Reconstitution of functional mammalian U4 small nuclear ribonucleoprotein: Sm protein binding is not essential for splicing in vitro.

Abstract

We have developed an in vitro splicing complementation assay to investigate the domain structure of the mammalian U4 small nuclear RNA (snRNA) through mutational analysis. The addition of affinity-purified U4 snRNP or U4 RNA to U4-depleted nuclear extract efficiently restores splicing activity. In the U4-U6 interaction domain of U4 RNA, only stem II was found to be essential for splicing activity; the 5' loop is important for spliceosome stability. In the central domain, we have identified a U4 RNA sequence element that is important for splicing and spliceosome assembly. Surprisingly, an intact Sm domain is not essential for splicing in vitro.Our data provide evidence that several distinct regions of U4 RNA contribute to snRNP assembly, spliceosome assembly and stability, and splicing activity.Nuclear pre-mRNA splicing requires the ordered assembly of the splicing substrate into a large ribonucleoprotein (RNP) complex, the spliceosome, containing small nuclear RNPs (Ul, U2, U4/U6, and U5 snRNPs) and non-snRNP splicing factors (for recent reviews, see references 6, 28, and 40). The Ul and U2 snRNPs, in conjunction with nonsnRNP splicing factors, recognize the 5' splice site and the branch point region, respectively. Most likely, the U4/U6 and U5 snRNPs interact to form the U4/U5/U6 multi-snRNP before they are incorporated into the spliceosome (4, 25, 37), apparently not through direct pre-mRNA contacts but through snRNP-snRNP interactions (5). The spliceosome proceeds, during its assembly, the two steps of the splicing reaction, and its disassembly, through multiple conformational stages, some of which may be driven by ATP-dependent RNA helicases (for reviews, see references 17 and 36). For example, a major conformational change during splicing destabilizes U4 binding in the spliceosome (8,11,26,35); U6 and U2 RNAs engage in a base-pairing interaction required for the assembly of a stable spliceosome and for splicing (12,21,46,47), and an additional U6-U2 interaction has recently been suggested (32).On the basis of extensive phylogenetic evidence, a secondary structure model has been proposed for U4 RNA base paired with U6 RNA (18) (for the human U4/U6 RNA hybrid, see Fig. 1). U4 RNA can be divided into three domains, the 5'-terminal U4-U6 interaction domain (stem II, 5' stem-loop, stem I), the central domain (single-stranded region, central stem-loop), and the 3'-terminal domain (Smbinding site, 3' stem-loop). Interestingly, free U4 RNA can also be folded into a conserved secondary structure, in which the 3'-terminal domain remains unchanged compared with the U4/U6 RNA hybrid structure but in which the stem I and stem II regions are partially base paired with each other, thereby extending the 5' stem-loop structure (33). There are several lines of indirect evidence that U6 RNA sequences play a catalytic role in splicing (10, 14, 42, 43; reviewed in reference 17). Since in the U4/U6 snRNP U6 * Corresponding author.RNA is stably associated with U4 RNA, U4 has been hypothesized to function as an antisense negative ...

Spliceosome activation: U4 is the path, stem I is the goal, and Prp8 is the keeper. Let's cheer for the ATPase Brr2!

“…Regardless, Hahn et al (2012) found that the 39 SL alone does not bind Brr2, implying that other RNA parts are required, and MozaffariJovin et al (2012) showed that the central domain of U4 plays a key role in Brr2 binding as well as in U4/U6 unwinding. Consistent with an important role for the central domain, bases in this domain adjacent to stem I have been shown to be important for splicing (Wersig and Bindereif 1992). Notably, however, the central domain of U4 can be endonucleolytically cleaved after formation of U4/U6 with little consequence for splicing (Hayduk et al 2012).…”

The determinants for Sm protein binding to Xenopus U1 and U5 snRNAs are complex and non-identical.

“…Wersig and Bindereif (1992) showed that a human U4 snRNA mutant, whose Sm core site was mutated such as to abolish immunoprecipitation with anti-Sm antibodies, was active in an in vitro splicing complementation assay. This result suggests that the common proteins bound to U4 snRNA play no essential role in splicing in vitro.…”

Modified nucleotides at the 5′ end of human U2 snRNA are required for spliceosomal E-complex formation

“…Neither the m 3 G cap nor internal modifications are essential for the function of U1 , U4 (Wersig and Bindereif 1992), U5 (Ségault et al 1995), or U6 (Wolff and Bindereif 1992) snRNAs in splicing in vitro. In contrast, post-transcriptional modifications are essential for U2 function in Xenopus oocytes (Pan and Prives 1989) and HeLa nuclear extract (Ségault et al 1995), but their role remains poorly understood.…”