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Genome-wide association between branch point properties and alternative splicing.

Corvelo A, Hallegger M, Smith CW, Eyras E - PLoS Comput. Biol. (2010)

Bottom Line: Finally, the comparison between exons of different evolutionary ages and pseudo exons suggests a key role of the BP in the pathway of exon creation in human.Our computational and experimental analyses suggest that BP recognition is more flexible than previously assumed, and it appears highly dependent on the presence of downstream polypyrimidine tracts.The reported association between BP features and the splicing outcome suggests that this, so far disregarded but yet crucial, element buries information that can complement current acceptor site models.

View Article: PubMed Central - PubMed

Affiliation: Computational Genomics, Universitat Pompeu Fabra, Barcelona, Spain.

ABSTRACT
The branch point (BP) is one of the three obligatory signals required for pre-mRNA splicing. In mammals, the degeneracy of the motif combined with the lack of a large set of experimentally verified BPs complicates the task of modeling it in silico, and therefore of predicting the location of natural BPs. Consequently, BPs have been disregarded in a considerable fraction of the genome-wide studies on the regulation of splicing in mammals. We present a new computational approach for mammalian BP prediction. Using sequence conservation and positional bias we obtained a set of motifs with good agreement with U2 snRNA binding stability. Using a Support Vector Machine algorithm, we created a model complemented with polypyrimidine tract features, which considerably improves the prediction accuracy over previously published methods. Applying our algorithm to human introns, we show that BP position is highly dependent on the presence of AG dinucleotides in the 3' end of introns, with distance to the 3' splice site and BP strength strongly correlating with alternative splicing. Furthermore, experimental BP mapping for five exons preceded by long AG-dinucleotide exclusion zones revealed that, for a given intron, more than one BP can be chosen throughout the course of splicing. Finally, the comparison between exons of different evolutionary ages and pseudo exons suggests a key role of the BP in the pathway of exon creation in human. Our computational and experimental analyses suggest that BP recognition is more flexible than previously assumed, and it appears highly dependent on the presence of downstream polypyrimidine tracts. The reported association between BP features and the splicing outcome suggests that this, so far disregarded but yet crucial, element buries information that can complement current acceptor site models.

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BP features and exon age.A – Mean SVM score for BPs preceding pseudo exons, primate specific exons and mammalian-conserved exons. B – BP features for the same three exon groups: sequence score (top left), pyrimidine content between BP and 3SS (top right), downstream PPT score (bottom left) and distance to the downstream PPT (bottom right). C – BP-3SS distance for exons in the three above mentioned categories.
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pcbi-1001016-g008: BP features and exon age.A – Mean SVM score for BPs preceding pseudo exons, primate specific exons and mammalian-conserved exons. B – BP features for the same three exon groups: sequence score (top left), pyrimidine content between BP and 3SS (top right), downstream PPT score (bottom left) and distance to the downstream PPT (bottom right). C – BP-3SS distance for exons in the three above mentioned categories.

Mentions: Recent studies have reported a strong relation between exon age and AS [18], [35], [36]. It has been suggested that the low inclusion observed for young exons is due to weaker splicing signals in general [18]. In order to investigate whether BP features are also related to the differences observed between exons with different evolutionary age, we predicted BPs in three exon sets: primate specific (PS) exons; mammalian conserved (MC) exons; and, as control, a set of pseudo exons, which have no inclusion evidence. In Figure 8A we show that BPs preceding real exons have in average higher SVM scores than those preceding pseudo exons (Mann-Whitney, p≈0). This difference is even greater when comparing to BP candidates preceding random AG dinucleotides (Figures 12B, 12C in Text S1), since pseudo exons are preceded by a PPT signal, contributing to a higher BP SVM score (see [18] for details on the pseudo exon set construction). Interestingly, BP preceding PS exons, which have low inclusion, have intermediate values between pseudo exons (Mann-Whitney, p = 6.18×10−5) and MC exons (Mann-Whitney, p = 0.022). As we show in Figure 8B, these differences are mainly explained by differences in sequence score (Mann-Whitney, pseudo vs. PS p = 7.58×10−5; PS vs. MC p = 0.039). Regarding intronic position, BPs preceding pseudo exons tend to be located closer to the 3SS compared to real exons (Mann-Whitney, p≈0). BPs preceding real exons show a distribution peak between positions 20 to 25 nts upstream of the 3SS, whereas in pseudo exons this peak is located at the smallest distance considered (15 nts). Finally, no differences were found between PS and MC exons (Figure 8C) regarding BP-3SS distance. This feature strongly correlates with AGEZ length, which does not differ significantly between sets (data not shown).


Genome-wide association between branch point properties and alternative splicing.

Corvelo A, Hallegger M, Smith CW, Eyras E - PLoS Comput. Biol. (2010)

BP features and exon age.A – Mean SVM score for BPs preceding pseudo exons, primate specific exons and mammalian-conserved exons. B – BP features for the same three exon groups: sequence score (top left), pyrimidine content between BP and 3SS (top right), downstream PPT score (bottom left) and distance to the downstream PPT (bottom right). C – BP-3SS distance for exons in the three above mentioned categories.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2991248&req=5

pcbi-1001016-g008: BP features and exon age.A – Mean SVM score for BPs preceding pseudo exons, primate specific exons and mammalian-conserved exons. B – BP features for the same three exon groups: sequence score (top left), pyrimidine content between BP and 3SS (top right), downstream PPT score (bottom left) and distance to the downstream PPT (bottom right). C – BP-3SS distance for exons in the three above mentioned categories.
Mentions: Recent studies have reported a strong relation between exon age and AS [18], [35], [36]. It has been suggested that the low inclusion observed for young exons is due to weaker splicing signals in general [18]. In order to investigate whether BP features are also related to the differences observed between exons with different evolutionary age, we predicted BPs in three exon sets: primate specific (PS) exons; mammalian conserved (MC) exons; and, as control, a set of pseudo exons, which have no inclusion evidence. In Figure 8A we show that BPs preceding real exons have in average higher SVM scores than those preceding pseudo exons (Mann-Whitney, p≈0). This difference is even greater when comparing to BP candidates preceding random AG dinucleotides (Figures 12B, 12C in Text S1), since pseudo exons are preceded by a PPT signal, contributing to a higher BP SVM score (see [18] for details on the pseudo exon set construction). Interestingly, BP preceding PS exons, which have low inclusion, have intermediate values between pseudo exons (Mann-Whitney, p = 6.18×10−5) and MC exons (Mann-Whitney, p = 0.022). As we show in Figure 8B, these differences are mainly explained by differences in sequence score (Mann-Whitney, pseudo vs. PS p = 7.58×10−5; PS vs. MC p = 0.039). Regarding intronic position, BPs preceding pseudo exons tend to be located closer to the 3SS compared to real exons (Mann-Whitney, p≈0). BPs preceding real exons show a distribution peak between positions 20 to 25 nts upstream of the 3SS, whereas in pseudo exons this peak is located at the smallest distance considered (15 nts). Finally, no differences were found between PS and MC exons (Figure 8C) regarding BP-3SS distance. This feature strongly correlates with AGEZ length, which does not differ significantly between sets (data not shown).

Bottom Line: Finally, the comparison between exons of different evolutionary ages and pseudo exons suggests a key role of the BP in the pathway of exon creation in human.Our computational and experimental analyses suggest that BP recognition is more flexible than previously assumed, and it appears highly dependent on the presence of downstream polypyrimidine tracts.The reported association between BP features and the splicing outcome suggests that this, so far disregarded but yet crucial, element buries information that can complement current acceptor site models.

View Article: PubMed Central - PubMed

Affiliation: Computational Genomics, Universitat Pompeu Fabra, Barcelona, Spain.

ABSTRACT
The branch point (BP) is one of the three obligatory signals required for pre-mRNA splicing. In mammals, the degeneracy of the motif combined with the lack of a large set of experimentally verified BPs complicates the task of modeling it in silico, and therefore of predicting the location of natural BPs. Consequently, BPs have been disregarded in a considerable fraction of the genome-wide studies on the regulation of splicing in mammals. We present a new computational approach for mammalian BP prediction. Using sequence conservation and positional bias we obtained a set of motifs with good agreement with U2 snRNA binding stability. Using a Support Vector Machine algorithm, we created a model complemented with polypyrimidine tract features, which considerably improves the prediction accuracy over previously published methods. Applying our algorithm to human introns, we show that BP position is highly dependent on the presence of AG dinucleotides in the 3' end of introns, with distance to the 3' splice site and BP strength strongly correlating with alternative splicing. Furthermore, experimental BP mapping for five exons preceded by long AG-dinucleotide exclusion zones revealed that, for a given intron, more than one BP can be chosen throughout the course of splicing. Finally, the comparison between exons of different evolutionary ages and pseudo exons suggests a key role of the BP in the pathway of exon creation in human. Our computational and experimental analyses suggest that BP recognition is more flexible than previously assumed, and it appears highly dependent on the presence of downstream polypyrimidine tracts. The reported association between BP features and the splicing outcome suggests that this, so far disregarded but yet crucial, element buries information that can complement current acceptor site models.

Show MeSH