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small nuclear RNA
While introns and splicing are present in nearly all eukaryotes, various aspects are more or less conserved between organisms. The main spliceosomal machinery is known to have arisen very far back in eukaryotic ancestry. Evolutionary analysis of spliceosomal proteins (snRNPs) suggests that group II intron splicing evolved in sophisticated organisms rather than having a more primitive origin (Collins and Penny 2005).
The snRNAs are extremely conserved in both primary and secondary structure. Moreover, some residues seem to be completely invariant between organisms. With the exception of Saccharomyces, the length of the snRNAs involved in pre-mRNA splicing is fairly conserved (RLP Adams et. al. 1997).
The snRNPs associated with their respective snRNA are so closely coupled with each other they are often refered to synonomously. The splicosome as a whole has debated number of components. With sensitive mass spectrometers becoming more widely used, new components are constantly added to the list. It is also unclear whether the spliceosome is pre-assembled in a cell or if all the parts have to come together for splicing to occur. Both models are debated.
For U2-type introns: U1RNP (ribonucleoproteins complexed with snRNA U1) base pairs with the 5' splice junction. This is the commited step but requires no ATP hydrolysis. Branch point binding protein (BBP) and U2 auxillary factor bind the 3' splice junction. U2snRNP displaces BBP and U2AF while base pairing with the branch point adenosine within the intron and hydrolyzing ATP. U4/U6-U5snRNP enters the complex and rearranges the pre-mRNA strand to allow the 2' OH on the branch point adenosine to nucleophillically attack the 3' most nucleotide on the 5' exon. This displaces the U1snRNA by hydrolyzing ATP. A lariat structure is formed in the intron and the entire reaction rearranges. Using U5snRNP to stabilize the two exons in proximity to each other, the free 2' OH on the 3' end of the 5' exon attacks the 5' end of the 3' exon, releasing the intron lariat and ligating together the exons.
U12-type introns are similarly removed but different consensus sequences in the pre-mRNA are recognized by U11 and U12 snRNPs rather than U1 and U12, respectively ( B Alberts et al 2008).
snRNAs are <200nt long, non-coding RNA molecules that are key for pre-mRNA splicing. Each snRNA (e.g. U1, U2, etc.) is complexed with at least seven snRNP forming a UsnRNp. UsnRNPs U1, U2, U4, U5 and U6 are involved in splicing the most abundant type of introns, U2-type introns. Lower in abundance UsnRNPs U11 and U12 splice a rarer class of introns called U12-type introns. Each has its own role during pre-mRNA splicing which is covered in the mechanism of action section. Because the spliceosome has over two hundred component of varying stability (MS Jurica & MS Moore 2003), it is unclear whether the proteins involved perform the catalysis or the snRNAs themselves. It has been shown, however, the U2 and U6 alone in vitro have very low splicing activity (Valakhan & Manely 2001). The main, undisputed roles of snRNAs are to recognize the 5' and 3' intron/exon boundaries and to recruit a number of RNPs to catalyze splicing.
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Sm class of snRNAs (U1, U2, U4 and U5) are synthesized by RNA Pol II. For Sm class, pre-snRNAs are transcribed and 5' monomethylguanosine capped in the nucleus, exported via multiple factors to the cytoplasm for further processing. After cytoplamic hypermethylation of 5' cap (trimethylguanosine) and 3' trimming, the snRNA is translocated back into the nucleus. snRNPs for Sm class snRNAs are also assembled in the cytosol.
Lsm snRNA (U6 and other snoRNAs) are transcribed by Pol III and keep the monomethylguanosine 5' cap and in the nucleus. Lsm snRNAs never leave the nucleus (Matera et. al. 2007, T Kiss 2004)
While there are a dozen or so U-RNAs, the most common are the U1, U2, U4, U5 and U6 snRNAs. These five snRNAs are involved extensively in the spliceosome and removal of group II introns (B Alberts et. al. 2008).
small nuclear (sn)RNAs, historically referred to as U-RNAs, derive their nomenclature from their discovery during studies of migration patterns of RNAs and their uridylate-rich sequence (H Busch et. al. 1982). More recently, snRNAs are further divided into two main categories based on shared sequences and associated proteins. Sm-class RNAs have a 5' trimethylguanosine cap and bind several Sm proteins. Lsm-RNAs possess a monomethylphosphate 5' cap and a uridine rich 3' end acting as a binding site for Lsm proteins.
While no tools per se have been developed using snRNAs, tissue specific splice variants have been recognized and targeted for therapies (MA Garcia-Bianco et al. 2004)
snRNAs were discovered during a study comparing of agarose gel electorphoresis to sucrose density gradient electrophoresis (AA Hadjilov et. al. 1966). Unknown RNAs (not rRNA or tRNA) were seen and envoked curiosity. Only later were the RNAs analyzed and found to be high in uridylate and localized to the nucleus and nucleolus (JL Hodnet et. al. 1968). Once these RNAs were shown not to be degradation products (RA Wienberg et. al. 1968), snRNAs became an interesting area for further research.
Since most proteins from the human genome undergo some extent of splicing, deleterious mutations can be expected to occur in many places along the splicing pathway. Single nucleotide changes or deletions have been seen to alter splicing effeciency, cause improper alternative splicing (connecting different combinations of exons), loss of splice site recognition, or severe frameshifts in the mature mRNA from an aberrent pre-mRNA (Faustino & Cooper 2003). Although many diseases stem from mutations in splicing machinary or in pre-mRNA but rarely in actual snRNA sequences.