Identification and analysis of splicing quantitative trait loci across multiple tissues in the human genome

Abstract

Alternative splicing (AS) is a fundamental step in eukaryotic mRNA biogenesis. Here, we develop an efficient and reproducible pipeline for the discovery of genetic variants that affect AS (splicing QTLs, sQTLs). We use it to analyze the GTEx dataset, generating a comprehensive catalog of sQTLs in the human genome. Downstream analysis of this catalog provides insight into the mechanisms underlying splicing regulation. We report that a core set of sQTLs is shared across multiple tissues. sQTLs often target the global splicing pattern of genes, rather than individual splicing events. Many also affect the expression of the same or other genes, uncovering regulatory loci that act through different mechanisms. sQTLs tend to be located in post-transcriptionally spliced introns, which would function as hotspots for splicing regulation. While many variants affect splicing patterns by altering the sequence of splice sites, many more modify the binding sites of RNA-binding proteins. Genetic variants affecting splicing can have a stronger phenotypic impact than those affecting gene expression.

References 87

1. 1.

   Nilsen TW, Graveley BR. Expansion of the eukaryotic proteome by alternative splicing. Nature. 2010;463:457-463.

   Not in our library10.1038/nature08909 (opens in a new tab)

2. 2.

   Keren H, Lev-Maor G, Ast G. Alternative splicing and evolution: diversification, exon definition and function. Nat. Rev. Genet. 2010;11:345-55.

   Not in our library10.1038/nrg2776 (opens in a new tab)

3. 3.

   Scotti MM, Swanson MS. RNA mis-splicing in disease. Nat. Rev. Genet. 2016;17:19-32.

   Not in our library10.1038/nrg.2015.3 (opens in a new tab)

4. 4.

   Chen M, Manley JL. Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches. Nat. Rev. Mol. Cell Biol. 2009;10:741-754.

   Not in our library10.1038/nrm2777 (opens in a new tab)

5. 5.

   Fu X-D, Ares M. Context-dependent control of alternative splicing by RNA-binding proteins. Nat. Rev. Genet. 2014;15:689-701.

   Not in our library10.1038/nrg3778 (opens in a new tab)

6. 6.

   Kornblihtt AR, et al. Alternative splicing: a pivotal step between eukaryotic transcription and translation. Nat. Rev. Mol. Cell Biol. 2013;14:153-165.

   Not in our library10.1038/nrm3525 (opens in a new tab)

7. 7.

   Lappalainen T, et al. Transcriptome and genome sequencing uncovers functional variation in humans. Nature. 2013;501:506-11.

   Not in our library10.1038/nature12531 (opens in a new tab)

8. 8.

   Battle A, et al. Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals. Genome Res. 2014;24:14-24.

   Not in our library10.1101/gr.155192.113 (opens in a new tab)

9. 9.
   Genome-wide identification of splicing QTLs in the human brain and their enrichment among schizophrenia-associated loci · 2017

   No notice
10. 10.

    Raj T, et al. Integrative transcriptome analyses of the aging brain implicate altered splicing in Alzheimer’s disease susceptibility. Nat. Genet. 2018;50:1584-1592.

    Not in our library10.1038/s41588-018-0238-1 (opens in a new tab)

11. 11.

    Tian J, et al. CancerSplicingQTL: a database for genome-wide identification of splicing QTLs in human cancer. Nucleic Acids Res. 2019;47:D909-D916.

    Not in our library10.1093/nar/gky954 (opens in a new tab)

12. 12.

    The GTEx Consortium. The GTEx Consortium atlas of genetic regulatory effects across human tissues. Science369, 1318–1330 (2020).

    Not in our library10.1126/science.aaz1776 (opens in a new tab)

13. 13.

    Ma L, Jia P, Zhao Z. Splicing QTL of human adipose-related traits. Sci. Rep. 2018;8:318.

    Not in our library10.1038/s41598-017-18767-z (opens in a new tab)

14. 14.

    Caswell JL, et al. Multiple breast cancer risk variants are associated with differential transcript isoform expression in tumors. Human Mol. Genet. 2015;24:7421-31.

    Not in our library10.1093/hmg/ddv432 (opens in a new tab)

15. 15.

    Li YI, et al. RNA splicing is a primary link between genetic variation and disease. Science. 2016;352:600-604.

    Not in our library10.1126/science.aad9417 (opens in a new tab)

16. 16.

    Rotival M, Quach H, Quintana-Murci L. Defining the genetic and evolutionary architecture of alternative splicing in response to infection. Nat. Commun. 2019;10:1671.

    Not in our library10.1038/s41467-019-09689-7 (opens in a new tab)

17. 17.

    Ongen H, Dermitzakis ET. Alternative splicing QTLs in European and African populations. Am. J. Human Genet. 2015;97:567-75.

    Not in our library10.1016/j.ajhg.2015.09.004 (opens in a new tab)

18. 18.

    Li YI, et al. Annotation-free quantification of RNA splicing using LeafCutter. Nat. Genet. 2018;50:151-158.

    Not in our library10.1038/s41588-017-0004-9 (opens in a new tab)

19. 19.

    López-Bigas N, Audit B, Ouzounis C, Parra G, Guigó R. Are splicing mutations the most frequent cause of hereditary disease? FEBS Lett. 2005;579:1900-1903.

    Not in our library10.1016/j.febslet.2005.02.047 (opens in a new tab)

20. 20.

    Monlong J, Calvo M, Ferreira PG, Guigó R. Identification of genetic variants associated with alternative splicing using sQTLseekeR. Nat. Commun. 2014;5:4698.

    Not in our library10.1038/ncomms5698 (opens in a new tab)

21. 21.

    Anderson M. A new method for non-parametric multivariate analysis of variance. Australian Ecol. 2001;26:32-46.

    Not in our library

22. 22.

    Anderson MJ, Robinson J. Generalized discriminant analysis based on distances. Australian N. Zealand J. Stat. 2003;45:301-318.

    Not in our library10.1111/1467-842x.00285 (opens in a new tab)

23. 23.

    Di Tommaso P, et al. Nextflow enables reproducible computational workflows. Nat. Biotechnol. 2017;35:316-319.

    Not in our library10.1038/nbt.3820 (opens in a new tab)

24. 24.
    Genetic effects on gene expression across human tissues · 2017

    Corrected
25. 25.
    xCell: digitally portraying the tissue cellular heterogeneity landscape · 2017

    No notice
26. 26.

    Jangi M, Sharp P. Building robust transcriptomes with master splicing factors. Cell. 2014;159:487-498.

    Not in our library10.1016/j.cell.2014.09.054 (opens in a new tab)

27. 27.
    Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells · 2016

    No notice
28. 28.
    Alternative start and termination sites of transcription drive most transcript isoform differences across human tissues · 2017

    No notice
29. 29.

    The GTEx Consortium. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science348, 648–60 (2015).

    Not in our library10.1126/science.1262110 (opens in a new tab)

30. 30.

    Urbut SM, Wang G, Carbonetto P, Stephens M. Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions. Nat. Genet. 2019;51:187-195.

    Not in our library10.1038/s41588-018-0268-8 (opens in a new tab)

31. 31.

    Yanai I, et al. Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics. 2005;21:650-659.

    Not in our library10.1093/bioinformatics/bti042 (opens in a new tab)

32. 32.

    Adzhubei IA, et al. A method and server for predicting damaging missense mutations. Nat. Methods. 2010;7:248-249.

    Not in our library10.1038/nmeth0410-248 (opens in a new tab)

33. 33.

    Sim N-L, et al. SIFT web server: predicting effects of amino acid substitutions on proteins. Nucleic Acids Res. 2012;40:W452-W457.

    Not in our library10.1093/nar/gks539 (opens in a new tab)

34. 34.

    Van Nostrand EL, et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat. Methods. 2016;13:508-514.

    Not in our library10.1038/nmeth.3810 (opens in a new tab)

35. 35.
    Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features · 2014

    Corrected
36. 36.

    Lee D, et al. A method to predict the impact of regulatory variants from DNA sequence. Nat. Genet. 2015;47:955-961.

    Not in our library10.1038/ng.3331 (opens in a new tab)

37. 37.

    Ghandi M, et al. gkmSVM: an R package for gapped-kmer SVM. Bioinformatics. 2016;32:2205-7.

    Not in our library10.1093/bioinformatics/btw203 (opens in a new tab)

38. 38.

    Yang E-W, et al. Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA. Nat. Commun. 2019;10:1338.

    Not in our library10.1038/s41467-019-09292-w (opens in a new tab)

39. 39.

    Wickramasinghe VO, et al. Regulation of constitutive and alternative mRNA splicing across the human transcriptome by PRPF8 is determined by 5’ splice site strength. Genome Biol. 2015;16:201.

    Not in our library10.1186/s13059-015-0749-3 (opens in a new tab)

40. 40.

    Tilgner H, et al. Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs. Genome Res. 2012;22:1616-1625.

    Not in our library10.1101/gr.134445.111 (opens in a new tab)

41. 41.

    Malone J, et al. Modeling sample variables with an Experimental Factor Ontology. Bioinformatics. 2010;26:1112-1118.

    Not in our library10.1093/bioinformatics/btq099 (opens in a new tab)

42. 42.

    Demenais F, et al. Multiancestry association study identifies new asthma risk loci that colocalize with immune-cell enhancer marks. Nature Genet. 2018;50:42-53.

    Not in our library10.1038/s41588-017-0014-7 (opens in a new tab)

43. 43.

    Michailidou K, et al. Association analysis identifies 65 new breast cancer risk loci. Nature. 2017;551:92-94.

    Not in our library10.1038/nature24284 (opens in a new tab)

44. 44.

    Schunkert H, et al. Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease. Nat. Genet. 2011;43:333-338.

    Not in our library10.1038/ng.784 (opens in a new tab)

45. 45.

    den Hoed M, et al. Identification of heart rate-associated loci and their effects on cardiac conduction and rhythm disorders. Nat. Genet. 2013;45:621-631.

    Not in our library10.1038/ng.2610 (opens in a new tab)

46. 46.

    Wood AR, et al. Defining the role of common variation in the genomic and biological architecture of adult human height. Nat. Genet. 2014;46:1173-1186.

    Not in our library10.1038/ng.3097 (opens in a new tab)

47. 47.

    The Global Lipids Genetics Consortium. Discovery and refinement of loci associated with lipid levels. Nat. Genet.45, 1274–1283 (2013).

    Not in our library10.1038/ng.2797 (opens in a new tab)

48. 48.

    Okada Y, et al. Genetics of rheumatoid arthritis contributes to biology and drug discovery. Nature. 2014;506:376-81.

    Not in our library10.1038/nature12873 (opens in a new tab)

49. 49.

    Schizophrenia Working Group of the Psychiatric Genomics Consortium. Biological insights from 108 schizophrenia-associated genetic loci. Nature511, 421–427 (2014).

    Not in our library10.1038/nature13595 (opens in a new tab)

50. 50.

    Pickrell J. Joint analysis of functional genomic data and genome-wide association studies of 18 human traits. Am. J. Human Genet. 2014;94:559-573.

    Not in our library10.1016/j.ajhg.2014.03.004 (opens in a new tab)

51. 51.

    Saleh NM, et al. Genetic association analyses of atopic illness and proinflammatory cytokine genes with type 1 diabetes. Diabetes. 2011;27:838-43.

    Not in our library10.1002/dmrr.1259 (opens in a new tab)

52. 52.

    McGovern DPB, et al. Genome-wide association identifies multiple ulcerative colitis susceptibility loci. Nat. Genet. 2010;42:332-7.

    Not in our library10.1038/ng.549 (opens in a new tab)

53. 53.

    Eyre S, et al. High-density genetic mapping identifies new susceptibility loci for rheumatoid arthritis. Nat. Genet. 2012;44:1336-40.

    Not in our library10.1038/ng.2462 (opens in a new tab)

54. 54.

    Panganiban RA, et al. A functional splice variant associated with decreased asthma risk abolishes the ability of gasdermin B to induce epithelial cell pyroptosis. J. Allergy Clin. Immunol. 2018;142:1469-1478.

    Not in our library10.1016/j.jaci.2017.11.040 (opens in a new tab)

55. 55.

    Das S, et al. GSDMB induces an asthma phenotype characterized by increased airway responsiveness and remodeling without lung inflammation. Proc. Natl Acad. Sci. USA. 2016;113:13132-13137.

    Not in our library10.1073/pnas.1610433113 (opens in a new tab)

56. 56.

    Ding J, et al. Pore-forming activity and structural autoinhibition of the gasdermin family. Nature. 2016;535:111-116.

    Not in our library10.1038/nature18590 (opens in a new tab)

57. 57.

    Gonzàlez-Porta M, Calvo M, Sammeth M, Guigó R. Estimation of alternative splicing variability in human populations. Genome Res. 2012;22:528-38.

    Not in our library10.1101/gr.121947.111 (opens in a new tab)

58. 58.

    Melé M, et al. Human genomics. The human transcriptome across tissues and individuals. Science. 2015;348:660-5.

    Not in our library10.1126/science.aaa0355 (opens in a new tab)

59. 59.

    Sibley CR. Regulation of gene expression through production of unstable mRNA isoforms. Biochem. Soc. Trans. 2014;42:1196-1205.

    Not in our library10.1042/bst20140102 (opens in a new tab)

60. 60.

    Bhatt DM, et al. Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions. Cell. 2012;150:279-290.

    Not in our library10.1016/j.cell.2012.05.043 (opens in a new tab)

61. 61.

    Pandya-Jones A, et al. Splicing kinetics and transcript release from the chromatin compartment limit the rate of Lipid A-induced gene expression. RNA. 2013;19:811-827.

    Not in our library10.1261/rna.039081.113 (opens in a new tab)

62. 62.

    Gerstberger S, Hafner M, Tuschl T. A census of human RNA-binding proteins. Nat. Rev. Genet. 2014;15:829-845.

    Not in our library10.1038/nrg3813 (opens in a new tab)

63. 63.
    Bayesian Test for Colocalisation between Pairs of Genetic Association Studies Using Summary Statistics · 2014

    No notice
64. 64.

    Pickrell JK, et al. Detection and interpretation of shared genetic influences on 42 human traits. Nat. Genet. 2016;48:709-17.

    Not in our library10.1038/ng.3570 (opens in a new tab)

65. 65.

    Hormozdiari F, et al. Colocalization of GWAS and eQTL signals detects target genes. Am. J. Human Genet. 2016;99:1245-1260.

    Not in our library10.1016/j.ajhg.2016.10.003 (opens in a new tab)

66. 66.

    Hormozdiari F, Kostem E, Kang EY, Pasaniuc B, Eskin E. Identifying causal variants at loci with multiple signals of association. Genetics. 2014;198:497-508.

    Not in our library10.1534/genetics.114.167908 (opens in a new tab)

67. 67.

    Brown AA, et al. Predicting causal variants affecting expression by using whole-genome sequencing and RNA-seq from multiple human tissues. Nat. Genet. 2017;49:1747-1751.

    Not in our library10.1038/ng.3979 (opens in a new tab)

68. 68.

    Wen X, Lee Y, Luca F, Pique-Regi R. Efficient integrative multi-SNP association analysis via deterministic approximation of posteriors. Am. J. Human Genet. 2016;98:1114-1129.

    Not in our library10.1016/j.ajhg.2016.03.029 (opens in a new tab)

69. 69.

    Jaganathan K, et al. Predicting splicing from primary sequence with deep learning. Cell. 2019;176:535-548.

    Not in our library10.1016/j.cell.2018.12.015 (opens in a new tab)

70. 70.
    MMSplice: modular modeling improves the predictions of genetic variant effects on splicing · 2019

    No notice
71. 71.

    Jagadeesh KA, et al. S-CAP extends pathogenicity prediction to genetic variants that affect RNA splicing. Nat. Genet. 2019;51:755-763.

    Not in our library10.1038/s41588-019-0348-4 (opens in a new tab)

72. 72.

    Dobin A, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29:15-21.

    Not in our library10.1093/bioinformatics/bts635 (opens in a new tab)

73. 73.
    RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome · 2011

    No notice
74. 74.

    Anderson MJ. Distance-based tests for homogeneity of multivariate dispersions. Biometrics. 2006;62:245-253.

    Not in our library10.1111/j.1541-0420.2005.00440.x (opens in a new tab)

75. 75.
    REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms · 2011

    No notice
76. 76.

    Storey JD, Tibshirani R. Statistical significance for genomewide studies. Proc. Natl Acad. Sci. USA. 2003;100:9440-5.

    Not in our library10.1073/pnas.1530509100 (opens in a new tab)

77. 77.
    A General Definition and Nomenclature for Alternative Splicing Events · 2008

    No notice
78. 78.

    The ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature489, 57–74 (2012).

    Not in our library10.1038/nature11247 (opens in a new tab)

79. 79.

    Davis CA, et al. The Encyclopedia of DNA elements (ENCODE): data portal update. Nucleic Acids Res. 2018;46:D794-D801.

    Not in our library10.1093/nar/gkx1081 (opens in a new tab)

80. 80.
    dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering · 2015

    No notice
81. 81.

    Parra G, Blanco E, Guigó R. GeneId in Drosophila. Genome Res. 2000;10:511-515.

    Not in our library10.1101/gr.10.4.511 (opens in a new tab)

82. 82.

    Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Mol. Biol. Evol. 2013;30:772-80.

    Not in our library10.1093/molbev/mst010 (opens in a new tab)

83. 83.
    ontologyX: a suite of R packages for working with ontological data · 2016

    No notice
84. 84.
    Identification and analysis of splicing quantitative trait loci across multiple tissues in the human genome · 2021

    No notice
85. 85.
    Identification and analysis of splicing quantitative trait loci across multiple tissues in the human genome · 2021

    No notice
86. 86.
    ggsashimi: Sashimi plot revised for browser- and annotation-independent splicing visualization · 2018

    No notice
87. 87.
    Identification of Common Genetic Variation That Modulates Alternative Splicing · 2007

    No notice

Cited by papers we hold 3

• Genetic control of RNA splicing and its distinct role in complex trait variation · 2022
  No notice
• Extensive Variation in Gene Expression is Revealed in 13 Fertility-Related Genes Using RNA-Seq, ISO-Seq, and CAGE-Seq From Brahman Cattle · 2022
  Not checked
• Clinical implementation of RNA sequencing for Mendelian disease diagnostics · 2022
  No notice

Questions about this paper

Reads

A person counts once a day per paper. We keep no cookie and no address: a reader is a hash that changes every day. Any month under five reads shows no number.