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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.


Related in: MedlinePlus

TS score explanation. a Hypothetical examples of time course transcript expression profiles from a gene to illustrate the concept of the TS score. The primary transcript is shown in blue. Minor transcripts are shown in other colours. The red line would have a high TS score since it has reasonably high expression relative to the primary transcript but with a different shape. The green transcript would have a Low TS score since although it has high general expression it has the same shape as the primary transcript. The purple transcript would have a low TS score since although it has a different shape it has low expression relative to the primary transcript. b, Example of a secondary isoform taken from the ‘sdt’ gene with a high TS score when compared to the primary isoform. The legend IDs between brackets are FlyBase transcript ID’s. Along the x-axis the first 24 hours correspond to embryogenesis stages; time points labelled ‘L’ correspond to subsequent Larval developmental stages; WPP indicates the white prepupae and,‘P’ indicates pupal stage, ‘F’ and ‘M’ are for female and male adult stages respectively (see Additional file 1: Figure S1 for an example of a gene with a low TS score)
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Fig1: TS score explanation. a Hypothetical examples of time course transcript expression profiles from a gene to illustrate the concept of the TS score. The primary transcript is shown in blue. Minor transcripts are shown in other colours. The red line would have a high TS score since it has reasonably high expression relative to the primary transcript but with a different shape. The green transcript would have a Low TS score since although it has high general expression it has the same shape as the primary transcript. The purple transcript would have a low TS score since although it has a different shape it has low expression relative to the primary transcript. b, Example of a secondary isoform taken from the ‘sdt’ gene with a high TS score when compared to the primary isoform. The legend IDs between brackets are FlyBase transcript ID’s. Along the x-axis the first 24 hours correspond to embryogenesis stages; time points labelled ‘L’ correspond to subsequent Larval developmental stages; WPP indicates the white prepupae and,‘P’ indicates pupal stage, ‘F’ and ‘M’ are for female and male adult stages respectively (see Additional file 1: Figure S1 for an example of a gene with a low TS score)

Mentions: In this article we develop tools for bridging this gap and allowing more detailed functional analysis of splicing. We develop a pipeline that identifies alternative splice variants with significantly different expression profiles. Here we make use of isoform expression profiles over a developmental time series in D.melanogaster [22] to identify alternative protein isoforms that have expression profiles indicative of function. The idea of gene expression divergence corresponding to functional divergence is often found in the literature (for example [23]), and in this study we adapt these ideas for comparing intra gene expression profiles rather than inter gene. The score we developed for this we name the Time-course Switch (TS) score (see Eq. 1 and Fig. 1a) which takes into account both the magnitude and expression profile differences between primary and minor transcript expression profiles in its calculation.Fig. 1


Identifying and characterising key alternative splicing events in Drosophila development.

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

TS score explanation. a Hypothetical examples of time course transcript expression profiles from a gene to illustrate the concept of the TS score. The primary transcript is shown in blue. Minor transcripts are shown in other colours. The red line would have a high TS score since it has reasonably high expression relative to the primary transcript but with a different shape. The green transcript would have a Low TS score since although it has high general expression it has the same shape as the primary transcript. The purple transcript would have a low TS score since although it has a different shape it has low expression relative to the primary transcript. b, Example of a secondary isoform taken from the ‘sdt’ gene with a high TS score when compared to the primary isoform. The legend IDs between brackets are FlyBase transcript ID’s. Along the x-axis the first 24 hours correspond to embryogenesis stages; time points labelled ‘L’ correspond to subsequent Larval developmental stages; WPP indicates the white prepupae and,‘P’ indicates pupal stage, ‘F’ and ‘M’ are for female and male adult stages respectively (see Additional file 1: Figure S1 for an example of a gene with a low TS score)
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig1: TS score explanation. a Hypothetical examples of time course transcript expression profiles from a gene to illustrate the concept of the TS score. The primary transcript is shown in blue. Minor transcripts are shown in other colours. The red line would have a high TS score since it has reasonably high expression relative to the primary transcript but with a different shape. The green transcript would have a Low TS score since although it has high general expression it has the same shape as the primary transcript. The purple transcript would have a low TS score since although it has a different shape it has low expression relative to the primary transcript. b, Example of a secondary isoform taken from the ‘sdt’ gene with a high TS score when compared to the primary isoform. The legend IDs between brackets are FlyBase transcript ID’s. Along the x-axis the first 24 hours correspond to embryogenesis stages; time points labelled ‘L’ correspond to subsequent Larval developmental stages; WPP indicates the white prepupae and,‘P’ indicates pupal stage, ‘F’ and ‘M’ are for female and male adult stages respectively (see Additional file 1: Figure S1 for an example of a gene with a low TS score)
Mentions: In this article we develop tools for bridging this gap and allowing more detailed functional analysis of splicing. We develop a pipeline that identifies alternative splice variants with significantly different expression profiles. Here we make use of isoform expression profiles over a developmental time series in D.melanogaster [22] to identify alternative protein isoforms that have expression profiles indicative of function. The idea of gene expression divergence corresponding to functional divergence is often found in the literature (for example [23]), and in this study we adapt these ideas for comparing intra gene expression profiles rather than inter gene. The score we developed for this we name the Time-course Switch (TS) score (see Eq. 1 and Fig. 1a) which takes into account both the magnitude and expression profile differences between primary and minor transcript expression profiles in its calculation.Fig. 1

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