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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.


Example enriched function of High-TS Genes. Interactions between High-TS Genes annotated with the GO term “direct ligand regulated sequence-specific DNA binding transcription factor activity” (golden nodes). Predicted functionally related genes (predicted using Fun-L [43], see methods) are shown as blue nodes to help provide a more connected network
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Fig4: Example enriched function of High-TS Genes. Interactions between High-TS Genes annotated with the GO term “direct ligand regulated sequence-specific DNA binding transcription factor activity” (golden nodes). Predicted functionally related genes (predicted using Fun-L [43], see methods) are shown as blue nodes to help provide a more connected network

Mentions: Because of the lack of specific terms produced by this, we ran a second approach using Fisher’s exact test to look for GO terms enriched in the High-TS Genes compared to the multi protein genes as the background set. The most significantly enriched GO term for High-TS Genes was for “direct ligand regulated sequence-specific DNA binding transcription factor activity” (corrected p-value = 0.025). A narrow synonym given for this GO term in the QuickGo website is “nuclear hormone receptor”. We could see that this set includes many different nuclear hormone receptors that on ligand activation act as on-off switches for the genes they regulate when bound to DNA in a sequence specific manner (Fig. 4).Fig. 4


Identifying and characterising key alternative splicing events in Drosophila development.

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

Example enriched function of High-TS Genes. Interactions between High-TS Genes annotated with the GO term “direct ligand regulated sequence-specific DNA binding transcription factor activity” (golden nodes). Predicted functionally related genes (predicted using Fun-L [43], see methods) are shown as blue nodes to help provide a more connected network
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig4: Example enriched function of High-TS Genes. Interactions between High-TS Genes annotated with the GO term “direct ligand regulated sequence-specific DNA binding transcription factor activity” (golden nodes). Predicted functionally related genes (predicted using Fun-L [43], see methods) are shown as blue nodes to help provide a more connected network
Mentions: Because of the lack of specific terms produced by this, we ran a second approach using Fisher’s exact test to look for GO terms enriched in the High-TS Genes compared to the multi protein genes as the background set. The most significantly enriched GO term for High-TS Genes was for “direct ligand regulated sequence-specific DNA binding transcription factor activity” (corrected p-value = 0.025). A narrow synonym given for this GO term in the QuickGo website is “nuclear hormone receptor”. We could see that this set includes many different nuclear hormone receptors that on ligand activation act as on-off switches for the genes they regulate when bound to DNA in a sequence specific manner (Fig. 4).Fig. 4

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.