Abstract
Recent advances in long-read sequencing solve inaccuracies in alternative transcript identification of full-length transcripts in short-read RNA-Seq data, which encourages the development of methods for isoform-centered functional analysis. Here, we present tappAS, the first framework to enable a comprehensive Functional Iso-Transcriptomics (FIT) analysis, which is effective at revealing the functional impact of context-specific post-transcriptional regulation. tappAS uses isoform-resolved annotation of coding and non-coding functional domains, motifs, and sites, in combination with novel analysis methods to interrogate different aspects of the functional readout of transcript variants and isoform regulation. tappAS software and documentation are available at https://app.tappas.org.
Highlights
One of the most exciting aspects of transcriptome biology is the contextual adaptability of eukaryotic transcriptomes and proteomes by alternative splicing (AS), alternative polyadenylation (APA), and alternative transcription start sites (ATSS), jointly referred to here as alternative transcript expression mechanisms (AltTEM)
This is in contrast with the traditional approach to the functional assessment of differential splicing, in which analyses are restricted to the functional enrichment of spliced genes
We have included methods for the analysis of the variability in functional sites at genes with multiple transcript variants (FDA), strategies to evaluate the functional impact of the context-dependent expression of alternative isoforms, and ways to identify which functional elements change as a consequence of differential isoform usage (DFI)
Summary
One of the most exciting aspects of transcriptome biology is the contextual adaptability of eukaryotic transcriptomes and proteomes by alternative splicing (AS), alternative polyadenylation (APA), and alternative transcription start sites (ATSS), jointly referred to here as alternative transcript expression mechanisms (AltTEM). These three mechanisms determine which transcripts and isoforms are produced for a given gene in a given context. Molecular studies have revealed the mechanisms behind the dynamic changes in splicing patterns, identifying a large number of RNA-binding proteins (RBPs) as regulators of AS [11, 30,31,32,33,34]
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