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

Cell culture NAIL-MS allows insight into human tRNA and rRNA modification dynamics in vivo

Recently, studies about RNA modification dynamics in human RNAs are among the most controversially discussed. As a main reason, we identified the unavailability of a technique which allows the investigation of the temporal processing of RNA transcripts. Here, we present nucleic acid isotope labeling coupled mass spectrometry (NAIL-MS) for efficient, monoisotopic stable isotope labeling in both RNA and DNA in standard cell culture. We design pulse chase experiments and study the temporal placement of modified nucleosides in tRNAPhe and 18S rRNA. In existing RNAs, we observe a time-dependent constant loss of modified nucleosides which is masked by post-transcriptional methylation mechanisms and thus undetectable without NAIL-MS. During alkylation stress, NAIL-MS reveals an adaptation of tRNA modifications in new transcripts but not existing ones. Overall, we present a fast and reliable stable isotope labeling strategy which allows in-depth study of RNA modification dynamics in human cell culture.

Transcription and splicing: A two-way street

RNA synthesis by RNA polymerase II and RNA processing are closely coupled during the transcription cycle of protein-coding genes. This coupling affords opportunities for quality control and regulation of gene expression and the effects can go in both directions. For example, polymerase speed can affect splice site selection and splicing can increase transcription and affect the chromatin landscape. Here we review the many ways that transcription and splicing influence one another, including how splicing "talks back" to transcription. We will also place the connections between transcription and splicing in the context of other RNA processing events that define the exons that will make up the final mRNA. This article is categorized under: RNA Processing > Splicing Mechanisms RNA Processing > Splicing Regulation/Alternative Splicing.

Human adenovirus type 5 vectors deleted of early region 1 (E1) undergo limited expression of early replicative E2 proteins and DNA replication in non-permissive cells

Adenovirus (Ad) vectors deleted of the early region 1 (E1) are widely used for transgene delivery in preclinical and clinical gene therapy studies. Although proteins encoded within the E1 region are required for efficient virus replication, previous studies have suggested that certain viral or cellular proteins can functionally compensate for E1, leading to expression of the early region 2 (E2)-encoded replicative proteins and subsequent virus replication. We have generated a series of E1-encoding and E1-deficient Ad vectors containing a FLAG-epitope tag on each of the E2-encoded proteins: DNA-binding protein (DBP), terminal protein (TP) and DNA polymerase (Pol). Using these constructs, we show that for the replication-competent virus, the expression level of each E2-encoded protein declines with increasing distance from the E2 promoter, with E2A-encoded DBP expression being ~800-fold higher than E2B-encoded TP. Pol was expressed at extremely low levels in infected cells, and immunoprecipitation from cell lysates was required prior to its detection by immunoblot. We further show that DBP was expressed 200- to 400-fold less efficiently from an E1-deficient virus compared to a replication-competent virus in A549 and HepG2 cells, which was accompanied by a very small increase in genome copy number. For the E1-deficient virus, late gene expression (a marker of virus replication) was only observed at very high multiplicities of infection. These data show that E1-deleted Ad gives rise to limited expression of the E2-encoded genes and replication in infected cells, but highlight the importance of considering viral dose-dependent effects in gene therapy studies.

Co-transcriptional splicing and the CTD code

Transcription and splicing are fundamental steps in gene expression. These processes have been studied intensively over the past four decades, and very recent findings are challenging some of the formerly established ideas. In particular, splicing was shown to occur much faster than previously thought, with the first spliced products observed as soon as splice junctions emerge from RNA polymerase II (Pol II). Splicing was also found coupled to a specific phosphorylation pattern of Pol II carboxyl-terminal domain (CTD), suggesting a new layer of complexity in the CTD code. Moreover, phosphorylation of the CTD may be scarcer than expected, and other post-translational modifications of the CTD are emerging with unanticipated roles in gene expression regulation.

Single-Molecule Imaging of RNA Splicing in Live Cells

Expression of genetic information in eukaryotes involves a series of interconnected processes that ultimately determine the quality and amount of proteins in the cell. Many individual steps in gene expression are kinetically coupled, but tools are lacking to determine how temporal relationships between chemical reactions contribute to the output of the final gene product. Here, we describe a strategy that permits direct measurements of intron dynamics in single pre-mRNA molecules in live cells. This approach reveals that splicing can occur much faster than previously proposed and opens new avenues for studying how kinetic mechanisms impact on RNA biogenesis.

The timing of pre-mRNA splicing visualized in real-time

Since it became clear that intervening sequences or introns are spliced out from precursor pre-mRNA molecules in the nucleus before mature mRNAs are exported to the cytoplasm, questions were raised about the timing of splicing. Does splicing start while RNA polymerase II is still transcribing? Is splicing a slow or a fast process? Is timing important to control the splicing reaction? Although our understanding on the mechanism and function of splicing is largely based on data obtained using biochemical and large-scale "omic" approaches, microscopy has been instrumental to address questions related to timing. Experiments done with the electron microscope paved the way to the discovery of splicing and provided unequivocal evidence that splicing can occur co-transcriptionally. More recently, live-cell microscopy introduced a technical breakthrough that allows real-time visualization of splicing dynamics. We discuss here some of the microscopy advances that provided the basis for the current conceptual view of the splicing process and we outline a most recent development that permits direct measurement, in living cells, of the time it takes to synthesize and excise an intron from individual pre-mRNA molecules.

Live-cell visualization of pre-mRNA splicing with single-molecule sensitivity

Removal of introns from pre-messenger RNAs (pre-mRNAs) via splicing provides a versatile means of genetic regulation that is often disrupted in human diseases. To decipher how splicing occurs in real time, we directly examined with single-molecule sensitivity the kinetics of intron excision from pre-mRNA in the nucleus of living human cells. By using two different RNA labeling methods, MS2 and λN, we show that β-globin introns are transcribed and excised in 20-30 s. Furthermore, we show that replacing the weak polypyrimidine (Py) tract in mouse immunoglobulin μ (IgM) pre-mRNA by a U-rich Py decreases the intron lifetime, thus providing direct evidence that splice-site strength influences splicing kinetics. We also found that RNA polymerase II transcribes at elongation rates ranging between 3 and 6 kb min(-1) and that transcription can be rate limiting for splicing. These results have important implications for a mechanistic understanding of cotranscriptional splicing regulation in the live-cell context.

Functional and mechanistic insights from genome-wide studies of splicing regulation in the brain

We review here results arising from the systematic functional analysis of Nova, a neuron-specific RNA binding protein targeted in an autoimmune neurological disorder associated with cancer. We have developed a combination of biochemical, genetic and bioinformatic methods to generate a global understanding of Nova's role as a splicing regulator. Genome-wide identification and validation of Nova target RNAs has yielded unexpected insights into the protein's mechanism of action and into the functionally coherent role of Nova in the biology of the neuronal synapse. These studies provide us with a platform for understanding the role of RNA binding proteins in tissue-specific splicing regulation and in disease.

Cell-growth regulation of the hamster dihydrofolate reductase gene promoter by transcription factor Sp1

The dihydrofolate reductase (DHFR) gene (dhfr) promoter contains cis-acting elements for the transcription factors Sp1 and E2F. Given the ability of Sp1 to activate the dhfr promoter, we have evaluated the contribution of Sp1 to the cell-growth regulation of the dhfr gene. Using gel-mobility assays performed with DNA probes from the minimal promoter of the hamster dhfr gene and nuclear extracts from cultured hamster cells (CHO K1) we show that the binding of Sp1 to the dhfr promoter is cell-growth-phase regulated. Accordingly, dhfr transcription and mRNA levels in K1 cells increase upon serum stimulation. Cytological detection of Sp1 by immunofluorescence reveals a decrease of this protein in the process leading to the G0 state, and an increase upon serum stimulation of quiescent cells. These results were confirmed by western blot analysis. It is concluded that Sp1 progressively binds to the hamster dhfr promoter after stimulation of cell proliferation, which can account for the transcriptional regulation of the dhfr gene during the cell cycle. The role of Sp1 in the specific control of dhfr during the cell cycle was confirmed in vivo using cell lines derived from dhfr-negative cells transfected with dhfr plasmids carrying either the wild-type or mutated Sp1-binding or E2F-binding sites in the dhfr minimal promoter.

Order of intron removal during splicing of endogenous adenine phosphoribosyltransferase and dihydrofolate reductase pre-mRNA

Using a strategy based on reverse transcription and the polymerase chain reaction, we have determined the order of splicing of the four introns of the endogenous adenine phosphoribosyltransferase (aprt) gene in Chinese hamster ovary cells. The method involves a pairwise comparison of molecules that retain one intron and have either retained or spliced another intron(s). A highly preferred order of removal was found: intron 3 > 2 > 4 = 1. This order did not represent a linear progression from one end of the transcript to the other, nor did it correlate with the conformity of the splice site sequences to the consensus sequences or to the calculated energy of duplex formation with U1 small nuclear RNA. By using actinomycin D to inhibit RNA synthesis, the in vivo rate of the first step in splicing was estimated for all four introns; a half-life of 6 min was found for introns 2, 3, and 4. Intron 1 was spliced more slowly, with a 12-min half-life. A substantial amount of RNA that retained intron 1 as the sole intron was exported to the cytoplasm. In the course of these experiments, we also determined that intron 3, but not intron 4, is spliced before 3'-end formation is complete, probably on nascent transcripts. This result is consistent with the idea that polyadenylation is required for splicing of the 3'-most intron. We applied a similar strategy to determine the last intron to be spliced in a very large transcript, that of the endogenous dihydrofolate reductase (dhfr) gene in Chinese hamster ovary cells (25 kb). Here again, intron 1 was the last intron to be spliced.

Order of intron removal during splicing of endogenous adenine phosphoribosyltransferase and dihydrofolate reductase pre-mRNA

Using a strategy based on reverse transcription and the polymerase chain reaction, we have determined the order of splicing of the four introns of the endogenous adenine phosphoribosyltransferase (aprt) gene in Chinese hamster ovary cells. The method involves a pairwise comparison of molecules that retain one intron and have either retained or spliced another intron(s). A highly preferred order of removal was found: intron 3 > 2 > 4 = 1. This order did not represent a linear progression from one end of the transcript to the other, nor did it correlate with the conformity of the splice site sequences to the consensus sequences or to the calculated energy of duplex formation with U1 small nuclear RNA. By using actinomycin D to inhibit RNA synthesis, the in vivo rate of the first step in splicing was estimated for all four introns; a half-life of 6 min was found for introns 2, 3, and 4. Intron 1 was spliced more slowly, with a 12-min half-life. A substantial amount of RNA that retained intron 1 as the sole intron was exported to the cytoplasm. In the course of these experiments, we also determined that intron 3, but not intron 4, is spliced before 3'-end formation is complete, probably on nascent transcripts. This result is consistent with the idea that polyadenylation is required for splicing of the 3'-most intron. We applied a similar strategy to determine the last intron to be spliced in a very large transcript, that of the endogenous dihydrofolate reductase (dhfr) gene in Chinese hamster ovary cells (25 kb). Here again, intron 1 was the last intron to be spliced.

Effect of the cap structure on pre-mRNA splicing in Xenopus oocyte nuclei

The effect of the 5' cap structure on the splicing of precursor mRNAs was investigated after the RNAs were injected into Xenopus oocyte nuclei. The precursor mRNAs synthesized in vitro in a prokaryotic transcription system with a dinucleotide, ApppG, as a primer, were extremely stable when injected into the nuclei yet behaved like uncapped pre-mRNAs in the in vitro splicing reaction. The ApppG-primed precursor mRNAs served as a control (uncapped) in the injection experiments, and their splicing reactions were compared with those of their capped (m7GpppG-primed) counterparts. The capped precursors were spliced more efficiently than the uncapped precursors. Examination of splicing of the precursor mRNA that contained three exons and two introns with a single molecule has revealed that the cap structure exerts its effect primarily on the 5'-proximal intron. Thus, the cap structure not only stabilizes precursor mRNAs but also plays a positive role in the splicing of precursor mRNAs in cells.

The late spliced 19S and 16S RNAs of simian virus 40 can be synthesized from a common pool of transcripts

The late transcripts from the simian virus 40 (SV40) are alternatively spliced into two classes of spliced RNAs, 19S and 16S in size. We are interested in understanding the precursor-product relationships that result in the excision of different intervening sequences (introns) from the late transcripts. SV40 mutants containing precise deletions of the introns for each of the spliced 19S and 16S RNA species, including a previously undetected doubly spliced 19S RNA species, were isolated. Analysis by S1 mapping and a modified primer extension technique of the viral RNAs made in monkey cells transfected with each of these mutants led to the following conclusions. (i) Spliced late 19S RNA is not an intermediate in the synthesis of the late 16S RNAs. (ii) The 3' splice site used in the synthesis of the late 16S RNAs can join, albeit inefficiently, with alternative 5' splice sites in the absence of the 5' splice site normally used to synthesize 16S RNA. (iii) There is no obligatory order of excision of introns in the formation of the doubly spliced SV40 late 19S and 16S RNA species. A mutant was constructed by site-directed mutagenesis in which the 5'-proximal 3' splice site used in the synthesis of the doubly spliced RNAs is inactive. Cells transfected with this mutant processed transcripts into 19S RNA which, in wild-type-transfected cells, would have become doubly spliced 16S RNA. Therefore, we conclude that some of the spliced late 19S and 16S RNA can be synthesized from a common pool of transcripts.

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.

Alternative splicing of E1A transcripts of adenovirus requires appropriate ionic conditions in vitro

We have developed an in vitro splicing system using a HeLa cell nuclear extract that is highly active for the alternative splicing of the natural E1A transcripts. The efficiency of using the three alternative 5' splice sites is strongly dependent on the ionic conditions in the reaction, and the simultaneous production of the 13S, 12S, and 9S mRNA species is observed only at appropriate salt concentrations. All the intermediate and final splicing products have been extensively characterized and it has been demonstrated that the same major branch site is used for all the alternative reactions. The ratio of 13S to 9S mRNAs formed is close to that observed in vivo early in infection, suggesting that most of the mechanisms giving rise to alternative splicing are preserved in vitro.

Nuclear non-polyadenylated RNAs containing the first intervening sequence of the major late premessenger RNA from adenovirus-2: characterization and distribution in ribonucleoproteins

The nuclear non-polyadenylated RNA from HeLa cells infected with adenovirus-2 was examined for the presence of molecules containing the first intervening sequence (IVS1) of the major late premessenger RNA. Four molecules with the approximate size of free IVS1 in sucrose gradients (1021 nucleotides) were separated by polyacrylamide gel electrophoresis and characterized by complementary methods: S1 nuclease mapping, susceptibility to debranching enzyme, RNAase-H-directed cleavage. The results indicate that the most abundant RNA form is the excised lariat IVS1. We also find linear IVS1 and a randomly nicked lariat, the latter probably being made during RNA isolation. The fourth RNA is a leader 1-IVS1 molecule. No truncated IVS1 which might indicate that IVS1 is excised by several cycle of cleavage-ligation was detected. A study of the distribution of the four RNAs in hnRNP shows that they are part of RNPs of about 70 S. However, each RNP has distinct sedimentation characteristics and sensitivity to salt dissociation. Together, the results suggest that the excised lariat IVS1 is released from the large late premRNP under the form of a 70 S RNP, where it is linearized.

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.

The different intron 2 species excised in vivo from the E2A premRNA of adenovirus-2: an approach to analyse alternative splicing

In the early period of cellular infection by adenovirus 2, the E2A region gives rise to 2 major mRNA species of 2.0 and 2.3 kilobases, formed by alternative excisions of intron 2 (Gattoni et al., 1986, J. Mol. Biol. 187, 379-307). We have analysed the excision pathways of this intron. Two major intron species of 626 and 337 nucleotides, generated by the use of 2 consensus 3' splicing sites and a minor intron species of 520 nucleotides, generated by the use of another weaker 3' splicing site, are identified, the 3 species sharing a common 5' splicing site. They are detected predominantly in the lariat form. For the 2 major species we analyzed, the branched nucleotides are localized at consensus branching sequences, 26 or 25 nucleotides upstream from the 3' terminal AG. Our results confirm that the first reactions of cleavage at the 5' end of introns and branching occur in vivo as described in in vitro systems. The second predominant form of intron 2 is the linear segment, whereas the nicked lariat form which is very minor, might not be a genuine product of in vivo splicing. All intron 2 molecules show practically intact 5' and 3' terminal sequences, indicating that they are well protected against nuclease attack throughout their life. Therefore, these results indicate that the primary reaction following the excision of the lariat intron is debranching. In addition, the existence of a potential 5' splicing site contiguous to the major internal 3' splicing site raised the possibility of an elimination of the major 626 nucleotide intron in 2 cycles of excision. However, we demonstrate that intron 2 is systematically excised by a one cycle process, which is likely to represent the general rule for the production of correctly spliced mRNA.