Skip to main content
SpringerLink
Log in

Using RNA-Seq to Discover Genetic Polymorphisms That Produce Hidden Splice Variants

  • Protocol
  • First Online:
mRNA Processing

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1648))

Abstract

RNA-seq is a powerful and popular technology for studying posttranscriptional regulation of gene expression, such as alternative splicing. The first step in analyzing RNA-seq data is to map the sequenced reads back to the genome. However, commonly used RNA-seq aligners use the consensus splice site dinucleotide motifs to map reads across splice junctions. This can be deceiving due to genomic variants that create novel splice site dinucleotides, leaving the personal splice junction reads un-mapped to the reference genome. We developed and evaluated a method called RNA Personal Genome Alignment Analyzer (rPGA) to identify “hidden” splicing variations in personal transcriptomes, by mapping personal RNA-seq data to personal genomes. Our work demonstrates that the personal genome approach to RNA-seq read alignment enables the discovery of a large but previously unknown catalog of splicing variations in human populations.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Institutional subscriptions

References

  1. Nilsen TW, Graveley BR (2010) Expansion of the eukaryotic proteome by alternative splicing. Nature 463:457–463. Issn: 1476–4687 (Electronic) 0028–0836 (Linking)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Wang ET et al (2008) Alternative isoform regulation in human tissue transcriptomes. Nature 456:470–476. Issn: 1476–4687 (Electronic) 0028–0836 (Linking)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Hull J et al (2007) Identification of common genetic variation that modulates alternative splicing. PLoS Genet 3:e99. Issn: 1553–7404 (Electronic) 1553–7390 (Linking)

    Article  PubMed  PubMed Central  Google Scholar 

  4. Kwan T et al (2008) Genome-wide analysis of transcript isoform variation in humans. Nat Genet 40:225–231. Issn: 1546–1718 (Electronic) 1061–4036 (Linking)

    Article  CAS  PubMed  Google Scholar 

  5. Kwan T et al (2007) Heritability of alternative splicing in the human genome. Genome Res 17:1210–1218. Issn: 1088–9051 (Print) 1088–9051 (Linking) (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Garcia-Blanco MA, Baraniak AP, Lasda EL (2004) Alternative splicing in dis-ease and therapy. Nat Biotechnol 22:535–546. Issn: 1087–0156 (Print) 1087–0156 (Linking)

    Article  CAS  PubMed  Google Scholar 

  7. Ward AJ, Cooper TA (2010) The pathobiology of splicing. J Pathol 220:152–163. Issn: 1096–9896 (Electronic) 0022–3417 (Linking)

    Google Scholar 

  8. Lu ZX, Jiang P, Xing Y (2012) Genetic variation of pre-mRNA alternative splicing in human populations. Wiley Interdiscip Rev RNA 3:581–592. Issn: 1757–7012 (Electronic) 1757–7004 (Linking).

    Article  CAS  PubMed  Google Scholar 

  9. Sheth N et al (2006) Comprehensive splice-site analysis using comparative genomics. Nucleic Acids Res 34:3955–3967. Issn: 1362–4962 (Electronic) 0305–1048 (Linking)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Kurmangaliyev YZ, Sutormin RA, Naumenko SA, Bazykin GA, Gelfand MS (2013) Functional implications of splicing polymorphisms in the human genome. Hum Mol Genet 22:3449–3459. Issn: 1460–2083 (Electronic) 0964–6906 (Linking)

    Article  CAS  PubMed  Google Scholar 

  11. Krawczak M, Reiss J, Cooper DN (1992) The mutational spectrum of single base-pair substitutions in mRNA splice junctions of human genes: causes and consequences. Hum Genet 90:41–54. Issn: 0340–6717 (Print) 0340–6717 (Linking)

    Article  CAS  PubMed  Google Scholar 

  12. Katz Y, Wang ET, Airoldi EM, Burge CB (2010) Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat Methods 7:1009–1015. Issn: 1548–7105 (Electronic) 1548–7091 (Linking).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621–628. Issn: 1548–7105 (Electronic) 1548–7091 (Linking)

    Article  CAS  PubMed  Google Scholar 

  14. Shen S et al (2012) MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data. Nucleic Acids Res 40:e61

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Shen S et al (2014) rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data. Proc Natl Acad Sci U S A 111:E5593–E5601. Issn: 1091–6490 (Electronic) 0027–8424 (Linking)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Dobin A et al (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29:15–21. Issn: 1367–4811 (Electronic) 1367–4803 (Linking).

    Article  CAS  PubMed  Google Scholar 

  17. Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25:1105–1111. Issn: 1367–4811 (Electronic) 1367–4803 (Linking)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Stein S, Lu ZX, Bahrami-Samani E, Park JW, Xing Y (2015) Discover hidden splicing variations by mapping personal transcriptomes to personal genomes. Nucleic Acids Res 43:10612–10622. Issn: 1362–4962 (Electronic) 0305–1048 (Linking)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, 650 Charles E. Young Drive South, Los Angeles, CA, 90095, USA

    Shayna Stein, Emad Bahrami-Samani & Yi Xing

Authors
  1. Shayna Stein
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Emad Bahrami-Samani
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yi Xing
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yi Xing .

Editor information

Editors and Affiliations

  1. Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, California, USA

    Yongsheng Shi

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer Science+Business Media LLC

About this protocol

Cite this protocol

Stein, S., Bahrami-Samani, E., Xing, Y. (2017). Using RNA-Seq to Discover Genetic Polymorphisms That Produce Hidden Splice Variants. In: Shi, Y. (eds) mRNA Processing. Methods in Molecular Biology, vol 1648. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7204-3_10

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-7204-3_10

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7203-6

  • Online ISBN: 978-1-4939-7204-3

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation