scholarly journals Spliceosome Assembly Pathways for Different Types of Alternative Splicing Converge during Commitment to Splice Site Pairing in the A Complex

2008 ◽  
Vol 29 (4) ◽  
pp. 1072-1082 ◽  
Author(s):  
Matthew V. Kotlajich ◽  
Tara L. Crabb ◽  
Klemens J. Hertel

ABSTRACT Differential splice site pairing establishes alternative splicing patterns resulting in the generation of multiple mRNA isoforms. This process is carried out by the spliceosome, which is activated by a series of sequential structural rearrangements of its five core snRNPs. To determine when splice sites become functionally paired, we carried out a series of kinetic trap experiments using pre-mRNAs that undergo alternative 5′ splice site selection or alternative exon inclusion. We show that commitment to splice site pairing in both cases occurs in the A complex, which is characterized by the ATP-dependent association of the U2 snRNP with the branch point. Interestingly, the timing of splice site pairing is independent of the intron or exon definition modes of splice site recognition. Using the ATP analog ATPγS, we showed that ATP hydrolysis is required for splice site pairing independent from U2 snRNP binding to the pre-mRNA. These results identify the A complex as the spliceosomal assembly step dedicated to splice site pairing and suggest that ATP hydrolysis locks splice sites into a splicing pattern after stable U2 snRNP association to the branch point.

2001 ◽  
Vol 21 (6) ◽  
pp. 1986-1996 ◽  
Author(s):  
Luiz O. F. Penalva ◽  
Maria José Lallena ◽  
Juan Valcárcel

ABSTRACT Maintenance of female sexual identity in Drosophila melanogaster involves an autoregulatory loop in which the protein Sex-lethal (SXL) promotes skipping of exon 3 from its own pre-mRNA. We have used transient transfection of Drosophila Schneider cells to analyze the role of exon 3 splice sites in regulation. Our results indicate that exon 3 repression requires competition between the 5′ splice sites of exons 2 and 3 but is independent of their relative strength. Two 3′ splice site AG's precede exon 3. We report here that, while the distal site plays a critical role in defining the exon, the proximal site is preferentially used for the actual splicing reaction, arguing for a switch in 3′ splice site recognition between exon definition and splicing catalysis. Remarkably, the presence of the two 3′ splice sites is important for the efficient regulation by SXL, suggesting that SXL interferes with molecular events occurring between initial splice site communication across the exon and the splice site pairing that leads to intron removal.


2019 ◽  
Vol 21 (Supplement_6) ◽  
pp. vi41-vi41
Author(s):  
Tobias Bonifert ◽  
Sonali Arora ◽  
Matthew Fitzgibbon ◽  
Patrick Paddison

Abstract Chemical or genetic perturbation of the spliceosome function may represent a therapeutic opportunity for Glioblastoma multiforme (GBM) and other cancers. We and others have shown that oncogenic MYC activity causes spliceosome vulnerability and leads to deficits in 3’ splice site recognition upon spliceosome perturbation. Several spliceosome inhibitors in pre-clinical development and in clinical trials target the U2 snRNP subcomplex SF3B, which is essential for 3’ splice site recognition. We showed that knockdown of one of its subunits, PHF5A, causes GBM-specific changes in splicing, including increases in exon skipping, intron retention and activation of alternative 3’ and 5’ splice sites. However, in depth analysis of these events revealed they are disproportionately enriched for “minor” introns. This class of ~800 introns is specifically excised by an alternative splicing pathway which involves the U12-dependent spliceosome. Remarkably, we provide evidence that inhibition of PHF5A in GBM stem-like cells causes increased retention of most minor introns, as well as activation of cryptic and alternative U2 snRNP-dependent splicing sites. We further demonstrate that components of the U12 snRNP complex are differentially required for GSC-specific viability. Our results suggest that regulation of the splicing of U12-type introns may be critically important for GBM tumor cell viability.


2017 ◽  
Vol 37 (9) ◽  
Author(s):  
Shu-Ching Huang ◽  
Henry S. Zhang ◽  
Brian Yu ◽  
Ellen McMahon ◽  
Dan T. Nguyen ◽  
...  

ABSTRACT Exon 16 of protein 4.1R encodes a spectrin/actin-binding peptide critical for erythrocyte membrane stability. Its expression during erythroid differentiation is regulated by alternative pre-mRNA splicing. A UUUUCCCCCC motif situated between the branch point and the 3′ splice site is crucial for inclusion. We show that the UUUU region and the last three C residues in this motif are necessary for the binding of splicing factors TIA1 and Pcbp1 and that these proteins appear to act in a collaborative manner to enhance exon 16 inclusion. This element also activates an internal exon when placed in a corresponding intronic position in a heterologous reporter. The impact of these two factors is further enhanced by high levels of RBM39, whose expression rises during erythroid differentiation as exon 16 inclusion increases. TIA1 and Pcbp1 associate in a complex containing RBM39, which interacts with U2AF65 and SF3b155 and promotes U2 snRNP recruitment to the branch point. Our results provide a mechanism for exon 16 3′ splice site activation in which a coordinated effort among TIA1, Pcbp1, and RBM39 stabilizes or increases U2 snRNP recruitment, enhances spliceosome A complex formation, and facilitates exon definition through RBM39-mediated splicing regulation.


Cells ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 936 ◽  
Author(s):  
Yongchao Liu ◽  
Donggun Kim ◽  
Namjeong Choi ◽  
Jagyeong Oh ◽  
Jiyeon Ha ◽  
...  

The ratio control of 4R-Tau/3R-Tau by alternative splicing of Tau exon 10 is important for maintaining brain functions. In this study, we show that hnRNP A1 knockdown induces inclusion of endogenous Tau exon 10, conversely, overexpression of hnRNP A1 promotes exon 10 skipping of Tau. In addition, hnRNP A1 inhibits splicing of intron 9, but not intron 10. Furthermore, hnRNP A1 directly interacts with the 3′ splice site of exon 10 to regulate its functions in alternative splicing. Finally, gene ontology analysis demonstrates that hnRNP A1-induced splicing and gene expression targets a subset of genes with neuronal function.


RNA Biology ◽  
2010 ◽  
Vol 7 (1) ◽  
pp. 56-64 ◽  
Author(s):  
Monika Heiner ◽  
Jingyi Hui ◽  
Silke Schreiner ◽  
Lee-Hsueh Hung ◽  
Albrecht Bindereif

2002 ◽  
Vol 22 (15) ◽  
pp. 5337-5346 ◽  
Author(s):  
Suzanne Furuyama ◽  
James P. Bruzik

ABSTRACT The trans-splicing reaction involves the association of 5′; and 3′; splice sites contained on separate transcripts. The mechanism by which these splice sites are juxtaposed during trans-spliceosome assembly and the role of SR proteins at each stage in this process have not been determined. Utilizing a system that allows for the separation of the RNA binding and RS domains of SR proteins, we have found that SR proteins are required for at least two stages of the trans-splicing reaction. They are important both prior to and subsequent to the addition of U2 snRNP to the 3′; acceptor. In addition, we have demonstrated a role for RS domain phosphorylation in both of these activities. Dephosphorylation of the RS domain led to a block in U2 snRNP binding to the substrate. In a separate experiment, RS domain phosphorylation was also determined to be necessary for trans splicing to proceed on a substrate that had U2 snRNP already bound. This newly identified role for phosphorylated SR proteins post-U2-snRNP addition coincides with the recruitment of the 5′; splice site contained on the SL RNP, suggesting a role for SR proteins in splice site communication in trans splicing.


1988 ◽  
Vol 8 (9) ◽  
pp. 3582-3590 ◽  
Author(s):  
X Y Fu ◽  
J D Colgan ◽  
J L Manley

We have determined the effects of a number of mutations in the small-t antigen mRNA intron on the alternative splicing pattern of the simian virus 40 early transcript. Expansion of the distance separating the small-t pre-mRNA lariat branch point and the shared large T-small t 3' splice site from 18 to 29 nucleotides (nt) resulted in a relative enhancement of small-t splicing in vivo. This finding, coupled with the observation that large-T pre-RNA splicing in vitro was not affected by this expansion, suggests that small-t splicing is specifically constrained by a short branch point-3' splice site distance. Similarly, the distance separating the 5' splice site and branch point (48 nt) was found to be at or near a minimum for small-t splicing, because deletions in this region as small as 2 nt dramatically reduced the ratio of small-t to large-T mRNA that accumulated in transfected cells. Finally, a specific sequence within the small-t intron, encompassing the upstream branch sites used in large-T splicing, was found to be an important element in the cell-specific pattern of early alternative splicing. Substitutions within this region reduced the ratio of small-t to large-T mRNA produced in HeLa cells but had only minor effects in human 293 cells.


2000 ◽  
Vol 20 (24) ◽  
pp. 9225-9235 ◽  
Author(s):  
Andrew J. McCullough ◽  
Susan M. Berget

ABSTRACT Intronic G triplets are frequently located adjacent to 5′ splice sites in vertebrate pre-mRNAs and have been correlated with splicing efficiency and specificity via a mechanism that activates upstream 5′ splice sites in exons containing duplicated sites (26). Using an intron dependent upon G triplets for maximal activity and 5′ splice site specificity, we determined that these elements bind U1 snRNPs via base pairing with U1 RNA. This interaction is novel in that it uses nucleotides 8 to 10 of U1 RNA and is independent of nucleotides 1 to 7. In vivo functionality of base pairing was documented by restoring activity and specificity to mutated G triplets through compensating U1 RNA mutations. We suggest that the G-rich region near vertebrate 5′ splice sites promotes accurate splice site recognition by recruiting the U1 snRNP.


2000 ◽  
Vol 20 (17) ◽  
pp. 6414-6425 ◽  
Author(s):  
Hanzhen Sun ◽  
Lawrence A. Chasin

ABSTRACT Splice site consensus sequences alone are insufficient to dictate the recognition of real constitutive splice sites within the typically large transcripts of higher eukaryotes, and large numbers of pseudoexons flanked by pseudosplice sites with good matches to the consensus sequences can be easily designated. In an attempt to identify elements that prevent pseudoexon splicing, we have systematically altered known splicing signals, as well as immediately adjacent flanking sequences, of an arbitrarily chosen pseudoexon from intron 1 of the human hprt gene. The substitution of a 5′ splice site that perfectly matches the 5′ consensus combined with mutation to match the CAG/G sequence of the 3′ consensus failed to get this model pseudoexon included as the central exon in a dhfr minigene context. Provision of a real 3′ splice site and a consensus 5′ splice site and removal of an upstream inhibitory sequence were necessary and sufficient to confer splicing on the pseudoexon. This activated context also supported the splicing of a second pseudoexon sequence containing no apparent enhancer. Thus, both the 5′ splice site sequence and the polypyrimidine tract of the pseudoexon are defective despite their good agreement with the consensus. On the other hand, the pseudoexon body did not exert a negative influence on splicing. The introduction into the pseudoexon of a sequence selected for binding to ASF/SF2 or its replacement with β-globin exon 2 only partially reversed the effect of the upstream negative element and the defective polypyrimidine tract. These results support the idea that exon-bridging enhancers are not a prerequisite for constitutive exon definition and suggest that intrinsically defective splice sites and negative elements play important roles in distinguishing the real splicing signal from the vast number of false splicing signals.


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