mapping revealed that the transcript is processed via two alternative splicing pathways within the insulin gene. About one-third of the total transcripts are processed normally with removal of the two insulin-specific introns. This transcript is apparently translated normally since immunoreactive proinsulin accumulates in the medium. About two-thirds of the transcripts are processed via an alternative splicing pathway involving a new splice acceptor site located within the coding region of the insulin gene. This results in a codon frameshift such that translation would produce a novel chimeric peptide containing the insulin NH2-terminal B chain, but a different COOH terminus containing human and SV40 sequences. A peptide of the predicted size is detected in the COS cell extract.

5,6-dichloro-1-beta-ribofuranosylbenzimidazole enhances premature termination of late transcription of simian virus 40 DNA

Short RNA chains initiating at the major promoter sites for simian virus 40 (SV40) late transcription are elongated to approximately 450 nucleotides in a molar ammount greater than that from any other region of the viral DNA. This conclusion is based on the following observations: (i) Transcriptional complexes isolated by Sarkosyl and by hypotonic leaching (minichromosomes) from nuclei of cells infected with SV40 as well as intact nuclei were pulse labeled in vitro with [alpha-32P]TUP and were observed to synthesize short RNA transcripts that hybridized predominantly to a SV40 DNA fragment spanning between 0.67 and 0.76 map units. (ii) In the presence of 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB), a drug known to accentuate premature transcriptional termination, accumulation of these short SV40 RNA chains was enhanced. When SV40-infected cells were pretreated with DRB and then labeled in vivo or in vitro, they synthesized short labeled viral RNAs that hydridized almost exclusively with the DNA fragment spanning between 0.67 and 0.76 map units. These observations suggest a mechanism in the regulation of SV40 late transcription.

Mechanism for circularization of linear DNAs: circular parvovirus MVM DNA is formed by a "noose" sliding in a "lasso"-like DNA structure

During an electron-microscopic survey with the aim of identifying the parvovirus MVM transcription template, we observed previously unidentified structures of MVM DNA in lysates of virus-infected cells. These included double-stranded "lasso"-like structures and relaxed circles. Both structures were of unit length MVM DNA, indicating that they were not intermediates formed during replication; they each represented about 5% of the total nuclear MVM DNA. The proportion of these structures was unchanged after digestion with sodium dodecyl sulfate/Pronase and RNase and after mild denaturation treatment. Cleavage of the "lasso" structures with EcoRI restriction endonuclease indicated that the "noose" part of the "lasso" structure is located on the 5' side of the genomic single-stranded MVM DNA. A model is presented for the molecular nature of the circularization process of MVM DNA in which the "lasso" structures are identified as intermediates during circle formation. This model proposes a mechanism for circularization of linear DNAs.

The frequencies of transcription from the E- and L-strands of polyoma DNA

Exhaustion type hybridization was used to measure the amount of nuclear virus RNA complementary to the early (E) and late (L) polyoma virus DNA strands. At 36 h after infection between 2.5 and 7.3% of the newly synthesized virus RNA was complementary to the E-strand (-strand) and between 92.7 and 97.5% was complementary to the L-strand (+strand). This proportion was independent of the labelling time, indicating similar accumulation of the E- and L-RNA transcripts in the nucleus. The nuclear E- and L-RNA transcripts sedimented in a similar manner through sucrose gradients.

Electron microscopic evidence for splicing of SV40 late mRNAs

Poly(A)-containing SV40 cytoplasmic RNA was hybridized with linear double-stranded SV40 DNA and formed RNA displacement loops (R loops). The structures visualized in the electron microscope are consistent with the conclusion that the leader sequences at the 5' ends of the 16S and 19S late mRNAs are not coded immediately adjacent to the main portions of the mRNAs. These data are consistent with either segmentation of the leaders or heterogeneity of their lengths. Measurements carried out on the R loop structures have provided the locations, on the physical map of SV40 DNA, for the bodies and leaders of the 16S and 19S late mRNAs, and the lengths of the bodies, leaders and the corresponding intervening DNA sequences.

Novel mechanism for RNA maturation: the leader sequences of simian virus 40 mRNA are not transcribed adjacent to the coding sequences

The 5'-terminal 100-200 ribonucleotides of late simian virus 40 (SV40) mRNAs are not transcribed immediately adjacent to their coding sequences. This conclusion is based on the following observations. The major late SV40 cytoplasmic RNA species, 16S and 19S, were purified from poly(A)-containing cytoplasmic RNA by hybridization to and elution from an SV40 DNA fragment that maps between 0.67 and 0.76. This fragment is remote from the DNA fragments that include the coding sequences. The RNA transcripts from the fragment located between 0.67 and 0.76 were found in abundance. Even though selected on oligo(dT)-cellulose columns, the 5'-terminal sequences did not contain poly(A) tails directly adjacent to their 3' termini. The 5' terminus of the 16S mRNA, as monitored by hybridization of the sequences adjacent to the "cap" structure, was found adjacent to the coding sequences when intact [3H]methyl-labeled RNA was hybridized with restriction fragments. However, after fragmentation, the methyl label of this same RNA hybridized with a fragment that is remote from the coding sequences and maps between 0.67 and 0.73. These results imply a novel mechanism for biosynthesis of SV40 mRNA.

Transcription of simian virus 40. V. Regulattion of simian virus 40 gene expression

RNA "exhaustion type" hybridization was used to measure the complementarity of nuclear and cytoplasmic viral RNA to the early (E) and late (L) simian virus 40 (SV40) DNA strands. This type of hybridization measures the amount of labeled RNA complementary to each of the two DNA strands, rather than the fraction of each SV40 DNA strand that is homologous to SV40 RNA. At 48 h after infection, about 5% of the nuclear newly synthesized viral RNA was complementary to the E-strand (- strand) and 95% was complementary to the L-strand (+ strand). This proportion was independent of the labeling time, indicating similar accumulation of the E- and L-RNA transcripts in the nucleus. The nuclear E- and L-viral RNA transcripts sedimented in a similar manner on sucrose gradients. Of the cytoplasmic viral RNA only about 1% was complementary to the E-strand, these molecules sedimenting at 19S, whereas 99% were complementary to the L-strand and sedimented at 19S and 16S. The abundance of E-RNA transcripts in nuclei of cells infected with serially passaged virus was about four times higher than that in nuclei of cells infected with plaque-purified virus; however, the size and proportion of the corresponding cytoplasmic E- and L-RNA transcripts was independent of the type of virus used to infect the cells. According to these results at least two control mechanisms regulate viral gene expression in productively infected cells, one operates at the trnascriptional level and the second at the post-transcriptional level.