The roles of RNA processing in translating genotype to phenotype

Abstract

A goal of human genetics studies is to determine the mechanisms by which genetic variation produces phenotypic differences that affect human health. Efforts in this respect have previously focused on genetic variants that affect mRNA levels by altering epigenetic and transcriptional regulation. Recent studies show that genetic variants that affect RNA processing are at least equally as common as, and are largely independent from, those variants that affect transcription. We highlight the impact of genetic variation on pre-mRNA splicing and polyadenylation, and on the stability, translation and structure of mRNAs as mechanisms that produce phenotypic traits. These results emphasize the importance of including RNA processing signals in analyses to identify functional variants.

Figure 1. Genetic variation alters gene output by affecting RNA processing

Genetic variants affect multiple steps of RNA processing and mRNA dynamics, including splicing, 3′ end processing, mRNA structure and stability, translation efficiency and regulation by RNA-binding proteins and by microRNAs (mi RNAs). Genetic variants that disrupt either cis-acting elements or key RNA secondary structures have downstream consequences in terms of protein composition and expression levels. UTR, untranslated region.

Figure 2. Genetic variants that affect RNA processing can have a range of effects on human health

These effects range from benign or unclassified variants to pathological variants that cause monogenic diseases. Selected examples of functional genetic variants that affect RNA processing are depicted, which have a range of consequences, such as causing disease^,,, altering prognosis or therapeutic response^,,, modifying disease severity^– or modifying disease risk^,,. BMP1, bone morphogenetic protein 1; CDKAL1, CDK5 regulatory subunit-associated protein 1-like 1; CFTR, cystic fibrosis transmembrane conductance regulator; ERCC5, ERCC excision repair 5, endonuclease; GWAS, genome-wide association studies; HMBS, hydroxymethylbilane synthase; HNRNPH1, heterogeneous nuclear ribonucleoprotein H1; ICAM1, intercellular adhesion molecule 1; IRGM1, immunity-realted GTPase M member 1; miRNA, microRNA; MPZ, myelin protein zero; OLR1, oxidized low-density lipoprotein receptor 1; OPRM1, opioid receptor mu 1; pri, primary; SNV, single-nucleotide variant.

Figure 3. Cis-acting splicing elements are not restricted to exon–intron boundaries

Consensus and auxiliary splicing elements are required for efficient and regulated pre-mRNA splicing. The consensus splice site sequences are shown below the pre-mRNA. The GT (GU in the pre-mRNA) and AG dinucleotides at either end of introns are crucial for splicing, but substitutions of other nucleotides within the consensus splicing elements, such as in the branch site or polypyrimidine tract, can also have an effect on splicing. Examples of auxiliary splicing element motifs within exons and introns are shown above the pre-mRNA, together with the RNA-binding proteins that bind to these motifs. ESE, exonic splicing enhancer; HNRNPA1, heterogeneous nuclear ribonucleoprotein A1; ISE, intronic splicing enhancer; ISS, intronic splicing silencer; RBFOX1, RNA-binding protein, fox-1 homologue 1; SRSF, serine/arginine-rich splicing factor. Sequence logos for auxiliary splicing elements for the RNA-binding protein SRSF1, SRSF2, HNRNPA1 and RBFOX1 are from REF. , and for the consensus splice sites are from REF. and http://weblogo.berkeley.edu/examples.html.

Figure 4. Genetic variants that create or abolish key RNA secondary structures affect multiple aspects of post-transcriptional regulation

RNA-binding proteins rely on sequence and structural information for binding to their target cis-acting elements. a | Secondary RNA structures created by a genetic variant can prevent access of a microRNA (miRNA) within the RNA-induced silencing complex (RISC), thereby affecting the level of miRNA-mediated repression. b | Similarly, the creation of a novel RNA structure by a single-nucleotide variant can prevent binding of an RNA-binding protein to its cognate site. Alternatively, the affinities of some RNA-binding proteins require a specific RNA structure, and genetic variants that disrupt this structure can decrease binding of the trans-acting factor. As outlined in the text, sequence-specific interactions of RNA with RNA-binding proteins are crucial for appropriate basal and regulated RNA processing steps; their disruption can result in altered RNA splicing, stability or localization. c | Genetic variants that alter RNA structure within the coding region can affect the translation rate by impairing ribosome progression.