Key Points
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Gene expression involves a cascade of chromosomal, transcriptional and post-transcriptional events. Genomic variants produce differences between individuals in terms of transcriptional and post-transcriptional events at equal frequency.
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Common genetic variation between individuals contributes to phenotypic diversity. Single-nucleotide variants can have functional consequences by affecting RNA processing, including effects on pre-mRNA splicing, 3′ end formation, and RNA stability, localization, structure and translation efficiency.
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Genomic variants affect RNA processing by altering the binding sites of sequence-specific RNA-binding proteins, by disrupting RNA structures required for processing or by introducing RNA structures that prevent RNA processing.
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Comparisons of genomic and transcriptomic sequences from a large number of individuals from diverse backgrounds will not only identify functional variants that are relevant to human health, but also catalogue the cis-acting elements that are required for basal and regulated RNA processing.
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Analysis of the effects of genomic variants on post-transcriptional regulation of gene expression is made possible by the recent rapid expansion of high-throughput experimental approaches and associated computational analyses.
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.
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Acknowledgements
The authors thank members of the Cooper laboratory as well as the reviewers for valuable input. The work of the authors is supported by the US National Institutes of Health (NIH) (R01AR045653, R01AR060733 and R01HL045565 to T.A.C.), the Muscular Dystrophy Association (MDA276796 to T.A.C.), NIH training grant T32 GM008231 (to K.S.M.) and Baylor Research Advocates for Student Scientists (to K.S.M.).
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Glossary
- Genome-wide association studies
-
(GWAS). Large studies across many individuals to determine whether the presence of a specific genotype is correlated with the manifestation of natural and pathological phenotypic traits or diseases.
- mRNA 3′ ends
-
The 3′ end of an mRNA is formed by endonucleolytic cleavage. The vast majority of protein-coding mRNAs have approximately 250 non-templated adenosines added to the last templated nucleotide at the site of endonucleolytic cleavage.
- Polyadenylation sites
-
Technically refers to the site of addition of the poly(A) tail at the last templated nucleotide of an mRNA. However, the term is sometimes used to refer to the AAUAAA hexanucleotide motif that is required for polyadenylation and that is typically located within 25 nucleotides of the last templated nucleotide.
- 5′ and 3′ untranslated regions
-
(5′ and 3′ UTRs). The open reading frames of protein-coding mRNAs can constitute less than half of their nucleotide sequence. The 5′ UTR is the mRNA region upstream of the translation start codon and the 3′ UTR is the region downstream of the translation stop codon.
- MicroRNAs
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(miRNAs). Small RNAs (about 22 nucleotides long) that base pair to their mRNA targets and reduce protein expression by mRNA destabilization or translational repression.
- Branch site
-
A consensus mRNA splicing element typically located within 30 nucleotides of the 3′ splice site. It is recognized by sequential binding of branch point-binding protein followed by the U2 small nuclear ribonucleoprotein by base pairing.
- Exonic splicing enhancer
-
(ESE). One of several auxiliary mRNA splicing elements that are bound by splicing factors to promote (ESE or intronic splicing enhancer (ISE)) or inhibit (exonic splicing silencer (ESS) or intronic splicing silencer (ISS)) splicing. Disruption of these motifs and the resulting effects on splicing indicate that genetic variants outside exon–intron junctions can affect gene output.
- Synonymous and non-synonymous variants
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Refers to variants in the coding region of a gene that either alter the encoded amino acid (non-synonymous) or do not affect the encoded amino acid (synonymous).
- Splicing quantitative trait loci
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(sQTLs). Genomic regions containing variants that affect the splicing patterns of the associated pre-mRNA.
- Expression QTLs
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(eQTLs). Genomic regions containing variants that affect the level of mRNA expression from one or more genes.
- HapMap-derived lymphoblastoid cell lines
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(HapMap-derived LCLs). Refers to the International HapMap Project, which derived LCLs from 270 individuals of European, African and Asian ancestry for analysis of genotype, gene expression and pharmacological response.
- Single-nucleotide variants
-
(SNVs). We use the term SNV to refer to any genetic variant that changes one nucleotide, which may or may not have functional or pathological consequences. We largely focus on examples of common variants (also known as single-nucleotide polymorphisms (SNPs)) that are associated with either disease risk or disease severity.
- GEUVADIS and GTEx
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Genetic European Variation in Health and Disease (GEUVADIS) and Genotype Tissue Expression (GTEx) are consortia for the high-throughput sequencing of human genomes and transcriptomes.
- Crosslinking immunoprecipitation
-
(CLIP). Used to identify the direct targets of an RNA-binding protein by covalently linking RNA and the protein in vivo by UV crosslinking, followed by immunoprecipitation and then high-throughput sequencing.
- Linkage disequilibrium
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The nonrandom association of two or more genetic variants, usually owing to close proximity on the same chromosome and reflecting shared ancestry of alleles at flanking loci.
- Cis-acting miRNA QTLs
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(Cis-mirQTLs). Genomic regions containing variants that affect the level of expression of individual microRNAs (miRNAs) located in cis with the variant.
- 1000 Genomes Project
-
This database was designed to identify genetic variants present in at least 1% of individuals across 26 populations, and contains DNA sequencing data for more than 2,500 individuals. This data set has been expanded by the addition of RNA sequencing data from the GEUVADIS consortium.
- Nonsense-mediated decay
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An RNA surveillance mechanism that recognizes and degrades RNA transcripts containing premature termination codons.
- Nonstop decay
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An RNA surveillance mechanism that recognizes and degrades RNA transcripts lacking a stop codon.
- No-go decay
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An RNA and translation quality control mechanism that recognizes and degrades RNA -transcripts containing stalled ribosomes.
- RNA-induced silencing complex
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(RISC). A ribonucleoprotein complex that mediates binding between a microRNA and its target mRNA.
- Protein QTLs
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Genomic regions containing variants that affect the expression level of protein from one or more genes.
- Kozak sequence
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A consensus sequence surrounding the start codon in eukaryotic mRNAs that promotes translation initiation.
- Endoplasmic reticulum-associated degradation pathway
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(ERAD pathway). A quality control system for misfolded proteins in the endoplasmic reticulum that marks them for degradation by the ubiquitin–proteasome system.
- RNA zipcode motifs
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Regulatory cis-acting RNA elements containing a specific sequence and secondary structure that are sufficient to confer mRNA subcellular localization.
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Manning, K., Cooper, T. The roles of RNA processing in translating genotype to phenotype. Nat Rev Mol Cell Biol 18, 102–114 (2017). https://doi.org/10.1038/nrm.2016.139
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DOI: https://doi.org/10.1038/nrm.2016.139
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