snRNAs are required for splicing

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A small nuclear RNA (snRNA) is one of many small RNA species confined to the nucleus; several of the snRNAs are involved in splicing or other RNA processing reactions.
Small cytoplasmic RNAs (scRNA) are present in the cytoplasm and (sometimes are also found in the nucleus).
snRNPs (snurp) are small nuclear ribonucleoproteins (snRNAs associated with proteins).
scRNPs (scyrp) are small cytoplasmic ribonucleoproteins (scRNAs associated with proteins).
The spliceosome is a complex formed by the snRNPs that are required for splicing together with additional protein factors.
Anti-Sm is an autoimmune antiserum that defines the Sm epitope that is common to a group of proteins found in snRNPs that are involved in RNA splicing.

The five snRNPs involved in splicing are U1, U2, U5, U4, and U6.
Together with some additional proteins, the snRNPs form the spliceosome.
All the snRNPs except U6 contain a conserved sequence that binds the Sm proteins that are recognized by antibodies generated in autoimmune disease.

The 5' and 3' splice sites and the branch sequence are recognized by components of the splicing apparatus that assemble to form a large complex. This complex brings together the 5' and 3' splice sites before any reaction occurs, explaining why a deficiency in any one of the sites may prevent the reaction from initiating. The complex assembles sequentially on the pre-mRNA, and several intermediates can be recognized by fractionating complexes of different sizes. Splicing occurs only after all the components have assembled (719).

The splicing apparatus contains both proteins and RNAs (in addition to the pre-mRNA). The RNAs take the form of small molecules that exist as ribonucleoprotein particles. Both the nucleus and cytoplasm of eukaryotic cells contain many discrete small RNA species. They range in size from 100-300 bases in higher eukaryotes, and extend in length to ~1000 bases in yeast. They vary considerably in abundance, from 10⁵-10⁶ molecules per cell to concentrations too low to be detected directly.

Those restricted to the nucleus are called small nuclear RNAs (snRNA); those found in the cytoplasm are called small cytoplasmic RNAs (scRNA). In their natural state, they exist as ribonucleoprotein particles (snRNP and scRNP). Colloquially, they are sometimes known as snurps and scyrps. There is also a class of small RNAs found in the nucleolus, called snoRNAs, which are involved in processing ribosomal RNA (see Small RNAs are required for rRNA processing).

The snRNPs involved in splicing, together with many additional proteins, form a large particulate complex, called the spliceosome. Isolated from the in vitro splicing systems, it comprises a 50-60S ribonucleoprotein particle. The spliceosome may be formed in stages as the snRNPs join, proceeding through several "presplicing complexes." The spliceosome is a large body, greater in mass than the ribosome.

Figure 24.8

The spliceosome is ~12 MDa. 5 snRNPs account for almost half of the mass. The remaining proteins include known splicing factors and also proteins that are involved in other stages of gene expression.

Figure 24.8 summarizes the components of the spliceosome (3210). The 5 snRNAs account for more than a quarter of the mass; together with their 41 associated proteins, they account for almost half of the mass. Some 70 other proteins found in the spliceosome are described as splicing factors. They include proteins required for assembly of the spliceosome, proteins required for it to bind to the RNA substrate, and proteins involved in the catalytic process. In addition to these proteins, another ~30 proteins associated with the spliceosome have been implicated in acting at other stages of gene expression, suggesting that the spliceosome may serve as a coordinating apparatus.

The spliceosome forms on the intact precursor RNA and passes through an intermediate state in which it contains the individual 5' exon linear molecule and the right lariat-intron-exon. Little spliced product is found in the complex, which suggests that it is usually released immediately following the cleavage of the 3' site and ligation of the exons.

We may think of the snRNP particles as being involved in building the structure of the spliceosome. Like the ribosome, the spliceosome depends on RNA-RNA interactions as well as protein-RNA and protein-protein interactions. Some of the reactions involving the snRNPs require their RNAs to base pair directly with sequences in the RNA being spliced; other reactions require recognition between snRNPs or between their proteins and other components of the spliceosome.

The importance of snRNA molecules can be tested directly in yeast by making mutations in their genes. Mutations in 5 snRNA genes are lethal and prevent splicing. All of the snRNAs involved in splicing can be recognized in conserved forms in animal, bird, and insect cells. The corresponding RNAs in yeast are often rather larger, but conserved regions include features that are similar to the snRNAs of higher eukaryotes.

The snRNPs involved in splicing are U1, U2, U5, U4, and U6. They are named according to the snRNAs that are present. Each snRNP contains a single snRNA and several (<20) proteins. The U4 and U6 snRNPs are usually found as a single (U4/U6) particle. A common structural core for each snRNP consists of a group of 8 proteins, all of which are recognized by an autoimmune antiserum called anti-Sm; conserved sequences in the proteins form the target for the antibodies. The other proteins in each snRNP are unique to it. The Sm proteins bind to the conserved sequence PuAU₃₆Gpu, which is present in all snRNAs except U6. The U6 snRNP contains instead a set of Sm-like (Lsm) proteins. The Sm proteins must be involved in the autoimmune reaction, although their relationship to the phenotype of the autoimmune disease is not clear (for review see 244; 245; 247).

Some of the proteins in the snRNPs may be involved directly in splicing; others may be required in structural roles or just for assembly or interactions between the snRNP particles. About one third of the proteins involved in splicing are components of the snRNPs. Increasing evidence for a direct role of RNA in the splicing reaction suggests that relatively few of the splicing factors play a direct role in catalysis; most are involved in structural or assembly roles.

Last Revised on June 2, 2004

244 Maniatis, T. and Reed, R. (1987). The role of small nuclear ribonucleoprotein particles in pre-mRNA splicing. Nature 325, 673-678. PubMed Journal
245 Guthrie, C. and Patterson, B. (1988). Spliceosomal snRNAs. Annu. Rev. Genet. 22, 387-419. PubMed Journal
247 Guthrie, C. (1991). Messenger RNA splicing in yeast: clues to why the spliceosome is a ribonucleoprotein. Science 253, 157-163. PubMed

719 Grabowski, P. J., Seiler, S. R., and Sharp, P. A. (1985). A multicomponent complex is involved in the splicing of messenger RNA precursors. Cell 42, 345-353. PubMed Journal
3210 Zhou, Z., Licklider, L. J., Gygi, S. P., and Reed, R. (2002). Comprehensive proteomic analysis of the human spliceosome. Nature 419, 182-185. PubMed Journal

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