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Identifying and characterising key alternative splicing events in Drosophila development.

Lees JG, Ranea JA, Orengo CA - BMC Genomics (2015)

Bottom Line: We have identified a subset of protein isoforms which appear to have high functional significance, particularly in regulation.The methods and analyses we present here represent important first steps in the development of tools to address the near complete lack of isoform specific function annotation.In turn the tools allow us to better characterise the regulatory functions of alternative splicing in more detail.

View Article: PubMed Central - PubMed

Affiliation: Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, UK. ucbcjle@live.ucl.ac.uk.

ABSTRACT

Background: In complex Metazoans a given gene frequently codes for multiple protein isoforms, through processes such as alternative splicing. Large scale functional annotation of these isoforms is a key challenge for functional genomics. This annotation gap is increasing with the large numbers of multi transcript genes being identified by technologies such as RNASeq. Furthermore attempts to characterise the functions of splicing in an organism are complicated by the difficulty in distinguishing functional isoforms from those produced by splicing errors or transcription noise. Tools to help prioritise candidate isoforms for testing are largely absent.

Results: In this study we implement a Time-course Switch (TS) score for ranking isoforms by their likelihood of producing additional functions based on their developmental expression profiles, as reported by modENCODE. The TS score allows us to better investigate functional roles of different isoforms expressed in multi transcript genes. From this analysis, we find that isoforms with high TS scores have sequence feature changes consistent with more deterministic splicing and functional changes and tend to gain domains or whole exons which could carry additional functions. Furthermore these functions appear to be particularly important for essential regulatory roles, establishing functional isoform switching as key for regulatory processes. Based on the TS score we develop a Transcript Annotations Pipeline for Alternative Splicing (TAPAS) that identifies functional neighbourhoods of potentially interesting isoforms.

Conclusions: We have identified a subset of protein isoforms which appear to have high functional significance, particularly in regulation. This has been made possible through the development of novel methods that make use of transcript expression profiles. The methods and analyses we present here represent important first steps in the development of tools to address the near complete lack of isoform specific function annotation. In turn the tools allow us to better characterise the regulatory functions of alternative splicing in more detail.

No MeSH data available.


TS scores for different splicing events. TS score distribution of retained intron and exon gain events for real (blue bars), and randomised (grey bars) data. The randomised scores were generated by randomly permuting the TS scores between genes. The box extends from the lower to upper quartile values of the data, with a line at the median. All values more than 1.5 IQR lower than the first quartile or 1.5 IQR higher than the third quartile are excluded as outliers for visualization purposes. The smallest and highest values that are not outliers are connected with a line. The notches correspond to 95 % confidence interval for the median
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Fig2: TS scores for different splicing events. TS score distribution of retained intron and exon gain events for real (blue bars), and randomised (grey bars) data. The randomised scores were generated by randomly permuting the TS scores between genes. The box extends from the lower to upper quartile values of the data, with a line at the median. All values more than 1.5 IQR lower than the first quartile or 1.5 IQR higher than the third quartile are excluded as outliers for visualization purposes. The smallest and highest values that are not outliers are connected with a line. The notches correspond to 95 % confidence interval for the median

Mentions: The gain of exons is known to potentially alter the precise functioning of a protein isoform by changing its interaction partners if certain sequence features are present [24]. Conversely, in the literature Intron retention (IR) is more often perceived as an aberrant, mis-splicing event compared to whole exon gain or loss [25]. For this reason we decided to assess IR events in relation to the TS score to see if we could see any differences from the background rate. We find that exon gains and intron retentions have significantly higher and lower TS scores respectively than expected by chance (Fig. 2), both with Mann–Whitney p-values <0.001. This feature was also observed if only evolutionarily conserved isoform specific exons were considered (see methods). This observation is important since, evolutionary conserved exons are more likely to be functional than those with low evolutionary conservation. Evolutionary conserved exons were detected using the Conservation Index score [26] (Table 2) which measures the evolutionary distance at which an exon is both genomically conserved and shows signs of expression.Fig. 2


Identifying and characterising key alternative splicing events in Drosophila development.

Lees JG, Ranea JA, Orengo CA - BMC Genomics (2015)

TS scores for different splicing events. TS score distribution of retained intron and exon gain events for real (blue bars), and randomised (grey bars) data. The randomised scores were generated by randomly permuting the TS scores between genes. The box extends from the lower to upper quartile values of the data, with a line at the median. All values more than 1.5 IQR lower than the first quartile or 1.5 IQR higher than the third quartile are excluded as outliers for visualization purposes. The smallest and highest values that are not outliers are connected with a line. The notches correspond to 95 % confidence interval for the median
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4537583&req=5

Fig2: TS scores for different splicing events. TS score distribution of retained intron and exon gain events for real (blue bars), and randomised (grey bars) data. The randomised scores were generated by randomly permuting the TS scores between genes. The box extends from the lower to upper quartile values of the data, with a line at the median. All values more than 1.5 IQR lower than the first quartile or 1.5 IQR higher than the third quartile are excluded as outliers for visualization purposes. The smallest and highest values that are not outliers are connected with a line. The notches correspond to 95 % confidence interval for the median
Mentions: The gain of exons is known to potentially alter the precise functioning of a protein isoform by changing its interaction partners if certain sequence features are present [24]. Conversely, in the literature Intron retention (IR) is more often perceived as an aberrant, mis-splicing event compared to whole exon gain or loss [25]. For this reason we decided to assess IR events in relation to the TS score to see if we could see any differences from the background rate. We find that exon gains and intron retentions have significantly higher and lower TS scores respectively than expected by chance (Fig. 2), both with Mann–Whitney p-values <0.001. This feature was also observed if only evolutionarily conserved isoform specific exons were considered (see methods). This observation is important since, evolutionary conserved exons are more likely to be functional than those with low evolutionary conservation. Evolutionary conserved exons were detected using the Conservation Index score [26] (Table 2) which measures the evolutionary distance at which an exon is both genomically conserved and shows signs of expression.Fig. 2

Bottom Line: We have identified a subset of protein isoforms which appear to have high functional significance, particularly in regulation.The methods and analyses we present here represent important first steps in the development of tools to address the near complete lack of isoform specific function annotation.In turn the tools allow us to better characterise the regulatory functions of alternative splicing in more detail.

View Article: PubMed Central - PubMed

Affiliation: Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, UK. ucbcjle@live.ucl.ac.uk.

ABSTRACT

Background: In complex Metazoans a given gene frequently codes for multiple protein isoforms, through processes such as alternative splicing. Large scale functional annotation of these isoforms is a key challenge for functional genomics. This annotation gap is increasing with the large numbers of multi transcript genes being identified by technologies such as RNASeq. Furthermore attempts to characterise the functions of splicing in an organism are complicated by the difficulty in distinguishing functional isoforms from those produced by splicing errors or transcription noise. Tools to help prioritise candidate isoforms for testing are largely absent.

Results: In this study we implement a Time-course Switch (TS) score for ranking isoforms by their likelihood of producing additional functions based on their developmental expression profiles, as reported by modENCODE. The TS score allows us to better investigate functional roles of different isoforms expressed in multi transcript genes. From this analysis, we find that isoforms with high TS scores have sequence feature changes consistent with more deterministic splicing and functional changes and tend to gain domains or whole exons which could carry additional functions. Furthermore these functions appear to be particularly important for essential regulatory roles, establishing functional isoform switching as key for regulatory processes. Based on the TS score we develop a Transcript Annotations Pipeline for Alternative Splicing (TAPAS) that identifies functional neighbourhoods of potentially interesting isoforms.

Conclusions: We have identified a subset of protein isoforms which appear to have high functional significance, particularly in regulation. This has been made possible through the development of novel methods that make use of transcript expression profiles. The methods and analyses we present here represent important first steps in the development of tools to address the near complete lack of isoform specific function annotation. In turn the tools allow us to better characterise the regulatory functions of alternative splicing in more detail.

No MeSH data available.