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PMID: 25730491 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, U.S. Gov't, Non-P.H.S.

Genome sequence-independent identification of RNA editing sites.

Nature methods ·Vol. 12 ·No. 4 ·2015-04-00 ·Pages 347-50

Zhang Q, Xiao X

Abstract

RNA editing generates post-transcriptional sequence changes that can be deduced from RNA-seq data, but detection typically requires matched genomic sequence or multiple related expression data sets. We developed the GIREMI tool (genome-independent identification of RNA editing by mutual information; https://www.ibp.ucla.edu/research/xiao/GIREMI.html) to predict adenosine-to-inosine editing accurately and sensitively from a single RNA-seq data set of modest sequencing depth. Using GIREMI on existing data, we observed tissue-specific and evolutionary patterns in editing sites in the human population.

MeSH Terms
Evolution, Molecular Genomics Humans RNA Editing/genetics Sequence Analysis, RNA/methods
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Zhang Qing
Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, USA.
Xiao Xinshu
1] Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, USA. [2] Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, USA. [3] Molecular Biology Institute, University of California, Los Angeles, Los Angeles, USA.
References (39)
39 references, click to expand
  1. RNA editome in rhesus macaque shaped by purifying selection.
    PLoS Genet. 2014 Apr;10(4):e1004274 PMID: 24722121
  2. Mammalian conserved ADAR targets comprise only a small fragment of the human editosome.
    Genome Biol. 2014;15(1):R5 PMID: 24393560
  3. RNA editing by adenosine deaminases that act on RNA.
    Annu Rev Biochem. 2002;71:817-46 PMID: 12045112
  4. Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts.
    Genome Res. 2009 Mar;19(3):381-94 PMID: 19116412
  5. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
    Genome Biol. 2009;10(3):R25 PMID: 19261174
  6. Recognition and coupling of A-to-I edited sites are determined by the tertiary structure of the RNA.
    Nucleic Acids Res. 2009 Nov;37(20):6916-26 PMID: 19740768
  7. Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping.
    Mol Cell. 2009 Dec 25;36(6):996-1006 PMID: 20064465
  8. U87MG decoded: the genomic sequence of a cytogenetically aberrant human cancer cell line.
    PLoS Genet. 2010 Jan;6(1):e1000832 PMID: 20126413
  9. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP.
    Cell. 2010 Apr 2;141(1):129-41 PMID: 20371350
  10. Molecular diversity through RNA editing: a balancing act.
    Trends Genet. 2010 May;26(5):221-30 PMID: 20395010
  11. Functions and regulation of RNA editing by ADAR deaminases.
    Annu Rev Biochem. 2010;79:321-49 PMID: 20192758
  12. iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution.
    Nat Struct Mol Biol. 2010 Jul;17(7):909-15 PMID: 20601959
  13. iCLIP predicts the dual splicing effects of TIA-RNA interactions.
    PLoS Biol. 2010;8(10):e1000530 PMID: 21048981
  14. Analysis and design of RNA sequencing experiments for identifying isoform regulation.
    Nat Methods. 2010 Dec;7(12):1009-15 PMID: 21057496
  15. Characterizing the RNA targets and position-dependent splicing regulation by TDP-43.
    Nat Neurosci. 2011 Apr;14(4):452-8 PMID: 21358640
  16. Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability.
    Mol Cell. 2011 Aug 5;43(3):327-39 PMID: 21723170
  17. RNA targets of wild-type and mutant FET family proteins.
    Nat Struct Mol Biol. 2011 Dec;18(12):1428-31 PMID: 22081015
  18. Analysis of transcriptome complexity through RNA sequencing in normal and failing murine hearts.
    Circ Res. 2011 Dec 9;109(12):1332-41 PMID: 22034492
  19. The UCSC Genome Browser database: extensions and updates 2011.
    Nucleic Acids Res. 2012 Jan;40(Database issue):D918-23 PMID: 22086951
  20. Accurate identification of A-to-I RNA editing in human by transcriptome sequencing.
    Genome Res. 2012 Jan;22(1):142-50 PMID: 21960545
  21. Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome.
    Nat Biotechnol. 2012 Mar;30(3):253-60 PMID: 22327324
  22. Comment on "Widespread RNA and DNA sequence differences in the human transcriptome".
    Science. 2012 Mar 16;335(6074):1302; author reply 1302 PMID: 22422962
  23. Comment on "Widespread RNA and DNA sequence differences in the human transcriptome".
    Science. 2012 Mar 16;335(6074):1302; author reply 1302 PMID: 22422963
  24. Comment on "Widespread RNA and DNA sequence differences in the human transcriptome".
    Science. 2012 Mar 16;335(6074):1302; author reply 1302 PMID: 22422964
  25. Identification of allele-specific alternative mRNA processing via transcriptome sequencing.
    Nucleic Acids Res. 2012 Jul;40(13):e104 PMID: 22467206
  26. DGCR8 HITS-CLIP reveals novel functions for the Microprocessor.
    Nat Struct Mol Biol. 2012 Aug;19(8):760-6 PMID: 22796965
  27. Accurate identification of human Alu and non-Alu RNA editing sites.
    Nat Methods. 2012 Jun;9(6):579-81 PMID: 22484847
  28. Landscape of transcription in human cells.
    Nature. 2012 Sep 6;489(7414):101-8 PMID: 22955620
  29. Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins.
    Cell Rep. 2012 Feb 23;1(2):167-78 PMID: 22574288
  30. LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance.
    Mol Cell. 2012 Oct 26;48(2):195-206 PMID: 22959275
  31. Mixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MOV10 PAR-CLIP data.
    Nucleic Acids Res. 2012 Nov 1;40(20):e160 PMID: 22844102
  32. An integrated map of genetic variation from 1,092 human genomes.
    Nature. 2012 Nov 1;491(7422):56-65 PMID: 23128226
  33. Identifying RNA editing sites using RNA sequencing data alone.
    Nat Methods. 2013 Feb;10(2):128-32 PMID: 23291724
  34. Analysis and design of RNA sequencing experiments for identifying RNA editing and other single-nucleotide variants.
    RNA. 2013 Jun;19(6):725-32 PMID: 23598527
  35. The Genotype-Tissue Expression (GTEx) project.
    Nat Genet. 2013 Jun;45(6):580-5 PMID: 23715323
  36. Characterization and comparison of human nuclear and cytosolic editomes.
    Proc Natl Acad Sci U S A. 2013 Jul 16;110(29):E2741-7 PMID: 23818636
  37. A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes.
    Genome Res. 2014 Mar;24(3):365-76 PMID: 24347612
  38. Genome-wide analysis of Alu editability.
    Nucleic Acids Res. 2014 Jun;42(11):6876-84 PMID: 24829451
  39. BLAT--the BLAST-like alignment tool.
    Genome Res. 2002 Apr;12(4):656-64 PMID: 11932250
Article Info
Journal
Nature methods
Abbr.
Nat Methods
ISSN
1548-7105
DOI
10.1038/nmeth.3314
Published
2015-04-00
Epub
2015-00-02
Pages
347-50
Language
English
Region
United States
NLM ID
101215604
PMCID
PMC4382388
Subset
IM
Grants
NHGRI NIH HHS · R01 HG006264 · United States
NHGRI NIH HHS · U01 HG007013 · United States
NHGRI NIH HHS · R01HG006264 · United States
NHGRI NIH HHS · U01HG007013 · United States
External Links
PubMed source DOI: 10.1038/nmeth.3314 PMC Full Text View journal details
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