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NONCODEv4: Annotation of Noncoding RNAs with Emphasis on Long Noncoding RNAs

  • Yi Zhao
  • Jiao Yuan
  • Runsheng ChenEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1402)

Abstract

The rapid development of high-throughput sequencing technologies and bioinformatics algorithms now enables detection and profiling of a large number of noncoding transcripts. Long noncoding RNAs (lncRNAs), which are longer than 200 nucleotides, are accumulating with important roles involved in biological processes and tissue physiology. In this chapter, we describe the use of NONCODEv4, a database that provide a comprehensive catalog of noncoding RNAs with particularly detailed annotations for lncRNAs. NONCODEv4 stores more than half million transcripts, of which more than 200,000 are lncRNAs. NONCODEv4 raises the concept of lncRNA genes and explores their expression and functions based on public transcriptome data. NONCODEv4 also integrated a series of online tools and have a web interface easy to use. NONCODEv4 is available at http://www.noncode.org/ http://www.bioinfo.org/noncode.

Key words

Sequencing lncRNA lncRNA gene Expression Function 

Notes

Acknowledgment

This work was supported by National High-tech Research and Development Projects 863 [2012AA020402, 2012AA022501], National Key Basic Research and Development Program 973 [2009CB825401], Training Program of the Major Research plan of the National Natural Science Foundation of China [91229120], and National Natural Science Foundation of China [31371320]. Funding for open access charge: Training Program of the Major Research plan of the National Natural Science Foundation of China [91229120].

References

  1. 1.
    Himeno H, Kurita D, Muto A (2014) tmRNA-mediated trans-translation as the major ribosome rescue system in a bacterial cell. Front Genet 5:66CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Jones TA, Otto W, Marz M, Eddy SR, Stadler PF (2009) A survey of nematode SmY RNAs. RNA Biol 6:5–8CrossRefPubMedGoogle Scholar
  3. 3.
    Christov CP, Gardiner TJ, Szuts D, Krude T (2006) Functional requirement of noncoding Y RNAs for human chromosomal DNA replication. Mol Cell Biol 26:6993–7004CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Mercer TR, Dinger ME, Mattick JS (2009) Long non-coding RNAs: insights into functions. Nat Rev Genet 10:155–159CrossRefPubMedGoogle Scholar
  5. 5.
    Croucher NJ, Thomson NR (2010) Studying bacterial transcriptomes using RNA-seq. Curr Opin Microbiol 13:619–624CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-seq. Nat Methods 5:621–628CrossRefPubMedGoogle Scholar
  7. 7.
    Xie C, Yuan J, Li H, Li M, Zhao G, Bu D, Zhu W, Wu W, Chen R, Zhao Y (2014) NONCODEv4: exploring the world of long non-coding RNA genes. Nucleic Acids Res 42:D98–D103CrossRefPubMedGoogle Scholar
  8. 8.
    Flicek P, Ahmed I, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S et al (2013) Ensembl 2013. Nucleic Acids Res 41:D48–D55CrossRefPubMedGoogle Scholar
  9. 9.
    Pruitt KD, Tatusova T, Brown GR, Maglott DR (2012) NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res 40:D130–D135CrossRefPubMedGoogle Scholar
  10. 10.
    Bu D, Yu K, Sun S, Xie C, Skogerbo G, Miao R, Xiao H, Liao Q, Luo H, Zhao G et al (2012) NONCODE v3.0: integrative annotation of long noncoding RNAs. Nucleic Acids Res 40:D210–D215CrossRefPubMedGoogle Scholar
  11. 11.
    Picardi E, D’Erchia AM, Gallo A, Montalvo A, Pesole G (2014) Uncovering RNA editing sites in long non-coding RNAs. Front Bioeng Biotechnol 2:64CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Lipman DJ, Pearson WR (1985) Rapid and sensitive protein similarity searches. Science 227:1435–1441CrossRefPubMedGoogle Scholar
  13. 13.
    Liao Q, Xiao H, Bu D, Xie C, Miao R, Luo H, Zhao G, Yu K, Zhao H, Skogerbo G et al (2011) ncFANs: a web server for functional annotation of long non-coding RNAs. Nucleic Acids Res 39:W118–W124CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410CrossRefPubMedGoogle Scholar
  15. 15.
    Sun L, Luo H, Bu D, Zhao G, Yu K, Zhang C, Liu Y, Chen R, Zhao Y (2013) Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts. Nucleic Acids Res 41(17):e166CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7:562–578CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  1. 1.Key Laboratory of Intelligent Information Processing, Institute of Computing TechnologyChinese Academy of SciencesBeijingChina
  2. 2.Laboratory of Noncoding RNA, Institute of BiophysicsChinese Academy of SciencesBeijingChina

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