scholarly journals Post-catalytic spliceosome structure reveals mechanism of 3'-splice site selection

2017 ◽  
Author(s):  
Max E. Wilkinson ◽  
Sebastian M. Fica ◽  
Wojciech P. Galej ◽  
Christine M. Norman ◽  
Andrew J. Newman ◽  
...  
Keyword(s):  
Branch Point ◽  
Splice Site ◽  
Site Selection ◽  
Catalytic Mechanism ◽  
Splice Site Selection ◽  
Terminal Domain ◽  
Exon Ligation ◽  
Site Recognition ◽  
U5 Snrna ◽  
Insight Into

AbstractIntrons are removed from eukaryotic mRNA precursors by the spliceosome in two transesterification reactions – branching and exon ligation. Following branching, the 5'-exon remains paired to U5 snRNA loop 1, but the mechanism of 3'-splice site recognition during exon ligation has remained unclear. Here we present the 3.7Å cryo-EM structure of the yeast P complex spliceosome immediately after exon ligation. The 3'-splice site AG dinucleotide is recognised through non-Watson-Crick pairing with the 5'-splice site and the branch point adenosine. A conserved loop of Prp18 together with the α-finger and the RNaseH domain of Prp8 clamp the docked 3'-splice site and 3'-exon. The step 2 factors Prp18 and Slu7 and the C-terminal domain of Yju2 stabilise a conformation competent for 3'-splice site docking and exon ligation. The structure accounts for the strict conservation of the GU and AG dinucleotides of the introns and provides insight into the catalytic mechanism of exon ligation.

scholarly journals Recurrent Spliceosome Mutations in Cancer: Mechanisms and Consequences of Aberrant Splice Site Selection

Cancers ◽  
2022 ◽  
Vol 14 (2) ◽  
pp. 281
Author(s):  
Carlos A. Niño ◽  
Rossella Scotto di Perrotolo ◽  
Simona Polo
Keyword(s):  
Splice Site ◽  
Site Selection ◽  
Aberrant Splice ◽  
Splice Site Selection ◽  
Exon Ligation ◽  
Complex Process ◽  
U1 Snrna ◽  
Intron Removal ◽  
Tumor Types ◽  
Site Recognition

Splicing alterations have been widely documented in tumors where the proliferation and dissemination of cancer cells is supported by the expression of aberrant isoform variants. Splicing is catalyzed by the spliceosome, a ribonucleoprotein complex that orchestrates the complex process of intron removal and exon ligation. In recent years, recurrent hotspot mutations in the spliceosome components U1 snRNA, SF3B1, and U2AF1 have been identified across different tumor types. Such mutations in principle are highly detrimental for cells as all three spliceosome components are crucial for accurate splice site selection: the U1 snRNA is essential for 3′ splice site recognition, and SF3B1 and U2AF1 are important for 5′ splice site selection. Nonetheless, they appear to be selected to promote specific types of cancers. Here, we review the current molecular understanding of these mutations in cancer, focusing on how they influence splice site selection and impact on cancer development.

scholarly journals Scanning and competition between AGs are involved in 3' splice site selection in mammalian introns.

1993 ◽  
Vol 13 (8) ◽  
pp. 4939-4952 ◽  
Author(s):  
C W Smith ◽  
T T Chu ◽  
B Nadal-Ginard
Keyword(s):  
Branch Point ◽  
Splice Site ◽  
Site Selection ◽  
Wild Type ◽  
Splice Site Selection ◽  
Sequence Context ◽  
Scanning Process ◽  
Close Proximity ◽  
Type 3 ◽  
Scanning Mechanism

In mammalian intron splicing, the mechanism by which the 3' splice site AG is accurately and efficiently identified has remained unresolved. We have previously proposed that the 3' splice site in mammalian introns is located by a scanning mechanism for the first AG downstream of the branch point-polypyrimidine tract. We now present experiments that lend further support to this model while identifying conditions under which competition can occur between adjacent AGs. The data show that the 3' splice site is identified as the first AG downstream from the branch point by a mechanism that has all the characteristics expected of a 5'-to-3' scanning process that starts from the branch point rather than the pyrimidine tract. Failure to recognize the proximal AG may arise, however, from extreme proximity to the branch point or sequestration within a hairpin. Once an AG has been encountered, the spliceosome can still see a limited stretch of downstream RNA within which an AG more competitive than the proximal one may be selected. Proximity to the branch point is a major determinant of competition, although steric effects render an AG less competitive in close proximity (approximately 12 nucleotides). In addition, the nucleotide preceding the AG has a striking influence upon competition between closely spaced AGs. The order of competitiveness, CAG congruent to UAG > AAG > GAG, is similar to the nucleotide preference at this position in wild-type 3' splice sites. Thus, 3' splice site selection displays properties of both a scanning process and competition between AGs based on immediate sequence context. This refined scanning model, incorporating elements of competition, is the simplest interpretation that is consistent with all of the available data.

scholarly journals Wobble Splicing Reveals the Role of the Branch Point Sequence-to-NAGNAG Region in 3′ Tandem Splice Site Selection

2007 ◽  
Vol 27 (16) ◽  
pp. 5835-5848 ◽  
Author(s):  
Kuo-Wang Tsai ◽  
Woan-Yuh Tarn ◽  
Wen-chang Lin
Keyword(s):  
Branch Point ◽  
Splice Site ◽  
Site Selection ◽  
Protein Function ◽  
Upstream Region ◽  
Nucleotide Polymorphisms ◽  
Splice Site Selection ◽  
Independent Manner ◽  
Branch Point Sequence

ABSTRACT Alternative splicing involving the 3′ tandem splice site NAGNAG sequence may play a role in the structure-function diversity of proteins. However, how 3′ tandem splice site utilization is determined is not well understood. We previously demonstrated that 3′ NAGNAG-based wobble splicing occurs mostly in a tissue- and developmental stage-independent manner. Bioinformatic analysis reveals that the nucleotide preceding the AG dinucleotide may influence 3′ splice site utilization; this is also supported by an in vivo splicing assay. Moreover, we found that the intron sequence plays an important role in 3′ splice site selection for NAGNAG wobble splicing. Mutations of the region between the branch site and the NAGNAG 3′ splice site, indeed, affected the ratio of the distal/proximal AG selection. Finally, we found that single nucleotide polymorphisms around the NAGNAG motif could affect the splice site choice, which may lead to a change in mRNA patterns and influence protein function. We conclude that the NAGNAG motif and its upstream region to the branch point sequence are required for 3′ tandem splice site selection.

Scanning and competition between AGs are involved in 3' splice site selection in mammalian introns

1993 ◽  
Vol 13 (8) ◽  
pp. 4939-4952
Author(s):  
C W Smith ◽  
T T Chu ◽  
B Nadal-Ginard
Keyword(s):  
Branch Point ◽  
Splice Site ◽  
Site Selection ◽  
Wild Type ◽  
Splice Site Selection ◽  
Sequence Context ◽  
Scanning Process ◽  
Close Proximity ◽  
Type 3 ◽  
Scanning Mechanism

In mammalian intron splicing, the mechanism by which the 3' splice site AG is accurately and efficiently identified has remained unresolved. We have previously proposed that the 3' splice site in mammalian introns is located by a scanning mechanism for the first AG downstream of the branch point-polypyrimidine tract. We now present experiments that lend further support to this model while identifying conditions under which competition can occur between adjacent AGs. The data show that the 3' splice site is identified as the first AG downstream from the branch point by a mechanism that has all the characteristics expected of a 5'-to-3' scanning process that starts from the branch point rather than the pyrimidine tract. Failure to recognize the proximal AG may arise, however, from extreme proximity to the branch point or sequestration within a hairpin. Once an AG has been encountered, the spliceosome can still see a limited stretch of downstream RNA within which an AG more competitive than the proximal one may be selected. Proximity to the branch point is a major determinant of competition, although steric effects render an AG less competitive in close proximity (approximately 12 nucleotides). In addition, the nucleotide preceding the AG has a striking influence upon competition between closely spaced AGs. The order of competitiveness, CAG congruent to UAG > AAG > GAG, is similar to the nucleotide preference at this position in wild-type 3' splice sites. Thus, 3' splice site selection displays properties of both a scanning process and competition between AGs based on immediate sequence context. This refined scanning model, incorporating elements of competition, is the simplest interpretation that is consistent with all of the available data.

scholarly journals Cancer-Associated SF3B1 Hotspot Mutations Induce Cryptic 3′ Splice Site Selection through Use of a Different Branch Point

Cell Reports ◽  
2015 ◽  
Vol 13 (5) ◽  
pp. 1033-1045 ◽  
Author(s):  
Rachel B. Darman ◽  
Michael Seiler ◽  
Anant A. Agrawal ◽  
Kian H. Lim ◽  
Shouyong Peng ◽  
...  
Keyword(s):  
Branch Point ◽  
Splice Site ◽  
Site Selection ◽  
Splice Site Selection ◽  
Hotspot Mutations

scholarly journals The anti-angiogenic isoforms of VEGF in health and disease

2009 ◽  
Vol 37 (6) ◽  
pp. 1207-1213 ◽  
Author(s):  
Yan Qiu ◽  
Coralie Hoareau-Aveilla ◽  
Sebastian Oltean ◽  
Steven J. Harper ◽  
David O. Bates
Keyword(s):  
Splice Site ◽  
Site Selection ◽  
Age Related Macular Degeneration ◽  
Splicing Factor ◽  
Splice Site Selection ◽  
Age Related ◽  
Normal Human ◽  
Radical Revision

Anti-angiogenic VEGF (vascular endothelial growth factor) isoforms, generated from differential splicing of exon 8, are widely expressed in normal human tissues but down-regulated in cancers and other pathologies associated with abnormal angiogenesis (cancer, diabetic retinopathy, retinal vein occlusion, the Denys–Drash syndrome and pre-eclampsia). Administration of recombinant VEGF165b inhibits ocular angiogenesis in mouse models of retinopathy and age-related macular degeneration, and colorectal carcinoma and metastatic melanoma. Splicing factors and their regulatory molecules alter splice site selection, such that cells can switch from the anti-angiogenic VEGFxxxb isoforms to the pro-angiogenic VEGFxxx isoforms, including SRp55 (serine/arginine protein 55), ASF/SF2 (alternative splicing factor/splicing factor 2) and SRPK (serine arginine domain protein kinase), and inhibitors of these molecules can inhibit angiogenesis in the eye, and splice site selection in cancer cells, opening up the possibility of using splicing factor inhibitors as novel anti-angiogenic therapeutics. Endogenous anti-angiogenic VEGFxxxb isoforms are cytoprotective for endothelial, epithelial and neuronal cells in vitro and in vivo, suggesting both an improved safety profile and an explanation for unpredicted anti-VEGF side effects. In summary, C-terminal distal splicing is a key component of VEGF biology, overlooked by the vast majority of publications in the field, and these findings require a radical revision of our understanding of VEGF biology in normal human physiology.

Are vertebrate exons scanned during splice-site selection?

Nature ◽  
1992 ◽  
Vol 360 (6401) ◽  
pp. 277-280 ◽  
Author(s):  
Maho Niwa ◽  
Clinton C. MacDonald ◽  
Susan M. Berget
Keyword(s):  
Splice Site ◽  
Site Selection ◽  
Splice Site Selection
Sign in / Sign up

Export Citation Format

Share Document