Key Points
-
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.
-
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.
-
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.
-
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.
-
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.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 print issues and online access
$189.00 per year
only $15.75 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Edwards, S. L., Beesley, J., French, J. D. & Dunning, A. M. Beyond GWASs: illuminating the dark road from association to function. Am. J. Hum. Genet. 93, 779–797 (2013).
Kwan, T. et al. Genome-wide analysis of transcript isoform variation in humans. Nat. Genet. 40, 225–231 (2008). One of the early genome-wide comparisons showed that genomic variation between individuals correlated with differences in mRNA levels and structure.
Li, Y. I. et al. RNA splicing is a primary link between genetic variation and disease. Science 352, 600–604 (2016). A systematic analysis of LCLs from 68 individuals identified genomic variants that correlate with differences in up to eight molecular features of the gene regulatory cascade.
Lappalainen, T. et al. Transcriptome and genome sequencing uncovers functional variation in humans. Nature 501, 506–511 (2013). This study identified the genomic causes of variation in the transcriptome using RNA-seq and genomic sequence data from LCLs of 462 individuals in the 1000 Genomes Project.
Wang, E. T. et al. Alternative isoform regulation in human tissue transcriptomes. Nature 456, 470–476 (2008).
Tian, B., Hu, J., Zhang, H. & Lutz, C. S. A large-scale analysis of mRNA polyadenylation of human and mouse genes. Nucleic Acids Res. 33, 201–212 (2005).
Derti, A. et al. A quantitative atlas of polyadenylation in five mammals. Genome Res. 22, 1173–1183 (2012).
Halbeisen, R. E., Galgano, A., Scherrer, T. & Gerber, A. P. Post-transcriptional gene regulation: from genome-wide studies to principles. Cell. Mol. Life Sci. 65, 798–813 (2008).
Cooper, T. A., Wan, L. & Dreyfuss, G. RNA and disease. Cell 136, 777–793 (2009).
Scotti, M. M. & Swanson, M. S. RNA mis-splicing in disease. Nat. Rev. Genet. 17, 19–32 (2016).
Lim, L. P. & Burge, C. B. A computational analysis of sequence features involved in recognition of short introns. Proc. Natl Acad. Sci. USA 98, 11193–11198 (2001).
Wang, G.-S. & Cooper, T. A. Splicing in disease: disruption of the splicing code and the decoding machinery. Nat. Rev. Genet. 8, 749–761 (2007).
Wang, Z. & Burge, C. B. Splicing regulation: from a parts list of regulatory elements to an integrated splicing code. RNA 14, 802–813 (2008).
Xiong, H. Y. et al. RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease. Science 347, 1254806 (2015). A computational model was developed to predict splicing patterns based on genomic elements, which identified a large number of genetic variants among more than 650,000 SNVs that affect splicing and are associated with human disease.
Busch, A. & Hertel, K. J. Splicing predictions reliably classify different types of alternative splicing. RNA 21, 813–823 (2015).
Supek, F., Miñana, B., Valcárcel, J., Gabaldón, T. & Lehner, B. Synonymous mutations frequently act as driver mutations in human cancers. Cell 156, 1324–1335 (2014).
Takata, A., Ionita-Laza, I., Gogos, J. A., Xu, B. & Karayiorgou, M. De novo synonymous mutations in regulatory elements contribute to the genetic etiology of autism and schizophrenia. Neuron 89, 940–947 (2016).
Bali, V. & Bebok, Z. Decoding mechanisms by which silent codon changes influence protein biogenesis and function. Int. J. Biochem. Cell Biol. 64, 58–74 (2015).
Lim, K. H., Ferraris, L., Filloux, M. E., Raphael, B. J. & Fairbrother, W. G. Using positional distribution to identify splicing elements and predict pre-mRNA processing defects in human genes. Proc. Natl Acad. Sci. USA 108, 11093–11098 (2011).
Cartegni, L., Chew, S. L. & Krainer, A. R. Listening to silence and understanding nonsense: exonic mutations that affect splicing. Nat. Rev. Genet. 3, 285–298 (2002).
Zemojtel, T. et al. Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome. Sci. Transl Med. 6, 252ra123 (2014).
Li, M.-X. et al. Predicting Mendelian disease-causing non-synonymous single nucleotide variants in exome sequencing studies. PLoS Genet. 9, e1003143 (2013).
Cargill, M. et al. Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat. Genet. 22, 231–238 (1999).
Wu, X. & Hurst, L. D. Determinants of the usage of splice-associated cis-motifs predict the distribution of human pathogenic SNPs. Mol. Biol. Evol. 33, 518–529 (2016).
Zhang, X. et al. Identification of common genetic variants controlling transcript isoform variation in human whole blood. Nat. Genet. 47, 345–352 (2015).
Ulirsch, J. C. et al. Systematic functional dissection of common genetic variation affecting red blood cell traits. Cell 165, 1530–1545 (2016).
Fraser, H. B. & Xie, X. Common polymorphic transcript variation in human disease. Genome Res. 19, 567–575 (2009).
Zhang, W. et al. Identification of common genetic variants that account for transcript isoform variation between human populations. Hum. Genet. 125, 81–93 (2009).
ElSharawy, A. et al. Systematic evaluation of the effect of common SNPs on pre-mRNA splicing. Hum. Mutat. 30, 625–632 (2009).
Rivas, M. A. et al. Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome. Science 348, 666–669 (2015).
Hsiao, Y.-H. E. et al. Alternative splicing modulated by genetic variants demonstrates accelerated evolution regulated by highly conserved proteins. Genome Res. 26, 440–450 (2016). The authors identified more than 600 exons for which the splicing is affected by SNVs using a computational approach to measure allele-specific gene expression, including splicing differences, in ENCODE RNA-seq data sets. The results demonstrate the prominence of variant-driven splicing differences and present a powerful approach to analyse allele-specific expression.
Matesanz, F. et al. A functional variant that affects exon-skipping and protein expression of SP140 as genetic mechanism predisposing to multiple sclerosis. Hum. Mol. Genet. 24, 5619–5627 (2015).
Paraboschi, E. M. et al. Functional variations modulating PRKCA expression and alternative splicing predispose to multiple sclerosis. Hum. Mol. Genet. 23, 6746–6761 (2014).
Bojesen, S. E. et al. Multiple independent variants at the TERT locus are associated with telomere length and risks of breast and ovarian cancer. Nat. Genet. 45, 371–384 (2013).
Di Giacomo, D. et al. Functional analysis of a large set of BRCA2 exon 7 variants highlights the predictive value of hexamer scores in detecting alterations of exonic splicing regulatory elements. Hum. Mutat. 34, 1547–1557 (2013).
Monlong, J., Calvo, M., Ferreira, P. G. & Guigó, R. Identification of genetic variants associated with alternative splicing using sQTLseekeR. Nat. Commun. 5, 4698 (2014).
Tejedor, J. R., Tilgner, H., Iannone, C., Guigó, R. & Valcárcel, J. Role of six single nucleotide polymorphisms, risk factors in coronary disease, in OLR1 alternative splicing. RNA 21, 1187–1202 (2015).
Gregory, S. G. et al. Interleukin 7 receptor α chain (IL7R) shows allelic and functional association with multiple sclerosis. Nat. Genet. 39, 1083–1091 (2007).
Gretarsdottir, S. et al. A splice region variant in LDLR lowers non-high density lipoprotein cholesterol and protects against coronary artery disease. PLoS Genet. 11, e1005379 (2015).
Shi, Y. & Manley, J. L. The end of the message: multiple protein-RNA interactions define the mRNA polyadenylation site. Genes Dev. 29, 889–897 (2015).
Mu, X. J., Lu, Z. J., Kong, Y., Lam, H. Y. K. & Gerstein, M. B. Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project. Nucleic Acids Res. 39, 7058–7076 (2011).
Lu, J. & Clark, A. G. Impact of microRNA regulation on variation in human gene expression. Genome Res. 22, 1243–1254 (2012).
Sheets, M. D., Ogg, S. C. & Wickens, M. P. Point mutations in AAUAAA and the poly (A) addition site: effects on the accuracy and efficiency of cleavage and polyadenylation in vitro. Nucleic Acids Res. 18, 5799–5805 (1990).
Higgs, D. R. et al. α-Thalassaemia caused by a polyadenylation signal mutation. Nature 306, 398–400 (1983).
Yoon, O. K., Hsu, T. Y., Im, J. H. & Brem, R. B. Genetics and regulatory impact of alternative polyadenylation in human B-lymphoblastoid cells. PLoS Genet. 8, e1002882 (2012).
Zhernakova, D. V. et al. DeepSAGE reveals genetic variants associated with alternative polyadenylation and expression of coding and non-coding transcripts. PLoS Genet. 9, e1003594 (2013).
Graham, R. R. et al. Three functional variants of IFN regulatory factor 5 (IRF5) define risk and protective haplotypes for human lupus. Proc. Natl Acad. Sci. USA 104, 6758–6763 (2007).
Cunninghame Graham, D. S. et al. Association of IRF5 in UK SLE families identifies a variant involved in polyadenylation. Hum. Mol. Genet. 16, 579–591 (2007).
Hellquist, A. et al. The human GIMAP5 gene has a common polyadenylation polymorphism increasing risk to systemic lupus erythematosus. J. Med. Genet. 44, 314–321 (2007).
Fahiminiya, S. et al. A polyadenylation site variant causes transcript-specific BMP1 deficiency and frequent fractures in children. Hum. Mol. Genet. 24, 516–524 (2015).
Garin, I. et al. Recessive mutations in the INS gene result in neonatal diabetes through reduced insulin biosynthesis. Proc. Natl Acad. Sci. USA 107, 3105–3110 (2010).
Stacey, S. N. et al. A germline variant in the TP53 polyadenylation signal confers cancer susceptibility. Nat. Genet. 43, 1098–1103 (2011).
Uitte de Willige, S., Rietveld, I. M., De Visser, M. C. H., Vos, H. L. & Bertina, R. M. Polymorphism 10034C>T is located in a region regulating polyadenylation of FGG transcripts and influences the fibrinogen γ′/γA mRNA ratio. J. Thromb. Haemost. 5, 1243–1249 (2007).
Friedman, R. C., Farh, K. K.-H., Burge, C. B. & Bartel, D. P. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res. 19, 92–105 (2009).
John, B. et al. Human microRNA targets. PLoS Biol. 2, e363 (2004).
Lewis, B. P., Shih, I.-H., Jones-Rhoades, M. W., Bartel, D. P. & Burge, C. B. Prediction of mammalian microRNA targets. Cell 115, 787–798 (2003).
Lewis, B. P., Burge, C. B. & Bartel, D. P. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120, 15–20 (2005).
Huan, T. et al. Genome-wide identification of microRNA expression quantitative trait loci. Nat. Commun. 6, 6601 (2015).
Wagschal, A. et al. Genome-wide identification of microRNAs regulating cholesterol and triglyceride homeostasis. Nat. Med. 21, 1290–1297 (2015).
Duan, J. et al. A rare functional noncoding variant at the GWAS-implicated MIR137/MIR2682 locus might confer risk to schizophrenia and bipolar disorder. Am. J. Hum. Genet. 95, 744–753 (2014).
Gamazon, E. R. et al. Genetic architecture of microRNA expression: implications for the transcriptome and complex traits. Am. J. Hum. Genet. 90, 1046–1063 (2012).
Ghanbari, M. et al. Genetic variations in microRNA-binding sites affect microRNA-mediated regulation of several genes associated with cardio-metabolic phenotypes. Circ. Cardiovasc. Genet. 8, 473–486 (2015).
Thomas, L. F. & Sætrom, P. Single nucleotide polymorphisms can create alternative polyadenylation signals and affect gene expression through loss of microRNA-regulation. PLoS Comput. Biol. 8, e1002621 (2012).
Arnold, M., Ellwanger, D. C., Hartsperger, M. L., Pfeufer, A. & Stümpflen, V. Cis-acting polymorphisms affect complex traits through modifications of microRNA regulation pathways. PLoS ONE 7, e36694 (2012).
Houlston, R. S. et al. Meta-analysis of three genome-wide association studies identifies susceptibility loci for colorectal cancer at 1q41, 3q26.2, 12q13.13 and 20q13.33. Nat. Genet. 42, 973–977 (2010).
Parkes, M. et al. Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility. Nat. Genet. 39, 830–832 (2007).
Brest, P. et al. A synonymous variant in IRGM alters a binding site for miR-196 and causes deregulation of IRGM-dependent xenophagy in Crohn's disease. Nat. Genet. 43, 242–245 (2011).
Kulkarni, S. et al. Differential microRNA regulation of HLA-C expression and its association with HIV control. Nature 472, 495–498 (2011).
Caussy, C. et al. An APOA5 3′ UTR variant associated with plasma triglycerides triggers APOA5 downregulation by creating a functional miR-485-5p binding site. Am. J. Hum. Genet. 94, 129–134 (2014).
Gartner, J. J. et al. Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma. Proc. Natl Acad. Sci. USA 110, 13481–13486 (2013).
Wang, G. et al. Variation in the miRNA-433 binding site of FGF20 confers risk for Parkinson disease by overexpression of α-synuclein. Am. J. Hum. Genet. 82, 283–289 (2008).
Haghnejad, L. et al. Variation in the miRNA-433 binding site of FGF20 is a risk factor for Parkinson's disease in Iranian population. J. Neurol. Sci. 355, 72–74 (2015).
Pai, A. A. et al. The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels. PLoS Genet. 8, e1003000 (2012).
Capon, F. et al. A synonymous SNP of the corneodesmosin gene leads to increased mRNA stability and demonstrates association with psoriasis across diverse ethnic groups. Hum. Mol. Genet. 13, 2361–2368 (2004).
van Hoof, A. & Wagner, E. J. A brief survey of mRNA surveillance. Trends Biochem. Sci. 36, 585–592 (2011).
Jacobs, E., Mills, J. D. & Janitz, M. The role of RNA structure in posttranscriptional regulation of gene expression. J. Genet. Genomics 39, 535–543 (2012).
Lu, Z. et al. RNA duplex map in living cells reveals higher-order transcriptome structure. Cell 165, 1267–1279 (2016).
Sharma, E., Sterne-Weiler, T., O'Hanlon, D. & Blencowe, B. J. Global mapping of human RNA–RNA interactions. Mol. Cell 62, 618–626 (2016).
Spitale, R. C. et al. Structural imprints in vivo decode RNA regulatory mechanisms. Nature 519, 486–490 (2015).
Wan, Y. et al. Landscape and variation of RNA secondary structure across the human transcriptome. Nature 505, 706–709 (2014). This study identified more than 1,900 SNVs that affected local RNA structure using high-throughput analysis of RNA structure in LCLs from a family trio.
Halvorsen, M., Martin, J. S., Broadaway, S. & Laederach, A. Disease-associated mutations that alter the RNA structural ensemble. PLoS Genet. 6, e1001074 (2010).
Rogler, L. E. et al. Small RNAs derived from lncRNA RNase MRP have gene-silencing activity relevant to human cartilage–hair hypoplasia. Hum. Mol. Genet. 23, 368–382 (2014).
Martin, J. S. et al. Structural effects of linkage disequilibrium on the transcriptome. RNA 18, 77–87 (2012).
Kutchko, K. M. et al. Multiple conformations are a conserved and regulatory feature of the RB1 5′ UTR. RNA 21, 1274–1285 (2015).
Duan, J. et al. Synonymous mutations in the human dopamine receptor D2 (DRD2) affect mRNA stability and synthesis of the receptor. Hum. Mol. Genet. 12, 205–216 (2003).
Akdeli, N. et al. A 3′UTR polymorphism modulates mRNA stability of the oncogene and drug target polo-like kinase 1. Mol. Cancer 13, 87 (2014).
Niu, T. et al. Identification of a novel FGFRL1 microRNA target site polymorphism for bone mineral density in meta-analyses of genome-wide association studies. Hum. Mol. Genet. 24, 4710–4727 (2015).
Sabarinathan, R. et al. Transcriptome-wide analysis of UTRs in non-small cell lung cancer reveals cancer-related genes with SNV-induced changes on RNA secondary structure and miRNA target sites. PLoS ONE 9, e82699 (2014).
Wu, L. et al. Variation and genetic control of protein abundance in humans. Nature 499, 79–82 (2013).
Battle, A. et al. Genomic variation. Impact of regulatory variation from RNA to protein. Science 347, 664–667 (2015).
Suhl, J. A. et al. A 3′ untranslated region variant in FMR1 eliminates neuronal activity-dependent translation of FMRP by disrupting binding of the RNA-binding protein HuR. Proc. Natl Acad. Sci. USA 112, E6553–E6561 (2015).
Somers, J. et al. A common polymorphism in the 5′ UTR of ERCC5 creates an upstream ORF that confers resistance to platinum-based chemotherapy. Genes Dev. 29, 1891–1896 (2015).
Raj, A. et al. Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling. eLife 5, e13328 (2016).
Cenik, C. et al. Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans. Genome Res. 25, 1610–1621 (2015).
Zhang, F., Saha, S., Shabalina, S. A. & Kashina, A. Differential arginylation of actin isoforms is regulated by coding sequence-dependent degradation. Science 329, 1534–1537 (2010).
Mortimer, S. A., Kidwell, M. A. & Doudna, J. A. Insights into RNA structure and function from genome-wide studies. Nat. Rev. Genet. 15, 469–479 (2014).
Wen, J.-D. et al. Following translation by single ribosomes one codon at a time. Nature 452, 598–603 (2008).
Shabalina, S. A., Ogurtsov, A. Y. & Spiridonov, N. A. A periodic pattern of mRNA secondary structure created by the genetic code. Nucleic Acids Res. 34, 2428–2437 (2006).
Yu, C.-H. et al. Codon usage influences the local rate of translation elongation to regulate co-translational protein folding. Mol. Cell 59, 744–754 (2015).
Riordan, J. R. et al. Identification of the cystic fibrosis gene: cloning and characterization of complementary DNA. Science 245, 1066–1073 (1989).
Ward, C. L. & Kopito, R. R. Intracellular turnover of cystic fibrosis transmembrane conductance regulator. Inefficient processing and rapid degradation of wild-type and mutant proteins. J. Biol. Chem. 269, 25710–25718 (1994).
Bartoszewski, R. A. et al. A synonymous single nucleotide polymorphism in ΔF508 CFTR alters the secondary structure of the mRNA and the expression of the mutant protein. J. Biol. Chem. 285, 28741–28748 (2010). This study proposes that the effects on CFTR mRNA secondary structure induced by the ΔF508 mutation, rather than the deletion of Phe, destabilize the protein, leading to loss of its function.
Nackley, A. G. et al. Human catechol-O- methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure. Science 314, 1930–1933 (2006).
Wang, T., Zhou, T., Saadat, L. & Garcia, J. G. N. A MYLK variant regulates asthmatic inflammation via alterations in mRNA secondary structure. Eur. J. Hum. Genet. 23, 874–876 (2015).
Chiaruttini, C. et al. Dendritic trafficking of BDNF mRNA is mediated by translin and blocked by the G196A (Val66Met) mutation. Proc. Natl Acad. Sci. USA 106, 16481–16486 (2009).
Bergalet, J. & Lécuyer, E. The functions and regulatory principles of mRNA intracellular trafficking. Adv. Exp. Med. Biol. 825, 57–96 (2014).
Chabanon, H., Mickleburgh, I., Burtle, B., Pedder, C. & Hesketh, J. An AU-rich stem-loop structure is a critical feature of the perinuclear localization signal of c-myc mRNA. Biochem. J. 392, 475–483 (2005).
Chen, Z.-Y. et al. Genetic variant BDNF (Val66Met) polymorphism alters anxiety-related behavior. Science 314, 140–143 (2006).
Egan, M. F. et al. The BDNF val66met polymorphism affects activity-dependent secretion of BDNF and human memory and hippocampal function. Cell 112, 257–269 (2003).
Notaras, M., Hill, R. & van den Buuse, M. The BDNF gene Val66Met polymorphism as a modifier of psychiatric disorder susceptibility: progress and controversy. Mol. Psychiatry 20, 916–930 (2015).
Mallei, A. et al. Expression and dendritic trafficking of BDNF-6 splice variant are impaired in knock-in mice carrying human BDNF Val66Met polymorphism. Int. J. Neuropsychopharmacol. 18, pyv069 (2015).
Li, G. et al. Identification of allele-specific alternative mRNA processing via transcriptome sequencing. Nucleic Acids Res. 40, e104 (2012).
Maniatis, T. & Reed, R. An extensive network of coupling among gene expression machines. Nature 416, 499–506 (2002).
Braunschweig, U., Gueroussov, S., Plocik, A. M., Graveley, B. R. & Blencowe, B. J. Dynamic integration of splicing within gene regulatory pathways. Cell 152, 1252–1269 (2013).
Naftelberg, S., Schor, I. E., Ast, G. & Kornblihtt, A. R. Regulation of alternative splicing through coupling with transcription and chromatin structure. Annu. Rev. Biochem. 84, 165–198 (2015).
Mayr, C. & Bartel, D. P. Widespread shortening of 3′ UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell 138, 673–684 (2009).
Taliaferro, J. M. et al. Distal alternative last exons localize mRNAs to neural projections. Mol. Cell 61, 821–833 (2016).
Sterne-Weiler, T. et al. Frac-seq reveals isoform-specific recruitment to polyribosomes. Genome Res. 23, 1615–1623 (2013).
Simms, C. L., Thomas, E. N. & Zaher, H. S. Ribosome-based quality control of mRNA and nascent peptides. Wiley Interdiscip. Rev. RNA http://dx.doi.org/10.1002/wrna.1366 (2016).
Van Nostrand, E. L. et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat. Methods 13, 508–514 (2016).
de Klerk, E. & 't Hoen, P. A. C. Alternative mRNA transcription, processing, and translation: insights from RNA sequencing. Trends Genet. 31, 128–139 (2015).
Weng, L., Li, Y., Xie, X. & Shi, Y. Poly(A) code analyses reveal key determinants for tissue-specific mRNA alternative polyadenylation. RNA 22, 813–821 (2016).
Brar, G. A. & Weissman, J. S. Ribosome profiling reveals the what, when, where and how of protein synthesis. Nat. Rev. Mol. Cell Biol. 16, 651–664 (2015).
van der Maarel, S. M., Tawil, R. & Tapscott, S. J. Facioscapulohumeral muscular dystrophy and DUX4: breaking the silence. Trends Mol. Med. 17, 252–258 (2011).
Lemmers, R. J. L. F. et al. Digenic inheritance of an SMCHD1 mutation and an FSHD-permissive D4Z4 allele causes facioscapulohumeral muscular dystrophy type 2. Nat. Genet. 44, 1370–1374 (2012).
Lemmers, R. J. L. F. et al. A unifying genetic model for facioscapulohumeral muscular dystrophy. Science 329, 1650–1653 (2010). The authors demonstrate the role of allelic differences in a polyadenylation signal that allows expression of a toxic protein in muscle tissue of patients with FSHD. This followed a detailed genetic analysis to identify permissive and non-permissive alleles within complex genomic regions.
Spear, B. B., Heath-Chiozzi, M. & Huff, J. Clinical application of pharmacogenetics. Trends Mol. Med. 7, 201–204 (2001).
Tate, S. K. et al. Genetic predictors of the maximum doses patients receive during clinical use of the anti-epileptic drugs carbamazepine and phenytoin. Proc. Natl Acad. Sci. USA 102, 5507–5512 (2005).
Burkhardt, R. et al. Common SNPs in HMGCR in Micronesians and whites associated with LDL-cholesterol levels affect alternative splicing of exon13. Arterioscler. Thromb. Vasc. Biol. 28, 2078–2084 (2008).
Medina, M. W., Gao, F., Ruan, W., Rotter, J. I. & Krauss, R. M. Alternative splicing of 3-hydroxy-3-methylglutaryl coenzyme A reductase is associated with plasma low-density lipoprotein cholesterol response to simvastatin. Circulation 118, 355–362 (2008).
Yu, C.-Y. et al. HNRNPA1 regulates HMGCR alternative splicing and modulates cellular cholesterol metabolism. Hum. Mol. Genet. 23, 319–332 (2014).
Corrado, L. et al. A novel synonymous mutation in the MPZ gene causing an aberrant splicing pattern and Charcot–Marie–Tooth disease type 1b. Neuromuscul. Disord. 26, 516–520 (2016).
Llewellyn, D. H. et al. Acute intermittent porphyria caused by defective splicing of porphobilinogen deaminase RNA: a synonymous codon mutation at -22 bp from the 5′ splice site causes skipping of exon 3. J. Med. Genet. 33, 437–438 (1996).
Thanopoulou, E. et al. The single nucleotide polymorphism g.1548A>G (K469E) of the ICAM-1 gene is associated with worse prognosis in non-small cell lung cancer. Tumour Biol. 33, 1429–1436 (2012).
Boni, V. et al. Role of primary miRNA polymorphic variants in metastatic colon cancer patients treated with 5-fluorouracil and irinotecan. Pharmacogenomics J. 11, 429–436 (2010).
Xu, J. et al. A heroin addiction severity-associated intronic single nucleotide polymorphism modulates alternative pre-mRNA splicing of the μ opioid receptor gene OPRM1 via hnRNPH Interactions. J. Neurosci. 34, 11048–11066 (2014).
Chiba-Falek, O. et al. The molecular basis of disease variability among cystic fibrosis patients carrying the 3849 + 10 kb C>T mutation. Genomics 53, 276–283 (1998).
Hinzpeter, A. et al. Alternative splicing at a NAGNAG acceptor site as a novel phenotype modifier. PLoS Genet. 6, e1001153 (2010). This study demonstrates that selection of the upstream AG in the NAGNAG sequence at the 3′ splice site introduces a termination codon in the CFTR mRNA, thereby modifying disease severity.
Morini, E. et al. The human rs1050286 polymorphism alters LOX-1 expression through modifying miR-24 binding. J. Cell. Mol. Med. 20, 181–187 (2016).
Zhou, B. et al. Identification of a splicing variant that regulates type 2 diabetes risk factor CDKAL1 level by a coding-independent mechanism in human. Hum. Mol. Genet. 23, 4639–4650 (2014).
Ray, D. et al. A compendium of RNA-binding motifs for decoding gene regulation. Nature 499, 172–177 (2013). This study identified the preferred binding motifs of hundreds of RNA-binding proteins with broad implications regarding roles in post-transcriptional regulation. A high-throughput approach was used to interrogate more than 200 RNA-binding protein motifs from vertebrate and invertebrate organisms using a randomized pool of 30–41-nucleotide RNAs containing all possible 9-nucleotide combinations.
Stephens, R. M. & Schneider, T. D. Features of spliceosome evolution and function inferred from an analysis of the information at human splice sites. J. Mol. Biol. 228, 1124–1136 (1992).
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.).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing financial interests.
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
-
(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
-
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
-
(sQTLs). Genomic regions containing variants that affect the splicing patterns of the associated pre-mRNA.
- Expression QTLs
-
(eQTLs). Genomic regions containing variants that affect the level of mRNA expression from one or more genes.
- HapMap-derived lymphoblastoid cell lines
-
(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
-
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
-
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
-
(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
-
An RNA surveillance mechanism that recognizes and degrades RNA transcripts containing premature termination codons.
- Nonstop decay
-
An RNA surveillance mechanism that recognizes and degrades RNA transcripts lacking a stop codon.
- No-go decay
-
An RNA and translation quality control mechanism that recognizes and degrades RNA -transcripts containing stalled ribosomes.
- RNA-induced silencing complex
-
(RISC). A ribonucleoprotein complex that mediates binding between a microRNA and its target mRNA.
- Protein QTLs
-
Genomic regions containing variants that affect the expression level of protein from one or more genes.
- Kozak sequence
-
A consensus sequence surrounding the start codon in eukaryotic mRNAs that promotes translation initiation.
- Endoplasmic reticulum-associated degradation pathway
-
(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
-
Regulatory cis-acting RNA elements containing a specific sequence and secondary structure that are sufficient to confer mRNA subcellular localization.
Rights and permissions
About this article
Cite this article
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
Published:
Issue Date:
DOI: https://doi.org/10.1038/nrm.2016.139
This article is cited by
-
Combining full-length gene assay and SpliceAI to interpret the splicing impact of all possible SPINK1 coding variants
Human Genomics (2024)
-
Alternative splicing and environmental adaptation in wild house mice
Heredity (2024)
-
Regulation of pre-mRNA splicing: roles in physiology and disease, and therapeutic prospects
Nature Reviews Genetics (2023)
-
TEQUILA-seq: a versatile and low-cost method for targeted long-read RNA sequencing
Nature Communications (2023)
-
Mendelian inheritance revisited: dominance and recessiveness in medical genetics
Nature Reviews Genetics (2023)
