Splicing patterns of nuclear precursors to the mRNA for adenovirus 2 DNA binding protein

Change in the graphics of journal articles in the life sciences field: analysis of figures and tables in the journal "Cell"

The purpose of this study is to examine how trends in the use of images in modern life science journals have changed since the spread of computer-based visual and imaging technology. To this end, a new classification system was constructed to analyze how the graphics of a scientific journal have changed over the years. The focus was on one international peer-reviewed journal in life sciences, Cell, which was founded in 1974, whereby 1725 figures and 160 tables from the research articles in Cell were sampled. The unit of classification was defined as a graphic and the figures and tables were divided into 5952 graphics. These graphics were further classified into hierarchical categories, and the data in each category were aggregated every five years. The following categories were observed: (1) data graphics, (2) explanation graphics, and (3) hybrid graphics. Data graphics increased by more than sixfold between 1974 and 2014, and some types of data graphics including mechanical reproduction images and bar charts displayed notable changes. The representation of explanatory graphics changed from hand-painted illustrations to diagrams of Bezier-curves. It is suggested that in addition to the development of experimental technologies such as fluorescent microscopy and big data analysis, continuously evolving application software for image creation and researchers' motivation to convince reviewers and editors have influenced these changes.

Genetic test for involvement of intervening sequences in transport of nuclear RNA

The construction of a recombinant virus in the late region of simian virus 40 is presented. The small intervening sequence of late 19S RNA (0.760 to 0.765 map unit) was cloned and inserted into the EcoRI site (1.0 map unit) in the late region of simian virus 40. This is a mutant virus that now has two intervening sequences, one at the normal position (0.760 map unit) and another out of the context of its flanking sequence and now at 1.0 map unit. The recombinant appears poisonous, as repeated attempts to plaque it as a virus with a standard helper virus were unsuccessful. The transcription of this recombinant was, therefore, studied after direct DNA transfection onto CV-1 cells. Nuclease S1 analysis of mutant RNA indicates that the major nuclear transcript was a spliced but nuclear 16S RNA species. Normally, 16S RNA is not found in the nucleus. This result was shown to be an artifact of the DNA transfection protocol. When the glycerol shock was done after infection with virus, a similar alteration in the makeup of nuclear RNA was seen. A transient stock of this double-intron mutant was finally obtained, using a nonrevertable helper virus. The transcriptional analysis of this mutant showed that unspliced 19S RNA was not transported and remained within the nucleus, whereas spliced 19S and 16S RNAs were transported. We conclude that the retention of nuclear transcripts within the nucleus is not simply due to the presence of intronic sequences, as spliced 19S and 16S RNAs which contain the second intron were efficiently transported.

Genetic test for involvement of intervening sequences in transport of nuclear RNA

The construction of a recombinant virus in the late region of simian virus 40 is presented. The small intervening sequence of late 19S RNA (0.760 to 0.765 map unit) was cloned and inserted into the EcoRI site (1.0 map unit) in the late region of simian virus 40. This is a mutant virus that now has two intervening sequences, one at the normal position (0.760 map unit) and another out of the context of its flanking sequence and now at 1.0 map unit. The recombinant appears poisonous, as repeated attempts to plaque it as a virus with a standard helper virus were unsuccessful. The transcription of this recombinant was, therefore, studied after direct DNA transfection onto CV-1 cells. Nuclease S1 analysis of mutant RNA indicates that the major nuclear transcript was a spliced but nuclear 16S RNA species. Normally, 16S RNA is not found in the nucleus. This result was shown to be an artifact of the DNA transfection protocol. When the glycerol shock was done after infection with virus, a similar alteration in the makeup of nuclear RNA was seen. A transient stock of this double-intron mutant was finally obtained, using a nonrevertable helper virus. The transcriptional analysis of this mutant showed that unspliced 19S RNA was not transported and remained within the nucleus, whereas spliced 19S and 16S RNAs were transported. We conclude that the retention of nuclear transcripts within the nucleus is not simply due to the presence of intronic sequences, as spliced 19S and 16S RNAs which contain the second intron were efficiently transported.

In vitro splicing pathways of pre-mRNAs containing multiple intervening sequences?

We analyzed the in vitro splicing pathways of three multi-intervening-sequence (IVS) pre-mRNAs: human beta-globin, which contains two IVSs (K. M. Lang, V. L. van Santen, and R. A. Spritz, EMBO J. 4:1991-1996, 1985); rat alpha-lactalbumin, which contains three IVSs; and murine interleukin-3, which contains four IVSs. We found that there are highly preferred pathways of IVS removal from these multi-IVS pre-mRNAs in vitro. The three IVSs of rat alpha-lactalbumin pre-mRNA were excised sequentially from 5' to 3'; in most molecules, IVS1 was removed first, followed by IVS2 and finally by IVS3. The splicing pathway of interleukin-3 pre-mRNA in vitro was more complex. The four IVSs were excised in a highly preferred temporal order, but the order was not strictly sequential or directional. In most molecules, IVS1 and IVS4 were removed first, either simultaneously or in rapid succession. Subsequently, IVS2 was excised, followed by IVS3. The observed splicing pathways apparently resulted from differences in lag times and maximum excision rates of the different IVSs. We detected no exon skipping during splicing of these transcripts in vitro. These observations have implication for proposed models of splice site selection.

In vitro splicing pathways of pre-mRNAs containing multiple intervening sequences?

We analyzed the in vitro splicing pathways of three multi-intervening-sequence (IVS) pre-mRNAs: human beta-globin, which contains two IVSs (K. M. Lang, V. L. van Santen, and R. A. Spritz, EMBO J. 4:1991-1996, 1985); rat alpha-lactalbumin, which contains three IVSs; and murine interleukin-3, which contains four IVSs. We found that there are highly preferred pathways of IVS removal from these multi-IVS pre-mRNAs in vitro. The three IVSs of rat alpha-lactalbumin pre-mRNA were excised sequentially from 5' to 3'; in most molecules, IVS1 was removed first, followed by IVS2 and finally by IVS3. The splicing pathway of interleukin-3 pre-mRNA in vitro was more complex. The four IVSs were excised in a highly preferred temporal order, but the order was not strictly sequential or directional. In most molecules, IVS1 and IVS4 were removed first, either simultaneously or in rapid succession. Subsequently, IVS2 was excised, followed by IVS3. The observed splicing pathways apparently resulted from differences in lag times and maximum excision rates of the different IVSs. We detected no exon skipping during splicing of these transcripts in vitro. These observations have implication for proposed models of splice site selection.

Model for alternative RNA processing in human calcitonin gene expression

The alternative RNA processing pathways in human calcitonin gene (CALC-I gene) expression were investigated using steady state RNA isolated from human medullary thyroid carcinoma (MTC) and from a culture line derived from this tumor. On Northern blots the mature 1.0 kilobases (Kb) calcitonin (CT) - and 1.1 Kb calcitonin gene-related peptide (CGRP) mRNAs were detected with CALCI gene specific probes as well as high molecular weight poly (A) containing RNAs of 2.1, 2.3, 3.3, 4.2, 5.0 and 5.7 Kb. The 5.7 Kb RNA was identified as the poly(A) tailed primary transcript containing sequences corresponding to all 6 exons and 5 introns of the CALC-I gene. From the composition of the other RNAs the splicing order of the different introns could be deduced. The results suggest the following model. First all introns not involved in alternative processing (introns 1, 2 and 5) are spliced from the 5.7 Kb RNA in rapid successive reactions yielding a 3.3 Kb RNA, which accumulates. From this 3.3 Kb RNA, the last common intermediate in the alternative processing pathway, CT mRNA is formed by splicing of intron 3 and poly(A) addition at exon 4, in this order or the reverse order via 2.3 Kb or 2.1 Kb RNA intermediates respectively. Alternatively, the whole intron 3-exon 4-intron 4 region is spliced from the 3.3 Kb RNA yielding CGRP mRNA. The temporal sequence of poly(A) addition at exons 4 and 6 may relate to the observed structural differences between the poly(A) addition signals at these sites. The ratio of CT- to CGRP mRNA may relate also to the differences in the primary structures of the intron 3- and intron 4 splice acceptor sites.

Splicing of the E2A premessenger RNA of adenovirus serotype 2. Multiple pathways in spite of excision of the entire large intron

During the early period of infection, the 4.9 kb (kb = 10(3) bases) E2A premRNA of adenovirus serotype 2 is matured mainly into a 2.0 kb mRNA by excision of introns of 2233 and 626 nucleotides. In order to define all the possible steps of splicing occurring in vivo, we characterized splicing intermediates present after a limiting treatment of cells with cycloheximide. Three complementary methods of analysis were used: RNA transfer analysis, S1 nuclease mapping and complementary DNA-RNase assay. Our principal conclusions concerning the poly(A)+ species are as follows. The RNA intermediate family detected is more complex than expected, since two major RNA intermediates of 4.6 kb and 4.3 kb, two minor intermediates of 2.9 kb and 2.6 kb, and a 2.3 kb RNA, which represents a minor alternative mRNA form, are revealed. Despite its large size and the presence of multiple internal donor and acceptor signals, intron 1 is exclusively excised as a whole. Intron 2 is either primarily excised as a whole, removing the standard 626-nucleotide sequence, or a smaller sequence of 337 nucleotides is removed, generating the 2.3 kb alternative mRNA. Kinetics of the ligation reaction demonstrate that the minimal time for excision of intron 2 is no more than two minutes, indicating a high level of co-ordination of the multiple individual reactions occurring during excision of an intron. Besides the major pathway for E2A premRNA splicing, namely the excision first of intron 2, followed by the excision of intron 1 after a lag time of five minutes, a minor pathway (used with a frequency of 10%) can be detected where the order of intron excision was inverted. With the alternative variant of excision of intron 2, at least three different pathways are therefore used to mature the E2A premRNA. RNA intermediates resulting from the cleavage at the 5' end of introns and branching can be detected by S1 mapping experiments, but their low accumulative level (1% relatively to the initial premRNA) precluded their direction by RNA transfer experiments and their complete characterization.

Nuclei of adenovirus 2-infected cells contain an RNA species that corresponds to an intron excised intact from mRNA precursors

We used Northern and S1 nuclease analyses to identify a nuclear RNA species of the structure predicted for an intron excised from the precursor of adenovirus 2 E2A early mRNA. The structure of this excised intron demonstrated that the splicing of E2A mRNA can involve the removal of the intron sequences as single intact molecules. The concentration of the excised intron is 30 copies per nuclei, comparable to the levels of E2A polyadenylated splicing precursors, but 30-fold less than nuclear E2A mRNA. Late in infection, when the production of E2A early mRNA is dramatically elevated (Goldenberg et al., J. Virol. 38:932-939, 1981), the excess intron was not detected, indicating that either its stability or the mechanism of splicing is altered. We also identified a spliced nonpolyadenylated E2A nuclear RNA species with a structure similar to the mRNA, indicating that splicing may normally occur in the absence of polyadenylation.

Nuclei of adenovirus 2-infected cells contain an RNA species that corresponds to an intron excised intact from mRNA precursors

We used Northern and S1 nuclease analyses to identify a nuclear RNA species of the structure predicted for an intron excised from the precursor of adenovirus 2 E2A early mRNA. The structure of this excised intron demonstrated that the splicing of E2A mRNA can involve the removal of the intron sequences as single intact molecules. The concentration of the excised intron is 30 copies per nuclei, comparable to the levels of E2A polyadenylated splicing precursors, but 30-fold less than nuclear E2A mRNA. Late in infection, when the production of E2A early mRNA is dramatically elevated (Goldenberg et al., J. Virol. 38:932-939, 1981), the excess intron was not detected, indicating that either its stability or the mechanism of splicing is altered. We also identified a spliced nonpolyadenylated E2A nuclear RNA species with a structure similar to the mRNA, indicating that splicing may normally occur in the absence of polyadenylation.

Vectors for the direct selection of cDNA clones corresponding to mammalian cell mRNA of low abundance

We have constructed two cDNA cloning vectors which (1) carry the intergenic region of phage f1 and (2) permit efficient cloning (by the Okayama-Berg procedure) of full-length copies of mammalian mRNA in either orientation. Infection of cells harboring these vectors with f1 phage results in the encapsidation of single-stranded (ss) plasmid DNA carrying either the sense or the anti-sense sequence of the cDNA inserts. The complementary nature of the cDNA inserts in two such cDNA libraries facilitates preparative hybridization procedures. These vectors have general applicability to any eukaryotic system where changes in the abundance of mRNA transcripts are to be measured and the corresponding cDNA clones isolated.

Splicing in adenovirus and other animal viruses

Splicing provides viruses with great genetic versatility. It is still too early to say whether this versatility is derived from ingeneous mechanisms evolved by necessity by the viruses, or whether the viruses indeed mimic cellular mechanisms. In any event, it is unlikely that cells will provide a single genomic cluster of genes that utilize splicing in such diverse ways as adenovirus, or the other viruses discussed here. And we may speculate that when the full role of splicing in adenovirus gene expression program is known, its import will continue to be a source of amazement!

Inhibition of RNA cleavage but not polyadenylation by a point mutation in mRNA 3' consensus sequence AAUAAA

A single U leads to G transversion in the 3' consensus sequence AAUAAA of the adenovirus early region 1A gene was constructed and the effect of this mutation on processing of the 3' end of the nuclear early region 1A RNAs was analysed. The results demonstrate that the intact AAUAAA is not required for RNA polyadenylation but is required for the cleavage step preceding polyadenylation to occur efficiently.

Identification of adenovirus genes that require template replication for expression

The relationship between adenovirus type 2 DNA replication and expression of intermediate stage viral genes was investigated. The 1.03-kilobase mRNA from early region 1b (E1b) and the mRNAs coding for proteins IX and IVa2 were first detected between 6 and 8 h postinfection. Inhibition of viral DNA replication with hydroxyurea prevented expression of the IX and IVa2 mRNAs, but not of the E1b mRNA. Pulse-labeling experiments demonstrated that the block of IX and IVa2 expression in hydroxyurea-treated cells was at the level of transcription. By a series of superinfection experiments, it was determined that the viral and cellular factors present during the late stage of adenovirus infection are insufficient to activate IX gene expression. The viral DNA template must first replicate before IX transcription can begin.

Splicing of adenovirus 2 early region 1A mRNAs is non-sequential

The r-strand of early region 1A (E1A) of adenovirus serotype 2 is transcribed into three completely overlapping messenger RNA species, a 9S, a 12S and a 13S mRNA. These three mRNAs are processed from a common colinear RNA precursor and differ only with regard to the size of the intron removed during mRNA maturation. We have studied the processing pathways for the E1A mRNAs by using an assay for transient expression of recombinant plasmids containing the E1A region. All three region E1A mRNAs are synthesized and transported to the cytoplasm in sufficient quantities to permit a detailed study of their structure by S1 endonuclease analysis and primer extension. Additionally, we show that the 72 base-pair repeat from simian virus 40 (SV40), when located upstream of the E1A promoter stimulates expression of the E1A mRNAs five- to tenfold. In order to determine whether splicing of the E1A mRNAs is sequential, i.e. whether the 13S and 12S mRNAs can serve as intermediates in splicing, we constructed two plasmids that lack the intervening sequences that are removed during the maturation of the 12S and 13S mRNAs, respectively. From an analysis of the RNAs produced after transfection with these deletion mutants, the following major conclusions can be made. (1) Splicing of the E1A mRNAs is non-sequential, i.e. the 13S, 12S and 9S RNAs are generated by separate splicing events using the nuclear colinear transcript as the only precursor RNA. (2) RNA splicing is not a prerequisite for an efficient transport of the E1A mRNAs to the cytoplasm. (3) The 13S RNA can be further processed to 12S and 9S RNA species. These splicing events are, however, illegitimate and give rise to 12S and 9S RNAs that both lack one nucleotide at the splice junction. (4) A coupling between splicing and nuclear transport is most likely required in vivo to prevent illegitimate splicing of the 13S mRNA. (5) The 12S RNA does not serve as a precursor for further processing to the 9S RNA. (6) Splicing of the E1A mRNAs followed strictly the G-T-A-G rule.

Accurate and efficient in vitro splicing of purified precursor RNAs specified by early region 2 of the adenovirus 2 genome

Polyadenylated and deproteinized nuclear RNA precursors encoded by early region 2 of the adenovirus 2 genome are spliced in vitro by nuclear extracts prepared from MOPC-315 mouse myeloma cells. The in vitro reaction excises sequences from two introns and attaches 5' sequences to the mRNA body. The nucleotide sequence across the splice junctions in the E2 RNAs processed in vitro was investigated by performing primer extensions in the presence of dideoxynucleotides and direct sequencing on polyacrylamide gels. We conclude that the in vitro splicing reaction is accurate and has the same precision as that of in vivo E2 cytoplasmic mRNA prepared from Ad2 infected cells. The efficiency of in vitro splicing by the nuclear extracts is very high. Approximately 80% of E2 RNA precursor, on a molar basis, are spliced in vitro to a mature RNA. These findings provide evidence that a nuclear extract prepared from MOPC-315 mouse myeloma cells is capable of accurate and efficient splicing of E2 RNA precursors.

Alternative splicing pathways exist in the formation of adenoviral late messenger RNAs

Total rapidly labeled RNA was extracted from nuclei of HeLa cells late after infection with adenovirus type 2. Most of this nuclear RNA is transcribed from the major late transcription unit (16.2 to 100.0 map units (m.u.)). To study the cleavage reactions that are involved in RNA splicing, we used the S1 nuclease mapping technique with HindIII B (16.8 to 31.5 m.u.) and XhoI F (15.5 to 22.4 m.u.) restriction fragments as DNA probes. The S1 mapping data showed that both intron 1 (16.3 to 19.1 m.u.) and intron 2 (19.4 to 26.2 m.u.) can be excised in more than one step. Kinetic labeling and pulse--chase experiments demonstrated that certain cleavage sites in the RNA are used within three minutes after the start of transcription, while other cleavages occur only after a significant time-lag. The use of 5.6-dichloro-1-beta-D-ribofuranosylbenzimidazole enabled us to label the nuclear RNA exclusively from the 5' end. Such an approach showed that the first cleavages are introduced in the nascent RNA before the RNA polymerase has passed more than 2000 nucleotides beyond the cleavage site. The chronology of the appearance of processing intermediates that results from cleavage of the RNA indicates that preferentially intron 1 is removed before intron 2. This is an agreement with the finding that leader 1 is ligated to leader 2 before ligation of leader 2 to leader 3 takes place. However, we have found that alternative splicing pathways exist in the excision of introns 1 and 2, demonstrating that cleavage in intron 2 may occur before intron 1 is attacked by the splicing enzymes.

Analysis of expression of adenovirus DNA (fragments) by microinjection in Xenopus oocytes. Independent synthesis of minor early region 2 proteins

Injection of whole adenovirus DNA into Xenopus oocytes results in the synthesis of large amounts of the early region 2A DNA-binding protein (E2A-DBP) and smaller amounts of polypeptide IX. The lack of synthesis of any functional messenger RNAs transcribed from the major late promotor at 16.3 map units is remarkable. Cleavage of the adenovirus DNA outside the E2A gene proper by restriction enzymes decreases synthesis of the DBP to about 10% of the amount produced after injection of intact DNA. On the other hand, presence of the terminal (Bellett) protein on the injected template enhances DBP synthesis considerably. Experiments with injected DNA restriction fragments, as well as reconstructed genes cloned into pBR322, indicate that efficient synthesis of DBP in oocytes requires the presence of either or both of the two main promoters from which the E2A gene is transcribed plus an intact 3' end of the gene. In the absence of any known promotor, 100-fold lower amounts of otherwise normal DBP are produced. Unlike in a regular infection, synthesis of DBP in oocytes does not require the product of the E1A gene. The same series of experiments also demonstrates that the DBP, a phosphoprotein, is the substrate of a cellular rather than a virus-encoded protein kinase. Two minor E2A proteins, although colinear with the major DBP, are synthesized independently. Synthesis of a 44,000 Mr protein, probably corresponding to the carboxy-terminal 360 amino acid residues of the DBP, is not decreased after injection of "promotorless" E2A genes. Unlike the 44,000 Mr protein, production of a 67,000 Mr protein (carboxy-terminal 483 amino acid residues) by one DNA-construct is probably directed by a T-A-T-A-A-A-T-A sequence in the vector DNA.

Transcription of adenovirus 5 early region 1b is elevated in permissive cells infected by a mutant with an upstream deletion

Early region 1b (E1b) of adenovirus 5 consists of a single transcription unit that lies from 1,702 to 4,070 nucleotides from the conventional left end of the genome. The effect of mutations that map upstream of E1b on the production of E1b mRNA was examined in vivo with mutants defective in gene functions from the neighboring early region 1a (E1a) transcription unit (499 to 1,632 nucleotides from the left end). These host range mutants replicate in the adenovirus 5-transformed human cell line 293. E1b mRNA accumulation was assayed by DNA-RNA hybridization late after productive infection when the E1b transcripts are abundant in the cytoplasm. Cells infected by wild-type virus, mutant dl311, or mutant hr1. The elevated levels of E1b mRNA were also detected in steady-state nuclear RNA, pulse-labeled polyadenylated nuclear RNA, and pulse-labeled total nuclear RNA. These data indicate that E1b transcription was elevated in human 293 cells infected with dl312. There was no evidence of increases in genomic DNA in dl312-infected cells, suggesting that the rate of transcription may be elevated. When mixed infections with a 10-fold excess of either dl312 or wild-type virus were performed, the phenotype was that of the more abundant genome. This result suggests that the respective phenotypes were cis dominant. The increased rate of transcription can be attributed to cis-active regulatory effects of the deletion of nucleotides 448 to 1,349 in mutant dl312 DNA.

Herpes simplex virus-induced changes in cellular and adenovirus RNA metabolism in an adenovirus type 5-transformed human cell line

We used the viral transcripts (designated Ad-RNA) that accumulated in the cytoplasm of adenovirus type 5-transformed human embryonic kidney cells (cell line 291-31) as models for cellular RNAs to examine how herpes simplex virus modifies cellular RNA metabolism. Infection of 293-31 cells with herpes simplex virus type 1 strain 17 lead to extensive inhibition of Ad-RNA accumulation by 4 h postinfection. The major part of this inhibition was due to an immediate early or alpha gene function, which reduced the rate of transcription of Ad-RNA within the nuclei of the infected cells. In addition, host polyadenylic acid-containing RNA accumulation and rRNA accumulation were affected, but to a lesser extent and at lower rate than Ad-RNA accumulation. In conjunction with previous data, our experimental data allowed us to propose a general scheme for how herpes simplex virus type 1 alters the metabolism of cellular RNA, the possible mechanisms for these changes, and how they correlate with the regulation of herpes simplex virus gene expression.

The orderly splicing of the first three leaders of the adenovirus-2 major late transcript

A strategy based on the hybridization of labeled nucleoplasmic RNA to a short cloned cDNA probe was devised to study the ligation of the three first leader sequences (Le1, Le2, Le3) of the major late adenovirus-2 transcript. The hybridized RNA was subsequently fractionated by electrophoresis and identified with the aid of restriction fragments of the DNA probe. The ligations were shown to occur stepwise and in an orderly fashion. Le1 and Le2 were first ligated without detectable lag time. The tripartite leader was formed after a lag time of 10-15 min probably due, for a large part, to the stepwise excision of the intervening sequence between Le2 and Le3. The possible processing intermediate Le2-Le3 was not detected.

In vitro splicing of purified precursor RNAs specified by early region 2 of the adenovirus 2 genome

Early region 2 of the adenovirus 2 genome (map position 61-75) specifies two poly(A)+ nuclear RNAs (28S and 23S) that appear to be precursors of the 20S cytoplasmic mRNA [Goldenberg, C. J. & Raskas, H. J. (1979) Cell 16, 131-138]. Splicing of these nuclear RNAs in vitro has been obtained with a whole cell extract prepared from MOPC-315 mouse myeloma cells. The in vitro reaction excises sequences from two introns and attaches 5' sequences to the mRNA body. The splicing reaction was demonstrated by two procedures: (i) hybridization of pulse-labeled RNA fractionated by size and (ii) annealing of RNAs with radioactive DNA probes followed by nuclease digestion. The first procedure provided evidence that sequences from the large 2300-nucleotide intron (74.6-68.8) were excised and 5' transcripts were spliced to the mRNA body. Utilizing both S1 and Exo VII nucleases, the second procedure demonstrated excision of sequences from the smaller 720-nucleotide intron (68.5-66.3), the splicing of sequences from the second leader (68.8) to the mRNA body, and the formation of an mRNA body of 1700 nucleotides, the size found in vivo. These findings provide evidence that an in vitro system that splices viral RNAs to yield products comparable to those found in vivo is now available.

The use of restriction endonucleases to measure mitochondrial DNA sequence relatedness in natural populations. III. Techniques and potential applications

Restriction endonucleases and agarose gel electrophoresis have been used to demonstrate extensive nucleotide sequence diversity in mitochondrial DNA (mtDNA) within and between conspecific populations of rodents and other mammals. Cleavage of mtDNA samples with a relatively small number of endonucleases provides information concerning the phylogenetic relatedness of individual organisms which cannot now be readily obtained by any other type of molecular analysis. This information is qualitatively different from that available from the study of nuclear genes or gene products because the mitochondrial genome is inherited intact from the female parent and is not altered by recombination or meiotic segregation. The requirements for large tissue samples and laborious DNA purification procedures have imposed severe limitations on the kinds of population surveys in which this technique could be utilized. Here, we show that these difficulties can be overcome by using DNA-DNA hybridization to detect minute amounts of mtDNA in crude tissue fractions which can be more easily and rapidly prepared from very small amounts of tissue without the use of expensive and immobile laboratory equipment. The techniques are described in detail in an effort to make restriction analysis of mtDNA available to biologists who may be unfamiliar with current DNA technology.

Coordinate regulation of two cytoplasmic RNA species transcribed from early region 2 of the adenovirus 2 genome

Early region 2 (E2) of the adenovirus 2 genome specifies a 72,000-dalton DNA-binding protein that is required for viral DNA replication. Electron microscopy studies have detected two major forms of 20S E2 mRNA, one species with a 5' leader from map position 75 and a second form having a leader from position 72 (Chow et al., J. Mol. Biol. 134:265-303, 1979). Only the species with a leader from position 75 was detected at early times; however, both forms were found at late times. We have analyzed the temporal regulation of E2 expression by documenting mRNA accumulation in the cytoplasm. Kinetic studies of pulse-labeled RNAs demonstrated a peak of E2 cytoplasmic RNa synthesis at 10 to 12 h, coinciding with the time of maximal synthesis of the 72,000-dalton DNA binding protein and viral DNA. To estimate the relative abundances of the two major E2 RNA species at various times during infection, total E2 cytoplasmic and polysomal 20S RNAs were isolated by hybridization-selection with specific DNA probes. The leader sequences in the selected RNAs were then quantitated by further RNA-DNA hybridization. We found that the elevated accumulation rate for E2 cytoplasmic RNA at late times reflected an increase in formation of both major species. Moreover, for all time points examined 66% of the mRNA species had a 5' end from map position 75, and 33% had a 5' terminus from position 72. Continuous labeling experiments provided evidence that both RNA forms have comparable half-lives. The results suggest that the two major species encoded by E2 are regulated in a coordinate fashion late in infection.

The Role of the poly(A) sequence in mammalian messenger RNA

The poly(A) sequence is added to 3' termini of nuclear RNA segments destined to become part of the mRNA, and may play an essential role in the selection of these segments. It appears to be required for at least some of the splicing events involved in mRNA processing. In the cytoplasm, the poly(A) segment is the target of a degradation process which causes its gradual shortening, and leads to a heterogeneous steady-state poly(A)-size distribution. Complete loss of the poly(A) is probably followed by inactivation of the mRNA, since chains depleted of poly(A) do not accumulate in the cells. A role for this sequence in the promotion of mRNA stability is suggested by the behavior of globin mRNA depleted of poly(A) after injection into frog oocytes. The poly(A) shortening process may be part of the mRNA inactivation mechanism, as indicated by the greater sensitivity to degradation of the poly(A) of some short-lived mRNAs. However, the stochastic mRNA decay implies that new and old mRNA chains, with long and short poly(A) segments, respectively are equally susceptible to inactivation. The poly(A)-lacking histone mRNAs are stable only in cells engaged in DNA replication. Present knowledge favors a role for poly(A) in the control of mRNA stability. Loss of this sequence could be controlled through modulation of poly(A)-protein interactions or through masking of a sequence directly adjacent to the poly(A). In the nucleus, the poly(A) sequence could also serve as stabilizing agent, but, in addition, it might interact with the splicing machinery.

Leakage of nuclear transcripts late in simian virus 40-infected CV1 cells: quantitation of spliced and unspliced late 19S RNAs

During the late phase of simian virus 40 infections of CV1 cells, the relative ratios of the spliced to the unspliced RNA molecules of the 19S family were measured. In the cytoplasm, unspliced 19S RNA represented between 1 and 2% of spliced 19S RNA. This ratio could be altered by the use of different methods of RNA extraction such that unspliced RNA was observed at 10 to 20% of spliced RNA. The nuclear ratios of spliced to unspliced 19S RNA were also determined. In contrast to cytoplasmic RNA, nuclear unspliced RNA was several hundred percent that of nuclear spliced 19S RNA. Cytoplasmic unspliced 19S RNA appears to be of nuclear origin, and its presence in the cytoplasmic fraction is due to nuclear leakage during RNA fractionation.

Transcription and RNA processing by the DNA tumour viruses

Messenger RNA synthesis by the DNA tumour viruses proceeds by a complex but versatile series of transcription and RNA processing steps. The major mechanistic features of this pathway are probably very similar to those used by the animal cell host itself. The viruses have, however, evolved intricate arrangements of protein coding sequences and sites for RNA initiation, polyadenylation and splicing which allow them to use their genetic information to maximum advantage.

Secondary structures for splice junctions in eukaryotic and viral messenger RNA precursors

Thermodynamically stable secondary structures have been found for adjacent splice junctions of 17 introns from 10 eukaryotic and viral mRNA precursors. Complementary regions in these structures position the exons to be ligated in a favourable orientation for splicing. The possible role of these structures in a general splicing mechanism in described.

Could poly(A) align the splicing sites of messenger RNA precursors?

In general, poly(A)-mRNA appears to be derived from larger nuclear RNA precursors. The maturation of these precursors involves excision of sequences of variable length from within the molecule and splicing of the remaining structural and coding sequences. The mechanism by which this process occurs is not known. It does not appear to operate solely through the recognition of a defined primary sequence or through the formation of a consistent secondary structure. We propose an alternative model in which poly(A) facilitates the splicing event by promoting the formation of triple-stranded structures within the mRNA precursor.

Order of polyadenylic acid addition and splicing events in early adenovirus mRNA formation

A study of the processing of mRNA from two early adenovirus type 2 transcription units (regions 2 and 4 of adenovirus type 2 genome; [J. Flint, Cell 10:153--166, 1977]) revealed that polyadenylic acid [poly(A)] was added in most if not all cases to an unspliced nuclear RNA molecule whose coordinates extended from the apparent initiation site for RNA synthesis to the single poly(A) site in each transcription unit. An intermediate RNA molecule in the processing of the mRNA for the 72,000-M, single-stranded DNA binding protein showed that the first of the two intervening sequences, the one closest to the 5' end of the molecule, was removed first at least in the majority of the processed molecules. Finally, in cells labeled for 10 min and then treated with actinomycin D to stop further RNA synthesis, the majority, if not all, of the poly(A)-terminated nuclear RNA specific for region 2 was successfully processed and transported to the cytoplasm.