Abstract
Long noncoding RNAs (lncRNAs) are noncoding transcripts, usually longer than 200 nt, that constitute one of the largest and significantly heterogeneous RNA families. The annotation of lncRNAs and the characterization of their function is a constantly evolving field. LncRNA interplay with microRNAs (miRNAs) is thoroughly studied in several physiological and disease states. miRNAs are small noncoding RNAs (~22 nt) that posttranscriptionally regulate the expression of protein coding genes, through mRNA target cleavage, degradation or direct translational suppression. miRNAs can affect lncRNA half-life by promoting their degradation, or lncRNAs can act as miRNA “sponges,” reducing miRNA regulatory effect on target mRNAs. This chapter outlines the miRNA–lncRNA interplay and provides hands-on methodologies for experimentally supported and in silico-guided analyses. The proposed techniques are a valuable asset to further understand lncRNA functions and can be appropriately adapted to become the backbone for further downstream analyses.
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Abbreviations
- ceRNA:
-
Competing endogenous RNA
- CLIP:
-
Cross-linking immunoprecipitation
- lncRNA:
-
Long noncoding RNA
- miRNA:
-
microRNA
- MRE:
-
miRNA recognition element
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Acknowledgments
We acknowledge support of this work by the project “ELIXIR-GR: The Greek Research Infrastructure for Data Management and Analysis in Life Sciences” (MIS 5002780) which is implemented under the Action “Reinforcement of the Research and Innovation Infrastructure,” funded by the Operational Programme “Competitiveness, Entrepreneurship and Innovation” (NSRF 2014–2020) and cofinanced by Greece and the European Union (European Regional Development Fund).
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Karagkouni, D., Karavangeli, A., Paraskevopoulou, M.D., Hatzigeorgiou, A.G. (2021). Characterizing miRNA–lncRNA Interplay. In: Zhang, L., Hu, X. (eds) Long Non-Coding RNAs. Methods in Molecular Biology, vol 2372. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1697-0_21
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DOI: https://doi.org/10.1007/978-1-0716-1697-0_21
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