Analyzing MiRNA–LncRNA Interactions

  • Maria D. ParaskevopoulouEmail author
  • Artemis G. HatzigeorgiouEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1402)


Long noncoding RNAs (lncRNAs) are noncoding transcripts usually longer than 200 nts that have recently emerged as one of the largest and significantly diverse RNA families. The biological role and functions of lncRNAs are still mostly uncharacterized. Their target-mimetic, sponge/decoy function on microRNAs was recently uncovered. miRNAs are a class of noncoding RNA species (~22 nts) that play a central role in posttranscriptional regulation of protein coding genes by mRNA cleavage, direct translational repression and/or mRNA destabilization. LncRNAs can act as miRNA sponges, reducing their regulatory effect on mRNAs. This function introduces an extra layer of complexity in the miRNA–target interaction network. This chapter focuses on the study of miRNA–lncRNA interactions with either in silico or experimentally supported analyses. The proposed methodologies can be appropriately adapted in order to become the backbone of advanced multistep functional miRNA analyses.

Key words

microRNA lncRNA HITS-CLIP PAR-CLIP Sponge In-silico predictions Experimentally supported Interaction 



Crosslinking immunoprecipitation




Long noncoding RNA


miRNA recognition element



The authors would like to thank Ioannis S Vlachos, Dimitra Karagkouni, and Georgios Georgakilas for their helpful comments and suggestions.

This work has been supported from the project “TOM”, “ARISTEIA” Action of the “OPERATIONAL PROGRAMME EDUCATION AND LIFELONG LEARNING” and is cofunded by the European Social Fund (ESF) and National Resources.


  1. 1.
    ENCODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489(7414):57–74CrossRefGoogle Scholar
  2. 2.
    Huntzinger E, Izaurralde E (2011) Gene silencing by microRNAs: contributions of translational repression and mRNA decay. Nat Rev Genet 12(2):99–110CrossRefPubMedGoogle Scholar
  3. 3.
    Griffiths-Jones S (2010) miRBase: microRNA sequences and annotation. Curr Protoc Bioinformatics Chapter 12:Unit12.9.1–Unit12.9.10Google Scholar
  4. 4.
    Baker M (2011) Long noncoding RNAs: the search for function. Nat Methods 8(5):379–383CrossRefGoogle Scholar
  5. 5.
    Cabili MN et al (2011) Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 25(18):1915–1927CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Johnsson P et al (2014) Evolutionary conservation of long non-coding RNAs; sequence, structure, function. Biochim Biophys Acta 1840(3):1063–1071CrossRefPubMedGoogle Scholar
  7. 7.
    Rinn JL, Chang HY (2012) Genome regulation by long noncoding RNAs. Annu Rev Biochem 81:145–166CrossRefPubMedGoogle Scholar
  8. 8.
    Gutschner T, Diederichs S (2012) The hallmarks of cancer: a long non-coding RNA point of view. RNA Biol 9(6):703–719CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Wang J et al (2010) CREB up-regulates long non-coding RNA, HULC expression through interaction with microRNA-372 in liver cancer. Nucleic Acids Res 38(16):5366–5383CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Klein U et al (2010) The DLEU2/miR-15a/16-1 cluster controls B cell proliferation and its deletion leads to chronic lymphocytic leukemia. Cancer Cell 17(1):28–40CrossRefPubMedGoogle Scholar
  11. 11.
    Cai X, Cullen BR (2007) The imprinted H19 noncoding RNA is a primary microRNA precursor. RNA 13(3):313–316CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Salmena L et al (2011) A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language? Cell 146(3):353–358CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Paraskevopoulou MD et al (2013) DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long non-coding RNAs. Nucleic Acids Res 41(Database issue):D239–D245CrossRefPubMedGoogle Scholar
  14. 14.
    Vlachos IS et al (2012) DIANA miRPath v. 2.0: investigating the combinatorial effect of microRNAs in pathways. Nucleic Acids Res 40(Web Server issue):W498–W504CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Georgakilas G et al (2014) microTSS: accurate microRNA transcription start site identification reveals a significant number of divergent pri-miRNAs. Nat Commun 5:5700CrossRefPubMedGoogle Scholar
  16. 16.
    Hansen TB et al (2011) miRNA-dependent gene silencing involving Ago2-mediated cleavage of a circular antisense RNA. EMBO J 30(21):4414–4422CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Memczak S et al (2013) Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 495(7441):333–338CrossRefPubMedGoogle Scholar
  18. 18.
    Hansen TB et al (2013) Natural RNA circles function as efficient microRNA sponges. Nature 495(7441):384–388CrossRefPubMedGoogle Scholar
  19. 19.
    Calin GA et al (2007) Ultraconserved regions encoding ncRNAs are altered in human leukemias and carcinomas. Cancer Cell 12(3):215–229CrossRefPubMedGoogle Scholar
  20. 20.
    Faghihi MA et al (2010) Evidence for natural antisense transcript-mediated inhibition of microRNA function. Genome Biol 11(5):R56CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    Yoon JH et al (2012) LincRNA-p21 suppresses target mRNA translation. Mol Cell 47(4):648–655CrossRefPubMedPubMedCentralGoogle Scholar
  22. 22.
    Poliseno L et al (2010) A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature 465(7301):1033–1038CrossRefPubMedPubMedCentralGoogle Scholar
  23. 23.
    Cesana M et al (2011) A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell 147(2):358–369CrossRefPubMedPubMedCentralGoogle Scholar
  24. 24.
    Franco-Zorrilla JM et al (2007) Target mimicry provides a new mechanism for regulation of microRNA activity. Nat Genet 39(8):1033–1037CrossRefPubMedGoogle Scholar
  25. 25.
    Imig J et al (2015) miR-CLIP capture of a miRNA targetome uncovers a lincRNA H19-miR-106a interaction. Nat Chem Biol 11(2):107–114CrossRefPubMedGoogle Scholar
  26. 26.
    Kallen AN et al (2013) The imprinted H19 lncRNA antagonizes let-7 microRNAs. Mol Cell 52(1):101–112CrossRefPubMedGoogle Scholar
  27. 27.
    Zhou X et al (2014) Linc-RNA-RoR acts as a “sponge” against mediation of the differentiation of endometrial cancer stem cells by microRNA-145. Gynecol Oncol 133(2):333–339CrossRefPubMedGoogle Scholar
  28. 28.
    Wang K et al (2014) The long noncoding RNA CHRF regulates cardiac hypertrophy by targeting miR-489. Circ Res 114(9):1377–1388CrossRefPubMedGoogle Scholar
  29. 29.
    Wang X et al (2015) Silencing of long noncoding RNA MALAT1 by miR-101 and miR-217inhibits proliferation, migration and invasion of esophageal squamous cell carcinoma cells. J Biol Chem 290(7):3925–3935CrossRefPubMedGoogle Scholar
  30. 30.
    Leucci E et al (2013) MicroRNA-9 targets the long non-coding RNA MALAT1 for degradation in the nucleus. Sci Rep 3:2535CrossRefPubMedPubMedCentralGoogle Scholar
  31. 31.
    Han Y et al (2013) Hsa-miR-125b suppresses bladder cancer development by down-regulating oncogene SIRT7 and oncogenic long noncoding RNA MALAT1. FEBS LettGoogle Scholar
  32. 32.
    Wang T et al (2014) Hsa-miR-1 downregulates long non-coding RNA urothelial cancer associated 1 in bladder cancer. Tumour Biol 35(10):10075–10084CrossRefPubMedGoogle Scholar
  33. 33.
    Prensner JR et al (2014) The long non-coding RNA PCAT-1 promotes prostate cancer cell proliferation through cMyc. Neoplasia 16(11):900–908CrossRefPubMedPubMedCentralGoogle Scholar
  34. 34.
    Wang P et al (2015) Long non-coding RNA CASC2 suppresses malignancy in human gliomas by miR-21. Cell Signal 27(2):275–282CrossRefPubMedGoogle Scholar
  35. 35.
    Wang K et al (2014) MDRL lncRNA regulates the processing of miR-484 primary transcript by targeting miR-361. PLoS Genet 10(7), e1004467CrossRefPubMedPubMedCentralGoogle Scholar
  36. 36.
    Gao Y et al (2015) LncRNA-HOST2 regulates cell biological behaviors in epithelial ovarian cancer through a mechanism involving microRNA let-7b. Hum Mol Genet 24(3):841–852CrossRefPubMedGoogle Scholar
  37. 37.
    Chiyomaru T et al (2013) Genistein inhibits prostate cancer cell growth by targeting miR-34a and oncogenic HOTAIR. PLoS One 8(8), e70372CrossRefPubMedPubMedCentralGoogle Scholar
  38. 38.
    Ma MZ et al (2014) Long non-coding RNA HOTAIR, a c-Myc activated driver of malignancy, negatively regulates miRNA-130a in gallbladder cancer. Mol Cancer 13:156CrossRefPubMedPubMedCentralGoogle Scholar
  39. 39.
    Cao C et al (2015) The long intergenic noncoding RNA UFC1, a target of MicroRNA 34a, interacts with the mRNA stabilizing protein HuR to increase levels of beta-Catenin in HCC cells. Gastroenterology 148(2):415–26.e18CrossRefPubMedGoogle Scholar
  40. 40.
    Zhang Z et al (2013) Negative regulation of lncRNA GAS5 by miR-21. Cell Death Differ 20(11):1558–1568CrossRefPubMedPubMedCentralGoogle Scholar
  41. 41.
    Braconi C et al (2011) microRNA-29 can regulate expression of the long non-coding RNA gene MEG3 in hepatocellular cancer. Oncogene 30(47):4750–4756CrossRefPubMedPubMedCentralGoogle Scholar
  42. 42.
    Fan M et al (2013) A long non-coding RNA, PTCSC3, as a tumor suppressor and a target of miRNAs in thyroid cancer cells. Exp Ther Med 5(4):1143–1146CrossRefPubMedPubMedCentralGoogle Scholar
  43. 43.
    Vlachos IS et al (2015) DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions. Nucleic Acids Res 43(Database issue):D153–D159CrossRefPubMedGoogle Scholar
  44. 44.
    Chi SW et al (2009) Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 460(7254):479–486PubMedPubMedCentralGoogle Scholar
  45. 45.
    Hafner M et al (2010) Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141(1):129–141CrossRefPubMedPubMedCentralGoogle Scholar
  46. 46.
    Helwak A et al (2013) Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding. Cell 153(3):654–665CrossRefPubMedPubMedCentralGoogle Scholar
  47. 47.
    Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114–2120CrossRefPubMedPubMedCentralGoogle Scholar
  48. 48.
    Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25(9):1105–1111CrossRefPubMedPubMedCentralGoogle Scholar
  49. 49.
    Wu TD, Nacu S (2010) Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26(7):873–881CrossRefPubMedPubMedCentralGoogle Scholar
  50. 50.
    Paraskevopoulou MD et al (2013) DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows. Nucleic Acids Res 41(Web Server issue):W169–W173CrossRefPubMedPubMedCentralGoogle Scholar
  51. 51.
    Ding Y, Chan CY, Lawrence CE (2004) Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res 32(Web Server issue):W135–W141CrossRefPubMedPubMedCentralGoogle Scholar
  52. 52.
    Rehmsmeier M et al (2004) Fast and effective prediction of microRNA/target duplexes. RNA 10(10):1507–1517CrossRefPubMedPubMedCentralGoogle Scholar
  53. 53.
    Pollard KS et al (2010) Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res 20(1):110–121CrossRefPubMedPubMedCentralGoogle Scholar
  54. 54.
    Bu D et al (2012) NONCODE v3.0: integrative annotation of long noncoding RNAs. Nucleic Acids Res 40(Database issue):D210–D215CrossRefPubMedGoogle Scholar
  55. 55.
    Flicek P et al (2012) Ensembl 2012. Nucleic Acids Res 40(Database issue):D84–D90CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  1. 1.DIANA-Lab, Department of Electrical & Computer EngineeringUniversity of ThessalyVolosGreece

Personalised recommendations