Electron microscopic evidence for splicing of SV40 late mRNAs

RNA-dependent nuclear matrix contains a 33 kb globin full domain transcript as well as prosomes but no 26S proteasomes

Previously, we have shown that in murine myoblasts prosomes are constituents of the nuclear matrix; a major part of the latter was found to be RNase sensitive. Here, we further define the RNA-dependent matrix in avian erythroblastosis virus (AEV) transformed erythroid cells in relation to its structure, presence of specific RNA, prosomes and/or proteasomes. These cells transcribe but do not express globin genes prior to induction. Electron micrographs show little difference in matrices treated with DNase alone or with both, DNase and RNase. In situ hybridization with alpha globin riboprobes shows that this matrix includes globin transcripts. Of particular interest is that, apparently, a nearly 35 kb long globin full domain transcript (FDT), including genes, intergenic regions and a large upstream domain is a part of the RNA-dependent nuclear matrix. The 23K-type of prosomes, previously shown to be co-localized with globin transcripts in the nuclear RNA processing centers, were found all over the nuclear matrix. Other types of prosomes show different distributions in the intact cell but similar distribution patterns on the matrix. Globin transcripts and at least 80% of prosomes disappear from matrices upon RNase treatment. Interestingly, the 19S proteasome modulator complex is insensitive to RNase treatment. Only 20S prosomes but not 26S proteasomes are thus part of the RNA-dependent nuclear matrix. We suggest that giant pre-mRNA and FDTs in processing, aligning prosomes and other RNA-binding proteins are involved in the organization of the dynamic nuclear matrix. It is proposed that the putative function of RNA within the nuclear matrix and, thus, the nuclear dynamic architecture, might explain the giant size and complex organization of primary transcripts and their introns.

A new method for the routine spreading of DNA in protein-free conditions

Electron microscopic studies of DNA are hampered by difficulties encountered with the spreading of DNA under protein-free conditions. The established and currently popular technique of spreading DNA on carbon membranes treated by glow discharge in an atmosphere of pentylamine is limited with regard to its reproducibility and the proper distribution of spread molecules on the surface of the membranes. A new, reliable, and highly reproducible technique using tri-L-(dimethylaminomethyl)phenol (DMP 30), a promotor factor for spreading circular DNA, linear DNA, and DNA-protein complexes, is described in this paper. Monolayers of DMP 30 are formed at the air-water interface by a microdiffusion procedure on droplets. DNA molecules that diffuse on this monolayer can easily be picked up on hydrophobic carbon membranes. This method, which is easy, reproducible, and fast, will facilitate electron microscopic studies of DNA-protein interactions.

Sequence homology within the morbilliviruses

Double-stranded cDNA synthesized from total polyadenylate-containing mRNA extracted from monkey kidney cells infected with canine distemper virus (CDV) was cloned into the PstI site of Escherichia coli plasmid pBR322. Clones containing CDV DNA were identified by hybridization to a CDV-specific 32P-labeled cDNA. A cDNA clone containing an insert 1,700 base pairs (CDV 364) has been identified as the reverse transcript of the mRNA coding for the nucleocapsid protein. The size of the mRNA species complementary to this insert is 1,850 nucleotides, as determined by the Northern technique. Hybridization experiments and heteroduplex mapping indicated homology between the central region of the CDV and measles virus nucleocapsid gene. The completion of the nucleotide sequence analysis of the measles virus gene allowed the reconstruction of the entire coding region of the measles virus gene and a comparison with the counterpart sequence of CDV. This comparison delineated three regions: (i) a region of high homology (nucleotides 501 to 1215), in which 77% of the nucleotides and 88% of the encoded amino acids are identical; (ii) a region of moderate homology at the 5' end of the message (nucleotides 1 to 500), in which 59% of the nucleotides and 66% of the encoded amino acids are identical; (iii) a region of little or no homology (nucleotides 1216 to 1625) near the 3' end of the message.

Mapping of polyadenylated transcripts of a monkey lymphotropic papova virus

Polyadenylated transcripts of a monkey lymphotropic papovavirus (LPV), which can be propagated in monkey and human lymphoblastoid cell lines, were identified and mapped. Polyadenylated RNA was purified from cells of the human line BJA/B infected with LPV, and was hybridized with various LPV DNA fragments. The hybrids were treated with S1 endonuclease and analyzed by alkaline gel electrophoresis. This analysis revealed two groups of RNA molecules encoded in two regions of the LPV genome. One group includes four colinear transcripts of 2.3, 2.1, 1.85, and 1.2 kb, whose polyadenylated termini map at a single site on the LPV DNA. The second group includes two less-abundant transcripts of 1.8 and 1.95 kb. The polarities of the LPV transcripts were determined by hybridizing cDNA complementary to their 3' termini with LPV DNA fragments. The two groups were found to have opposite polarities. It is shown that the four major transcripts can be aligned with, and may be functionally related to, SV40 and polyoma virus "late" mRNAs. It is also inferred that the 1.8- and 1.95-kb RNA species may be functionally related to the "early" transcripts of these papovaviruses.

Cloning and characterization of DNA complementary to the measles virus mRNA encoding hemagglutinin and matrix protein

Since cloning and characterization of DNA complementary to measles virus mRNA encoding for the nucleocapsid protein (M. Gorecki and S. Rozenblatt, Proc, Natl. Acad, Sci, U.S.A. 77:3686--3690, 1980), two additional measles-specific clones containing different classes of sequences have been characterized. The cloned plasmids contain inserts of 480 and 530 base pairs as shown by agarose gel electrophoresis and electron microscopy. The sizes of the mRNA species complementary to these inserts are 1,700 and 1,550 nucleotides, respectively as determined by the Northern technique. The cloned DNA fragments were further identified as reverse transcripts of the mRNA coding for the glycoprotein and matrix protein of measles virus. The major cell-free translation products of mRNA selected by hybridization to the individual cloned DNAs comigrated with the 70K in vitro products and matrix proteins. One of the cell-free translation products (70K) was also immunoprecipitated specifically with monoclonal antibodies against measles virus glycoprotein.

Attenuation in the control of SV40 gene expression

Nuclei and viral transcriptional complexes were prepared from cells infected with simian virus 40 and incubated in vitro in the presence of alpha- 32P-UTP. The in vitro elongated viral RNA appeared with a peak of 5S in sucrose gradients and hybridized preferentially to a promoter-proximal region of SV40 DNA. Treatment of infected cells with proflavine led to transcription of elongated RNA, while treatment of cells with 5,6-dichloro-1-beta-d-ribofuranosylbenzimidazole, a drug known to enhance premature termination, augmented accumulation of the promoter-proximal RNA. The in vitro elongated RNA produced a major band of 93-95 nucleotides in length in acrylamide gel. This RNA was found to map between the major initiation site at nucleotide 243 and nucleotides 335-337. The significance of these observations with respect to the transcription termination signal and the control of SV40 gene expression is discussed.

Simian virus 40 early mRNA's in lytically infected and transformed cells contain six 5'-terminal caps

Late simian virus 40 (SV40) mRNA contains eight different cap structures which we have previously identified and mapped on the viral genome. As reported here, 5'-cap heterogeneity is a common feature to both the early and the late SV40 mRNA's. methyl-3H-labeled viral mRNA was purified from cells infected at 41 degrees C with SV40 mutant tsA209. Three different cap cores were identified: m7GpppGm, m7GpppCm, and m7GpppAm. An average of three to four m6A residues per mRNA molecule was found. RNase T2-resistant 32P-labeled early caps from tsA209-infected cells isolated and characterized. Six distinct cap I structures were identified: m7GpppCmpU (30%), m7GpppGmpC (24%), m7GpppAmpG (18%), m7GpppGmpU (13%), m7GpppGmpG (12%), and m7GpppAmpU (3%). A similar 5'-end heterogeneity was observed in early SV40 mRNA from BSC-1 cells infected with wild-type SV40 strain 777 in the presence of cytosine arabinoside and in the SV40 UV-transformed permissive line C-6. Five of these capped dinucleotides are complementary to DNA sequences at 0.66 map unit in a region previously identified by the primer extension method (Reddy et al., J. Virol. 30:279-296, 1979; Thompson et al., J. Virol. 31:437-438, 1979) as the 5' end of the early message. DNA sequences upstream from this region contain the TATTTAT (Hogness-Goldberg box), which is missing from upstream of the 5'-cap sites of late SV40 mRNA. Thus, 5'-end heterogeneity is not necessarily related to the presence or the absence of this putative transcriptional "initiation signal." When the possibility that SV40 5' caps represent transcriptional initiation sites is considered, the data also suggest that, on SV40 DNA, eucaryotic RNA polymerase II initiates transcription at multiple nucleotide sequences, including pyrimidines.

Cloning of DNA complementary to the measles virus mRNA encoding nucleocapsid protein

Double-stranded cDNA synthesized from total poly(A)-containing mRNA, extracted from monkey cells infected with measles virus, has been inserted into Pst cleavage site of Escherichia coli plasmid pBR322 and cloned. A clone containing measles virus DNA sequences was identified by hybridization to a measles virus-specific 32P-labeled cDNA probe prepared from the mRNA of measles virus-infected cells. Cellular sequences in the probe were neutralized by prehybridization with an excess of unlabeled mRNA from uninfected monkey cells. The insert of cloned cDNA isolated contans 1420 base pairs, as shown by agarose gel electrophoresis and electron microscopy. The size of the mRNA complementary to this cloned cDNA is 1750 nucleotides, as determined by the reverse Southern technique. The cloned DNA fragment was further identified as the reverse transcript of the mRNA coding for the nucleocapsid protein of measles virus on the basis that the major cell-free translation product of mRNA selected by hybridization to the cloned DNA comigrated with the nucleocapsid protein and was immunoprecipitated by measles virus-specific antibodies. Subsequently, the cloned DNA was used to detect specific measles virus sequences in the poly(A)-RNA extracted from brain autopsy material from a patient with subacute sclerosing panecephalitis. The cloned DNA can thus be used as a probe to study the structure and expression of the measles genome, and in particular, to study diseases of the central nervous system in which persistent infection with measles virus has been implicated.

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.

Structural organization of a 17 KB segment of the alpha 2 collagen gene: evaluation by R loop mapping

A recombinant phage, SpC3, containing a 17 kb genomic DNA insert representing approximately 60% of the 3' portion of the sheep collagen alpha 2 gene, was evaluated by electron microscopic R loop analysis. A minimum of 17 intervening sequences (introns) and 18 alpha 2 coding sequences (exons) were mapped. With the exception of the 850 base pair exon located at the extreme 3' end of the insert, all exons contained 250 base pairs or less. The total length of all the exons in SpC3 was 3,014 base pairs. The length distribution of the 17 introns ranged from 300 to 1600 base pairs; together, all of the introns comprised 14,070 base pairs of SpC3 DNA. Thus, the DNA region required for coding the interspersed 3 kb of alpha 2 collagen genetic information was 5.6 fold longer than the corresponding alpha 2 mRNA coding sequences.

On pre-messenger RNA and transcriptions. A review

From the present review integrating old and new data emerge a few principles of gene expression in eukaryotes, and an infinite variety of possible mechanistic details generating the overal pattern. The few principles, most of which are not fundamentally new, may thus be summarized. 1) The eukaryotic genome is subdivided into transcriptional units: into transcriptons which are subject to individual activation controlled at DNA level. 2) Viral genomes may contain one or a few transcriptons, while cells of multicellular organisms contain from 3 x 10(3) in diptera up to an estimated 2 x 10(5) in birds and mammals. 3) Transcriptons may include one or several coding sequences. 4) Transcriptons vary considerably in size: in mammals and birds their size spectrum falls into the 2,000 to 20,000 bp range. 5) Units of coding information constituting one message (genes) and, possibly, units of regulative information are frequently broken up and stored within the transcripton in sub-genic blocks (of so far unknown significance) in general located at a certain distance from the 5' and 3' transcript terminals which are determined by the promotor and terminator signals. 6) The gene, in its specific definition as the functional unit underlying the phenotype, is in general constituted posttranscriptionally by the processing mechanisms from the mosaic of its genomic subunits in the transcripton; segments of coding, service and regulative sequences are recombined within themselves and with each other, polygenic transcripts separate into their unit messages. 7) Activated transcriptons produce pre-mRNA; these primary transcripts are colinear with the DNA of the transcriptional unit. 8) Primary pre-mRNA is processed into secondary pre-mRNA's by extragenic cleavage and intragenic ("splicing") processing, giving rise stepwise to functional mRNA. During this process chemical modifications as methylation, 5'-terminal capping and 3'-terminal polyadenylation take place. 9) Translation yields either potentially functional polypeptides or polycistronic polyproteins subject to further processing. 10) Processing is a regulated process; it involves many of the possible phases and mechanisms of post-transcriptional regulation (cf. 39, 40).

Electron microscopic evidence for splicing of Moloney murine leukemia virus RNAs

Poly (A) containing RNA extracted from Moloney murine leukemia virus infected mouse cells was hybridized with long single-stranded complementary DNA, prepared in detergent disrupted virions. Visualization of the hybrids in the electron microscope revealed among the structures, circles and circles with tails. Measurements performed on the circular molecules revealed two major species with circumferences corresponding to 3 and 8.2 kilobases. The latter structures had identical size to circles obtained after annealing of cDNA with the viral genome, 35S RNA. Circularization of a small viral RNA (3 kb) from infected cells in the RNA-cDNA hybrids is a direct evidence that like the 35S RNA it shares similar nucleotide sequences at both the 5' and 3' ends. The presence of 5' end sequences common to the two RNA species indicates the existence of a spliced viral RNA. Furthermore, based on the circularization of viral RNA in the hybrids, we suggest a new way to quantitate and determine the lengths of spliced RNA in retrovirus infected cells.