Functional annotation of alternatively spliced isoforms of human G protein-coupled receptors (GPCRs)

Abstract

The functional differences that exist between alternatively spliced isoforms of genes can be substantial; it could be variations of the function of the “primary” full-length protein, its antagonist function or not directly related to its function. Regardless of the functions of spliced isoforms there is a need for proper annotation. G protein-coupled receptors (GPCRs) are important trans-membrane proteins with important biological and pharmaceutical implications. Incorrect alternative splicing has been associated with a number of human diseases including diabetes and cancers. In this dissertation is presented a framework and results for annotating transcripts of GPCR genes that have originated from alternative splicing of their pre-mRNA. This was achieved by first assessing the genomic landscape of the GPCRs to determine the type of alternative splicing event that exist and the localization of such events. In addition, the influences of exon-intron structures of GPCRs on the alternative splicing of the genes are evaluated. Then, the molecular level functions are ascertained via motif identification. Furthermore, the cellular state in which each isoform could function was determined using tissues of expression from RNA-sequencing data. Lastly, isoform function is inferred from cis regulatory elements predicted to influence the transcription of the isoform in the specific cellular state. The results are presented here and made publicly available in a PHP/MySQL relational database. Results from the research analyses indicate that the genomic structures of GPCRs are complex; their exon-intron structures are not arbitrarily arranged; rather they are ordered in such a manner as to ease the alternative splicing of the gene for functional purposes. Also, that GPCR isoforms expression patterns differ across tissues. Additionally it was evident that GPCR isoforms have multiple cellular pathways in which they may be involved depending on the cellular conditions. Overall, 1044 human GPCR isoforms were annotated. These results are now publicly available via the Internet in the database called the G protein-coupled receptor transcriptional annotation of genes (gpcrTAG) database. The results from these analyses offer the promise of transcriptional drug control, as well as offer the framework to study functional diversity between isoforms of other genes families.