Skip to main content
SpringerLink
Log in
Book cover

Transcriptome Data Analysis pp 101–108Cite as

Analysis of RNA Editing Sites from RNA-Seq Data Using GIREMI

  • Protocol
  • First Online:

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1751))

Abstract

RNA editing is a posttranscriptional modification process that alters the sequence of RNA molecules. RNA editing is related to many human diseases. However, the identification of RNA editing sites typically requires matched genomic sequence or multiple related expression data sets. Here we describe the GIREMI tool (genome-independent identification of RNA editing by mutual information; https://github.com/zhqingit/giremi) that is designed to accurately and sensitively predict adenosine-to-inosine editing from a single RNA-Seq data set.

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

Protocol
USD   49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   159.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Springer Nature is developing a new tool to find and evaluate Protocols. Learn more

References

  1. Keegan LP, Gallo A, O’Connell MA (2001) The many roles of an RNA editor. Nat Rev Genet 2:869–878

    Article  CAS  PubMed  Google Scholar 

  2. Wang Q, Miyakoda M, Yang W et al (2004) Stress-induced apoptosis associated with null mutation of ADAR1 RNA editing deaminase gene. J Biol Chem 279:4952–4961

    Article  CAS  PubMed  Google Scholar 

  3. Higuchi M, Maas S, Single FN et al (2000) Point mutation in an AMPA receptor gene rescues lethality in mice deficient in the RNA-editing enzyme ADAR2. Nature 406:78–81

    Article  CAS  PubMed  Google Scholar 

  4. Maas S, Kawahara Y, Tamburro KM, Nishikura K (2006) A-to-I RNA editing and human disease. RNA Biol 3:1–9

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Miyamura Y, Suzuki T, Kono M, Inagaki K, Ito S, Suzuki N et al (2003) Mutations of the RNA-specific adenosine deaminase gene (DSRAD) are involved in dyschromatosis symmetrica hereditaria. Am J Hum Genet 73:693–699

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Rice GI, Kasher PR, Forte GM, Mannion NM, Greenwood SM, Szynkiewicz M et al (2012) Mutations in ADAR1 cause Aicardi-Goutieres syndrome associated with a type I interferon signature. Nat Genet 44:1243–1248

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Chen L (2013) Characterization and comparison of human nuclear and cytosolic editomes. Proc Natl Acad Sci U S A 110:E2741–E2747

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Paz N, Levanon EY, Amariglio N, Heimberger AB, Ram Z, Constantini S et al (2007) Altered adenosine-to-inosine RNA editing in human cancer. Genome Res 17:1586–1595

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Paz-Yaacov N, Bazak L, Buchumenski I, Porath HT, Danan-Gotthold M, Knisbacher BA et al (2015) Elevated RNA editing activity is a major contributor to transcriptomic diversity in tumors. Cell Rep 13:267–276

    Article  CAS  PubMed  Google Scholar 

  10. Han L, Diao L, Yu S, Xu X, Li J, Zhang R et al (2015) The genomic landscape and clinical relevance of A-to-I RNA editing in human cancers. Cancer Cell 28:515–528

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Lee J-H, Ang JK, Xiao X (2013) Analysis and design of RNA sequencing experiments for identifying RNA editing and other single-nucleotide variants. RNA 19:725–732

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Ramaswami G, Zhang R, Piskol R, Keegan LP, Deng P, O'Connell MA, Li JB (2013) Identifying RNA editing sites using RNA sequencing data alone. Nat Methods 10:128–132

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Zhang Q, Xiao X (2015) Genome sequence-independent identification of RNA editing sites. Nat Methods 12:347–350

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25

    Article  PubMed  PubMed Central  Google Scholar 

  15. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics 25:1754–1760

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Kent WJ (2002) BLAT--the BLAST-like alignment tool. Genome Res 12(4):656–664

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010) The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297–1303

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. DePristo M, Banks E, Poplin R, Garimella K, Maguire J, Hartl C, Philippakis A, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell T, Kernytsky A, Sivachenko A, Cibulskis K, Gabriel S, Altshuler D, Daly M (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43:491–498

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Van der Auwera GA, Carneiro M, Hartl C, Poplin R, del Angel G, Levy-Moonshine A, Jordan T, Shakir K, Roazen D, Thibault J, Banks E, Garimella K, Altshuler D, Gabriel S, DePristo M (2013) From FastQ data to high-confidence variant calls: the genome analysis toolkit best practices pipeline. Curr Protoc Bioinformatics 43:11.10.1–11.10.33

    Google Scholar 

  20. Li H (2011) A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27(21):2987–2993

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Ahn J, Xiao X (2015) RASER: reads aligner for SNPs and editing sites of RNA. Bioinformatics 31(24):3906–3913

    CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Integrative Biology and Physiology, The University of California, Los Angeles (UCLA), Los Angeles, CA, USA

    Qing Zhang

Authors
  1. Qing Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Cell Biology and Genetics, School of Basic Medicine, Shenzhen University Health, Science Center, Shenzhen, China

    Yejun Wang

  2. Epigenomics and Computational Biology Lab, Biocomplexity Institute of Virginia Tech, Blacksburg, Virginia, USA

    Ming-an Sun

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Science+Business Media, LLC

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Zhang, Q. (2018). Analysis of RNA Editing Sites from RNA-Seq Data Using GIREMI. In: Wang, Y., Sun, Ma. (eds) Transcriptome Data Analysis. Methods in Molecular Biology, vol 1751. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7710-9_7

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-7710-9_7

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7709-3

  • Online ISBN: 978-1-4939-7710-9

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation