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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.


Other characteristics of High-TS Genes. Proportions of High-TS Genes, labelled ‘TS’, and all other multi-protein genes, labelled ‘Other’, which are essential, contain transcription factors domains or classical signalling domains (see methods). Lines and values connecting bars indicate Fisher’s exact test enrichment significance
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Fig5: Other characteristics of High-TS Genes. Proportions of High-TS Genes, labelled ‘TS’, and all other multi-protein genes, labelled ‘Other’, which are essential, contain transcription factors domains or classical signalling domains (see methods). Lines and values connecting bars indicate Fisher’s exact test enrichment significance

Mentions: We can also use protein domain assignments in a different way to that used previously. In earlier sections we used the domains to establish specific changes between isoforms, whilst here we can use all the domain assignments of a gene to show the genes overall general function. For certain domain types such as sequence specific DNA binding domains, the functions they carry out can be assigned with high confidence (DBD [38]). When we performed functional assignments to genes in this way, using the DBD [38], we found that there was a significant enrichment in transcription factor/sequence specific DNA binding domains for the High-TS Genes relative to other multi protein genes (Fig. 5). We also found enrichment for proteins containing domains involved in signalling [39].Fig. 5


Identifying and characterising key alternative splicing events in Drosophila development.

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

Other characteristics of High-TS Genes. Proportions of High-TS Genes, labelled ‘TS’, and all other multi-protein genes, labelled ‘Other’, which are essential, contain transcription factors domains or classical signalling domains (see methods). Lines and values connecting bars indicate Fisher’s exact test enrichment significance
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig5: Other characteristics of High-TS Genes. Proportions of High-TS Genes, labelled ‘TS’, and all other multi-protein genes, labelled ‘Other’, which are essential, contain transcription factors domains or classical signalling domains (see methods). Lines and values connecting bars indicate Fisher’s exact test enrichment significance
Mentions: We can also use protein domain assignments in a different way to that used previously. In earlier sections we used the domains to establish specific changes between isoforms, whilst here we can use all the domain assignments of a gene to show the genes overall general function. For certain domain types such as sequence specific DNA binding domains, the functions they carry out can be assigned with high confidence (DBD [38]). When we performed functional assignments to genes in this way, using the DBD [38], we found that there was a significant enrichment in transcription factor/sequence specific DNA binding domains for the High-TS Genes relative to other multi protein genes (Fig. 5). We also found enrichment for proteins containing domains involved in signalling [39].Fig. 5

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.