The secondary structure of a messenger RNA precursor probed with psoralen is melted in an in vitro splicing reaction

Chemical and computer probing of RNA structure

Ribonucleic acids (RNAs) are one of the most important types of biopolymers. RNAs play key roles in the storage and multiplication of genetic information. They are important in catalysis and RNA splicing and are the most important steps of translation. This chapter describes experimental methods for probing RNA structure and theoretical methods allowing the prediction of thermodynamically favorable RNA folding. These methods are complementary and together they provide a powerful approach to determine the structure of RNAs. The three-dimensional (tertiary) structure of RNA is formed by hydrogen-bonding among functional groups of nucleosides in different regions of the molecule, by coordination of polyvalent cations, and by stacking between the double-stranded regions present in the RNA. The tertiary structures of only some small RNAs have been determined by high-resolution X-ray crystallographic analysis and nuclear magnetic resonance analysis. The most widely used approach for the investigation of RNA structure is chemical and enzymatic probing, in combination with theoretical methods and phylogenetic studies allowing the prediction of variants of RNA folding. Investigations of RNA structures with different enzymatic and chemical probes can provide detailed data allowing the identification of double-stranded regions of the molecules and nucleotides involved in tertiary interactions.

Pre-mRNA secondary structure and the regulation of splicing

Nuclear pre-mRNAs must be precisely processed to give rise to mature cytoplasmic mRNAs. This maturation process, known as splicing, involves excision of intron sequences and ligation of the exon sequences. One of the major problems in understanding this process is how splice sites, the sequences which form the boundaries between introns and exons, can be accurately selected. A number of studies have defined conserved sequences within introns which were later shown to interact with small nuclear ribonucleoproteins (snRNPs). However, due to the simplicity of these conserved sequences it has become clear that other elements must be involved and a number of studies have indicated the importance of secondary structures within pre-mRNAs. Using various examples, we shall show that such structures can help to specify splice sites by modifying physical distances within introns or by being involved in the definition of exons and lastly, that they can be part of the regulation of alternative splicing.

Inhibition of SV40 gene expression by microinjected small antisense RNA and DNA molecules

We tested the impact of antisense RNA and DNA molecules on SV40 gene expression by microinjection into TC7 cells. Short antisense stretches, complementary to either hairpin or loop structures on the T antigen mRNA, inhibited T antigen synthesis. In contrast, full-length antisense RNA and DNA molecules did not effect T antigen synthesis.

The AU-rich sequences present in the introns of plant nuclear pre-mRNAs are required for splicing

Plant cells do not in general process the introns of transcripts expressed from introduced vertebrate genes. By studying the processing of model introns in transfected plant protoplasts, we have investigated the special requirements for intron recognition by plant cells. Our results indicate that the requirements for intron recognition in plants are different from those of both metazoa and yeast. A synthetic intron of arbitrary sequence but incorporating splice site consensus sequences and a high proportion of U and A nucleotides, a characteristic feature of plant introns, was efficiently spliced in protoplasts. We have studied the effects of various sequence alterations and conclude that AU-rich sequences are necessary for intron recognition. In addition, we find that the criteria for branch site selection are relaxed, as they are in vertebrates, but a polypyrimidine tract is not necessary.

Specificity of site directed psoralen addition to RNA

We describe the attachment of a psoralen derivative (site specific psoralen, SSP) to the 5' end of a DNA oligonucleotide and the hybridization and the photoreaction of this reagent with a complementary target site on an RNA molecule. SSP was coupled to a variety of DNA oligonucleotides to investigate the structural requirements for addition to the RNA. Efficient SSP photoadducts were made on specific uridines by designing an intercalation site at an unpaired nucleotide in the RNA strand within the heteroduplex region. The optimal location for this site was five nucleotides from the oligonucleotide 5' end and just 5' to the target uridine residue. Because the attachment of the SSP to the oligonucleotide is through a disulfide bond, the DNA oligonucleotide can be removed with reduction to leave SSP attached to the RNA strand. The SSP adduct made in this way will be useful for subsequent biochemical and biophysical experiments.

The ends of La Crosse virus genome and antigenome RNAs within nucleocapsids are base paired

The three La Crosse virus genomes are found as circular structures in the electron microscope, and the RNA ends of at least the small (S) and medium (M) segments are highly complementary. When examined for psoralen cross-linking, about half of the S, at most 1 to 2% of the M, and none of the large (L) nucleocapsid RNAs could be cross-linked in virions or at late times intracellularly, under conditions in which each free RNA reacted completely. For the S segment, genomes and antigenomes first detected intracellularly could not be cross-linked at all, and their cross-linkability increased gradually with time. Antigenomes behaved similarly to genomes in all respects. It appears that the majority of all three segments are base paired at their ends and that the limited cross-linkability reflects the accessability of the RNA within nucleocapsids to psoralen. The gradual increase in cross-linkability may be important in persistent mosquito cell infection, in which it correlates with decreased S mRNA synthesis rates, and may be part of the mechanism which this infection becomes self-limiting. The implications of double-stranded RNA panhandles within nucleocapsids are discussed.

Use of reverse transcription to determine the exact locations of psoralen photochemical crosslinks in RNA

We have studied the properties of avian myeloblastosis virus reverse transcriptase on Escherichia coli 16S ribosomal RNA that was known to contain a psoralen crosslink in a restricted region around residue 920. These crosslinked RNA molecules were purified on the basis of loop size by gel electrophoresis. Reverse transcription stopped at specific positions in the crosslinked molecules but not in control linear molecules. With the particular crosslink that was studied, at the earliest time of reverse transcription, the most frequent stopping site was G925. At later times two nearly equal stops at G925 and C924 were seen. The crosslinked site was an absolute stop since even at long times of incubation the reverse transcriptase was not able to proceed beyond G925/C924. An independent determination of the crosslinked site by directly sequencing a section of the crosslinked RNA indicated that C924 was the sole nucleotide involved in the crosslink. Therefore, reverse transcriptase was able to synthesize cDNA all the way up to and including the nucleotide that contained the psoralen crosslink. Thus, reverse transcription can be a rapid and precise method for determining psoralen crosslinking sites when prefractionated, crosslinked RNA templates are used.

Virus-specific splicing inhibitor in extracts from cells infected with HIV-1

Human immunodeficiency virus type 1 (HIV-1), in contrast with most other retroviruses, encodes trans-regulatory proteins for virus gene expression. It is shown in this study, by means of an in vitro splicing system, that nuclear extracts obtained from cells infected with HIV-1 contain a factor (or factors) that specifically inhibits splicing of a synthetic SP6/HIV pre-messenger RNA (pre-mRNA)-containing donor and acceptor splice sites in the coding region for the envelope protein. It is also shown that the SP6/HIV pre-mRNA is not capable of assembly in a ribonucleoprotein complex, spliceosome, in extracts from infected cells. These findings raise the possibility that specific inhibition of pre-mRNA splicing in the envelope protein coding region by HIV-1 trans-regulatory factors might be one control mechanism for efficient production of structural viral proteins and virion assembly.

Intron sequences and the length of the downstream second exon affect the binding of hnRNP C proteins in an in vitro splicing reaction

The proteins that are in direct contact with the pre-mRNA in an in vitro splicing reaction were analyzed by UV cross-linking experiments. Six major proteins (120, 55, 44, 42, 39 and 38 KD) and three minor polypeptides (84, 72 and 63 KD) were detected. The predominant proteins 44, 42 KD belong to the class of hnRNP C proteins since they were immunoprecipitated by monoclonal antibodies directed against hnRNP C proteins. The cross-linked proteins were not detected in the absence of Mg2+, ATP or when RNA lacking introns were used as substrates in the splicing reactions. The effect of exon sequences on the binding efficiency for the photocrosslinked proteins was investigated. Transcripts containing a second exon of 24 nucleotides for the beta-globin or 107 nucleotides for the mouse insulin, yielded a reduced amount of cross-linked proteins when compared with "full length" pre-mRNAs. Sequences within the first exon of the beta-globin pre-mRNA did not affect the binding efficiency of these proteins. The reduced binding efficiency of the cross-linked proteins for the truncated beta-globin or mouse insulin pre-mRNAs correlated with the lower efficiency for in vitro splicing. Substitutions with unrelated sequences in the beta-globin second exon restore the binding of the cross-linked proteins indicating that the length of the second exon and not specific sequences are relevant for the binding efficiency of these proteins. The SP6/mouse insulin oligonucleotides cross-linked to the hnRNP C proteins were isolated and sequenced. A 17-mer was located in the second exon (134 nucleotides downstream from the 3' splice site) and a 14-mer in the intron region (25 nucleotides downstream the 5' splice site). The beta-globin oligonucleotides cross-linked to the hnRNP C proteins were a 13-mer in the second exon (28 nucleotides downstream the 3' splice site) and an 8-mer in the first exon (81 nucleotides downstream the 5' end of the pre-mRNA). Our results indicate that the hnRNP C proteins interact with those oligonucleotides located in different regions of the pre-mRNA. The binding efficiency of those proteins, however, depends on the length of the second exon and the presence of intron sequences (secondary and/or tertiary pre-mRNA structure).