trans-splicing to spliceosomal U2 snRNA suggests disruption of branch site-U2 pairing during pre-mRNA splicing

Abstract

Pairing between U2 snRNA and the branch site of spliceosomal introns is essential for spliceosome assembly and is thought to be required for the first catalytic step of splicing. We have identified an RNA comprising the 5' end of U2 snRNA and the 3' exon of the ACT1-CUP1 reporter gene, resulting from a trans-splicing reaction in which a 5' splice site-like sequence in the universally conserved branch site-binding region of U2 is used in trans as a 5' splice site for both steps of splicing in vivo. Formation of this product occurs in functional spliceosomes assembled on reporter genes whose 5' splice sites are predicted to bind poorly at the spliceosome catalytic center. Multiple spatially disparate splice sites in U2 can be used, calling into question both the fate of its pairing to the branch site and the details of its role in splicing catalysis.

Figure 1. Trans-splicing in S. cerevisiae can generate an RNA species comprising the 5’ end of U2 snRNA and the 3’ exon of the ACT1-CUP1 reporter

(A). Schematic of RNA-RNA interactions that contribute to the first step of splicing (modified from Konarska et al., 2006) with the initial G of each of the three 5’ splice site-like sequences in the BS-binding region of U2 snRNA indicated by circles. (B). Schematic of ACT1-CUP1 reporter pre-mRNA and U2 snRNA, indicating the mutations used in panels C and D, and the location of the RT and PCR primers (arrows) used in panel C. (C). RT-PCR using the primers indicated in Fig. 1B can amplify a product, of the size expected for a trans-splicing product generated using the BS-binding region of U2 as a 5’SS, from total RNA from S. cerevisiae Y04999 cells carrying reporters with 5’SS mutations as indicated. (D). Primer extension analysis of RNA recovered from cells containing the ACT1-CUP1 reporters as indicated. Primer complimentary to the 3' exon was used to reveal levels of pre-mRNA, mRNA, and lariat intermediate. Strain Y04999 (Δdbr1) was used in order to accurately monitor the efficiency of the first step. (E). The 130 bp RT-PCR product corresponds to trans-spliced U2-ACT1-CUP1. Reverse-complemented sequencing trace from the purified 130 bp product. U2 snRNA and ACT1-CUP1 sequence, as well as the chromatogram read, are indicated above the trace; concordance between chromatogram and gene sequence is indicated by boxes, and the splice junction is highlighted on the chromatogram trace.

Figure 2. Trans-splicing does not occur in reporter genes with mutations outside the 5’SS

(A). Schematic of ACT1-CUP1 reporter pre-mRNA and U2 snRNA, indicating the mutations used in panels C and D, and the schematic location of RT and PCR primers (arrows) used in panel B. (B). Mutations at and around the branch site do not stimulate trans-splicing in an otherwise wild-type context, and inhibit it in the context of an accompanying 5’SS mutation. RT-PCR analysis of RNA recovered from Y04999 cells containing the ACT1-CUP1 reporters as indicated, as in Fig. 1C. (C). Primer extension analysis of RNA recovered from Y04999 cells containing the ACT1-CUP1 reporters as indicated, as in Fig. 1D.

Figure 3. U2 snRNA in functional spliceosomes is the substrate for trans-splicing

(A). Compensatory U2 and U6 snRNA mutations used in panels C and D. (B, C). Predicted behaviour of wild-type and mutant U2 snRNAs in strains carrying a wild-type (B) or mutant (C) U6 snRNA gene. (D, E). The trans-spliced product is generated by attack of U2 snRNA in functional spliceosomes. Reverse-complemented sequencing traces from purified trans-splicing product from yCQ62 cells carrying G5A ACT1-CUP1 reporter, both wild-type and mutant U2 snRNA genes, and a wild-type (D) or mutant (E) U6 snRNA gene. Concordance between chromatogram and wild-type gene sequence is indicated by boxes, and the mutated/wild-type helix Ib U2 snRNA nucleotides highlighted.

Figure 4. U2 snRNA sequence is a suboptimal 5’SS in the context of a reporter gene

(A). Schematic of ACT1-CUP1 reporter pre-mRNA and U2 snRNA, indicating the U2 sequence substitution into ACT1-CUP1 and 3’SS gAG/ mutation used in panels B and C, and the RT-PCR primers used in panel C. (B). Primer extension analysis of RNA recovered from Y04999 cells containing the ACT1-CUP1 reporters as indicated, as in Fig. 1D. (C). Spliced ACT1-U2-ACT1-CUP1 mRNA can be detected by RT-PCR (lane 3). Wild-type mRNA is shown for comparison (lane 1). (D, E). Schematic indicating 5’SS usage in U2 sequence in cis in the context of ACT1-U2-ACT1-CUP1 (D) and in trans in the context of U2 snRNA (E). n refers to the number of plasmids sequenced containing trans-spliced product that had used the 5’SS indicated by the arrow above, and circles indicate the predominant 5’SS detected in directly sequenced PCR products. (F). Proposed mechanisms of trans-splicing: (i) RNA-RNA interactions in the fully assembled spliceosome, with BS paired to U2. (iia) BS and U2 unpair and re-pair potentially inaccurately, with BS nucleophilically attacking U2 from within the resulting helix, or (iib) BS and U2 unpair, with new pairing established between BS and the 5’SS; BS, bulged from this new helix, attacks U2. (iii) 5’SS-U6 and BS-U2 pairing both having been disrupted, the ‘U2 5’ exon’ generated in step ii attacks the reporter gene 3’SS, generating (iv) a branched product comprising the 3’ end of U2 appended to the 5’ exon and intron of the reporter gene, and a linear product comprising the 5’ end of U2 appended to the reporter 3’ exon.