Limits...
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.


Related in: MedlinePlus

Predicted isoform gene neighbourhoods from TAPAS. a Output from the TAPAS algorithm for all minor isoforms from High-TS Genes. Only functional links between query isoforms (orange boxes) and co-expressed non query transcripts from different genes (grey boxes) identified by TAPAS are shown. Only links with a GOSS cut-off of > 6.0, a string score of >800 or an experimentally determined protein interaction (blue links) are shown. b The box shows a zoom in on two query isoforms scrb-PB and sdt-PE and their predicted functionally associated neighbours
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig7: Predicted isoform gene neighbourhoods from TAPAS. a Output from the TAPAS algorithm for all minor isoforms from High-TS Genes. Only functional links between query isoforms (orange boxes) and co-expressed non query transcripts from different genes (grey boxes) identified by TAPAS are shown. Only links with a GOSS cut-off of > 6.0, a string score of >800 or an experimentally determined protein interaction (blue links) are shown. b The box shows a zoom in on two query isoforms scrb-PB and sdt-PE and their predicted functionally associated neighbours

Mentions: Running the TAPAS algorithm on minor isoforms having a TS score >0.5 enables us to generate a reasonably large network of associations between isoforms from different genes (see Fig. 7). We can zoom in on a query isoform in this network, scrb-PB (Fig. 7b). This isoform is identified by TAPAS as having a similar expression pattern and functional associations with isoforms from other genes involved in processes such as adherens junction and zonular adherens assembly. The main expression peak for scrb-PB is from 2–8 hours covering developmental events such as cellularisation and gastrulation, where adherens junction and zonula adherens assembly is known to be important [45]. The primary isoform of scrb-PB is not identified as belonging to the same functional neighbourhood since it has a distinct expression profile. This allows us to infer that scrb-PB is more likely than its primary isoform to operate with these specific co-expressed partners (Fig. 7b) in adherens junction and zonula adherens assembly in early embryogenesis.Fig. 7


Identifying and characterising key alternative splicing events in Drosophila development.

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

Predicted isoform gene neighbourhoods from TAPAS. a Output from the TAPAS algorithm for all minor isoforms from High-TS Genes. Only functional links between query isoforms (orange boxes) and co-expressed non query transcripts from different genes (grey boxes) identified by TAPAS are shown. Only links with a GOSS cut-off of > 6.0, a string score of >800 or an experimentally determined protein interaction (blue links) are shown. b The box shows a zoom in on two query isoforms scrb-PB and sdt-PE and their predicted functionally associated neighbours
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig7: Predicted isoform gene neighbourhoods from TAPAS. a Output from the TAPAS algorithm for all minor isoforms from High-TS Genes. Only functional links between query isoforms (orange boxes) and co-expressed non query transcripts from different genes (grey boxes) identified by TAPAS are shown. Only links with a GOSS cut-off of > 6.0, a string score of >800 or an experimentally determined protein interaction (blue links) are shown. b The box shows a zoom in on two query isoforms scrb-PB and sdt-PE and their predicted functionally associated neighbours
Mentions: Running the TAPAS algorithm on minor isoforms having a TS score >0.5 enables us to generate a reasonably large network of associations between isoforms from different genes (see Fig. 7). We can zoom in on a query isoform in this network, scrb-PB (Fig. 7b). This isoform is identified by TAPAS as having a similar expression pattern and functional associations with isoforms from other genes involved in processes such as adherens junction and zonular adherens assembly. The main expression peak for scrb-PB is from 2–8 hours covering developmental events such as cellularisation and gastrulation, where adherens junction and zonula adherens assembly is known to be important [45]. The primary isoform of scrb-PB is not identified as belonging to the same functional neighbourhood since it has a distinct expression profile. This allows us to infer that scrb-PB is more likely than its primary isoform to operate with these specific co-expressed partners (Fig. 7b) in adherens junction and zonula adherens assembly in early embryogenesis.Fig. 7

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.


Related in: MedlinePlus