Alternative Transcripts Diversify Genome Function for Phenome Relevance to Health and Diseases

Abstract

Manipulation using alternative exon splicing (AES), alternative transcription start (ATS), and alternative polyadenylation (APA) sites are key to transcript diversity underlying health and disease. All three are pervasive in organisms, present in at least 50% of human protein-coding genes. In fact, ATS and APA site use has the highest impact on protein identity, with their ability to alter which first and last exons are utilized as well as impacting stability and translation efficiency. These RNA variants have been shown to be highly specific, both in tissue type and stage, with demonstrated importance to cell proliferation, differentiation and the transition from fetal to adult cells. While alternative exon splicing has a limited effect on protein identity, its ubiquity highlights the importance of these minor alterations, which can alter other features such as localization. The three processes are also highly interwoven, with overlapping, complementary, and competing factors, RNA polymerase II and its CTD (C-terminal domain) chief among them. Their role in development means dysregulation leads to a wide variety of disorders and cancers, with some forms of disease disproportionately affected by specific mechanisms (AES, ATS, or APA). Challenges associated with the genome-wide profiling of RNA variants and their potential solutions are also discussed in this review.

Keywords: RNA variants; challenges and solutions; genome–phenome bridges; health and disease relevance.

Figure 1

Three mechanisms impacted by ATS sites and ORFs. Leaky scanning can occur when translation begins at a start codon with a weak Kozak sequence, allowing a portion of the ribosomal subunits to skip over (leak) and initiate translation at an alternative start codon. Upstream ORFs and strong secondary structures from ATS sites/promoters can stop or stall the PIC complex, causing it to fall off and repressing gene expression downstream of it. Lastly, short uORFs separated from the main ORF can cause the ribosomal subunit to remain associated after termination and resume scanning, which is termed reinitiation. Abbreviations: ORF (open reading frame), dORF/uORF (downstream/upstream ORF), TIS (transcription initiation site), aTIS (alternative TIS).

Figure 2

Different forms of polyadenylation, locations of typical polyadenylation signals (PASs) for each, and average lengths of untranslated regions (UTRs) based on tissue type and number of UTRs. The two most common forms, 3′ tandem UTR and alternative last exon (ALE), display common tissue associations and traits. The upper left shows the typical intragenic location of each form of alternative polyadenylation (APA) site. The lower left displays the average UTR length for single- and multi-UTR genes as well as ubiquitous versus tissue-specific genes. The right shows common associations for 3′ tandem UTR and ALE APA isoforms. Some ALE isoforms are the result of intronic APA site selection, as detailed on the right.

Figure 3

Distribution of post-transcriptional modification RNA elements. The layout of gene regions and distribution of the RNA elements within those regions for the three types of modification discussed here, alternative exon splicing, alternative transcription start sites, and alternative polyadenylation. It provides a visual representation of start rich and stop rich regions as the regions between the 1st and last start codon, and the 1st and last stop codon, respectively. It also denotes areas of coupling between these elements. Abbreviations: UTR (untranslated region).