Detection and Characterization of Ribosome-Associated Long Noncoding RNAs

  • Chao Zeng
  • Michiaki HamadaEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 2254)


Ribosome profiling shows potential for studying the function of long noncoding RNAs (lncRNAs). We introduce a bioinformatics pipeline for detecting ribosome-associated lncRNAs (ribo-lncRNAs) from ribosome profiling data. Further, we describe a machine-learning approach for the characterization of ribo-lncRNAs based on their sequence features. Scripts for ribo-lncRNA analysis can be accessed at (

Key words

lncRNA Machine learning Ribosome-associated Ribosome profiling Sequence feature 



This work was supported by the Ministry of Education, Culture, Sports, Science and Technology (KAKENHI) [grant numbers JP17K20032, JP16H05879, JP16H01318, and JP16H02484 to MH].


  1. 1.
    Bu D, Yu K, Sun S et al (2012) NONCODE v3.0: integrative annotation of long noncoding RNAs. Nucleic Acids Res 40:D210–D215CrossRefGoogle Scholar
  2. 2.
    Iyer MK, Niknafs YS, Malik R et al (2015) The landscape of long noncoding RNAs in the human transcriptome. Nat Genet 47:199–208CrossRefGoogle Scholar
  3. 3.
    Hon C-C, Ramilowski JA, Harshbarger J et al (2017) An atlas of human long non-coding RNAs with accurate 5′ ends. Nature 543:199–204CrossRefGoogle Scholar
  4. 4.
    O’Leary NA, Wright MW, Brister JR et al (2016) Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res 44:D733–D745CrossRefGoogle Scholar
  5. 5.
    You B-H, Yoon S-H, Nam J-W (2017) High-confidence coding and noncoding transcriptome maps. Genome Res 27:1050–1062CrossRefGoogle Scholar
  6. 6.
    Frankish A, Diekhans M, Ferreira A-M et al (2019) GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Res 47:D766–D773CrossRefGoogle Scholar
  7. 7.
    Ingolia NT, Ghaemmaghami S, Newman JRS, Weissman JS (2009) Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324:218–223CrossRefGoogle Scholar
  8. 8.
    Ingolia NT, Lareau LF, Weissman JS (2011) Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 147:789–802CrossRefGoogle Scholar
  9. 9.
    Zhou P, Zhang Y, Ma Q et al (2013) Interrogating translational efficiency and lineage-specific transcriptomes using ribosome affinity purification. Proc Natl Acad Sci U S A 110:15395–15400CrossRefGoogle Scholar
  10. 10.
    Aspden JL, Eyre-Walker YC, Phillips RJ et al (2014) Extensive translation of small open reading frames revealed by poly-ribo-seq. elife 3:e03528CrossRefGoogle Scholar
  11. 11.
    Zeng C, Fukunaga T, Hamada M (2018) Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data. BMC Genomics 19:414CrossRefGoogle Scholar
  12. 12.
    Zeng C, Hamada M (2018) Identifying sequence features that drive ribosomal association for lncRNA. BMC Genomics 19:906CrossRefGoogle Scholar
  13. 13.
    Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 17:10–12CrossRefGoogle Scholar
  14. 14.
    Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359CrossRefGoogle Scholar
  15. 15.
    Li B, Dewey CN (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12:323CrossRefGoogle Scholar
  16. 16.
    Camacho C, Coulouris G, Avagyan V et al (2009) BLAST+: architecture and applications. BMC Bioinformatics 10:421CrossRefGoogle Scholar
  17. 17.
    Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26:841–842CrossRefGoogle Scholar
  18. 18.
    Kawaguchi R, Kiryu H (2016) Parallel computation of genome-scale RNA secondary structure to detect structural constraints on human genome. BMC Bioinformatics 17:203CrossRefGoogle Scholar
  19. 19.
    Zhou Y, Zeng P, Li Y-H et al (2016) SRAMP: prediction of mammalian N6-methyladenosine (m6A) sites based on sequence-derived features. Nucleic Acids Res 44:e91CrossRefGoogle Scholar
  20. 20.
    Kikin O, D’Antonio L, Bagga PS (2006) QGRS Mapper: a web-based server for predicting G-quadruplexes in nucleotide sequences. Nucleic Acids Res 34:W676–W682CrossRefGoogle Scholar
  21. 21.
    Park J-E, Yi H, Kim Y et al (2016) Regulation of poly(A) tail and translation during the somatic cell cycle. Mol Cell 62:462–471CrossRefGoogle Scholar
  22. 22.
    Ingolia NT, Brar GA, Stern-Ginossar N et al (2014) Ribosome profiling reveals pervasive translation outside of annotated protein-coding genes. Cell Rep 8:1365–1379CrossRefGoogle Scholar
  23. 23.
    Guttman M, Russell P, Ingolia NT et al (2013) Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins. Cell 154:240–251CrossRefGoogle Scholar
  24. 24.
    Smit AFA, Hubley R, Green P (1996) RepeatMasker. Accessed 31 Mar 2019

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2021

Authors and Affiliations

  1. 1.AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL)TokyoJapan
  2. 2.Faculty of Science and EngineeringWaseda UniversityTokyoJapan
  3. 3.Artificial Intelligence Research CenterNational Institute of Advanced Industrial Science and Technology (AIST)TokyoJapan
  4. 4.Institute for Medical-oriented Structural BiologyWaseda UniversityTokyoJapan
  5. 5.Graduate School of MedicineNippon Medical SchoolTokyoJapan

Personalised recommendations