Login Register Cart 0
Letter Article

Common Variants of the Plant microRNA-168a Exhibit Differing Silencing Efficacy for Human Low-Density Lipoprotein Receptor Adaptor Protein 1 (LDLRAP1)

Author(s): Claudia Lang, Sakuntala Karunairetnam, Kim R. Lo, Andrew V. Kralicek, Ross N. Crowhurst, Andrew Peter Gleave, Robin M. MacDiarmid and John Ronald Ingram*

Volume 8, Issue 2, 2019

Page: [166 - 170] Pages: 5

DOI: 10.2174/2211536608666181203103233

Abstract

Background: The discovery that a plant microRNA (miRNAs) from rice (Oryza sativa miR168a) can modify post-transcriptional expression of the mammalian. Low-Density Lipoprotein Receptor Adaptor Protein 1 (LDLRAP1) gene highlights the potential for cross-kingdom miRNAmRNA interactions.

Objective: To investigate whether common variants of the conserved miR168a family have the capability for similar cross-kingdom regulatory functions, we selected sequences from three dietary plant sources: rice (Oryza sativa), tomato (Solanum lycopersicum), apple (Malus domestica) and compared their ability to regulate human LDLRAP1 expression.

Methods: Target prediction software intaRNA and RNAhybrid were used to analyze and calculate the energy and alignment score between the miR168a variants and human LDLRAP1 mRNA. An in vitro cell-based Dual-Luciferase® Reporter Assay (pmirGLO, Promega), was then used to validate the miRNA-mRNA interaction experimentally.

Results: Computational analyses revealed that a single nucleotide difference at position 14 (from the 5’ end of the miRNA) creates a G:U wobble in the miRNA-mRNA duplex formed by tomato and apple miR168a variants. This G:U wobble had only a small effect on the free energy score (-33.8–34.7 kcal/mol). However, despite reasonable hybridization energy scores (<-20 kcal/mol) for all miR168a variants, only the rice miR168a variant lacking a G:U wobble significantly reduced LDLRAP1 transcript expression by 25.8 + 7.3% (p<0.05), as measured by relative luciferase activity.

Conclusion: In summary, single nucleotide differences at key positions can have a marked influence on regulatory function despite similar predicted energy scores and miRNA-mRNA duplex structures.

Keywords: Cross-kingdom regulation, gene-reporter assay, LDLRAP1, miR-168a, miRNA variants, miRNA.

« Previous Next »
Graphical Abstract

[1]
Bartel D. MicroRNAs: target recognition and regulatory functions. Cell 2009; 136: 215-33.
[2]
Friedman JM, Jones PA. MicroRNAs: critical mediators of differentiation, development and disease. Swiss Med Wkly 2009; 139: 466-72.
[3]
Garzon R, Heaphy CE, Havelange V, et al. MicroRNA 29b functions in acute myeloid leukemia. Blood 2009; 114: 5331-41.
[4]
Ambros V. MicroRNAs and developmental timing. Curr Opin Genet Dev 2011; 21: 511-7.
[5]
Starega-Roslan J, Krol J, Koscianska E, et al. Structural basis of microRNA length variety. Nucleic Acids Res 2011; 39: 257-68.
[6]
Wang K, Li H, Yuan Y, et al. The complex exogenous RNA spectra in human plasma: an interface with human gut biota? PLoS One 2012; 7: e51009.
[7]
Freedman JE, Gerstein M, Mick E, et al. Corrigendum: diverse human extracellular RNAs are widely detected in human plasma. Nat Commun 2016; 7: 11902.
[8]
Buck AH, Coakley G, Simbari F, et al. Exosomes secreted by nematode parasites transfer small RNAs to mammalian cells and modulate innate immunity. Nat Commun 2011; 5: 5488.
[9]
Zhang L, Hou D, Chen X, et al. Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA. Cell Res 2012; 22: 107-26.
[10]
Zhou Z, Li X, Liu J. Honeysuckle-encoded atypical microRNA2911 directly targets influenza A viruses. Cell Res 2015; 25: 39-49.
[11]
Chin AR, Fong MY, Somlo G, et al. Cross-kingdom inhibition of breast cancer growth by plant miR159. Cell Res 2016; 26: 217-28.
[12]
Yang J, Hotz T, Broadnax L, Yarmarkovich M, Elbaz-Younes I, Hirschi KD. Anomalous uptake and circulatory characteristics of the plant-based small RNA MIR2911. Sci Rep 2016; 6: 26834.
[13]
Liu YC, Chen WL, Kung WH, Huang HD. Plant miRNAs found in human circulating system provide evidences of cross kingdom RNAi. BMC Genomics 2017; 18: 112.
[14]
Cavalieri D, Rizzetto L, Tocci N, et al. Plant microRNAs as novel immunomodulatory agents. Sci Rep 2016; 6: 25761.
[15]
Duan R, Pak C, Jin P. Single nucleotide polymorphism associated with mature miR-125a alters the processing of pri-miRNA. Hum Mol Genet 2007; 16: 1124-31.
[16]
Hu Z, Chen J, Tian T, et al. Genetic variants of miRNA sequences and non-small cell lung cancer survival. J Clin Invest 2008; 118: 2600-8.
[17]
Xu T, Zhu Y, Wei QK, et al. A functional polymorphism in the miR-146a gene is associated with the risk for hepatocellular carcinoma. Carcinogenesis 2008; 29: 2126-31.
[18]
Manikandan M, Munirajan AK. Single nucleotide polymorphisms in microRNA binding sites of oncogenes: implications in cancer and pharmacogenomics. OMICS 2014; 18: 142-54.
[19]
Chavez Montes RA, de Fatima Rosas-Cardenas F, De Paoli E, et al. Sample sequencing of vascular plants demonstrates widespread conservation and divergence of microRNAs. Nat Commun 2014; 5: 3722.
[20]
Qu D, Yan F, Li MA, Varotto C, Zhao ZY. Comparative analysis of MIR168 promoters in three plant species. Genet Mol Res 2016; 15(2)
[http://dx.doi.org/10.4238/gmr.15027684]
[21]
Javed M, Solanki M, Sinha A, Shukla LI. Position based nucleotide analysis of miR168 family in higher plants and its targets in mammalian transcripts. MicroRNA 2017; 6: 136-42.
[22]
Busch A, Richter AS, Backofen R. IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. Bioinformatics 2008; 24: 2849-56.
[23]
Wright PR, Georg J, Mann M, et al. CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domainsNucleic Acids Res 2014; 42(Web server issue): W119-23
[24]
Richter AS, Backofen R. Accessibility and conservation: general features of bacterial small RNA-mRNA interactions? RNA Biol 2012; 9: 954-65.
[25]
Rehmsmeier M, Steffen P, Hochsmann M, Giegerich R. Fast and effective prediction of microRNA/target duplexes. RNA 2004; 10: 1507-17.
[26]
Krüger J, Rehmsmeier M. RNA hybrid: microRNA target prediction easy, fast and flexible. Nucleic Acids Res 2006; 34: W451-54.
[27]
Shin C, Nam JW, Farh KH, Chiang H, Shkumatava A, Bartel D. Expanding the microRNA targeting code: functional sites with centered pairing. Mol Cell 2010; 38: 789-802.
[28]
Martin H, Wani S, Steptoe A, et al. Imperfect centered miRNA binding sites are common and can mediate repression of target mRNAs. Genome Biol 2014; 15: R51.
[29]
Doench JG, Sharp PA. Specificity of microRNA target selection in translational repression. Genes Dev 2004; 18: 504-11.
[30]
Shu J, Xia Z, Li L, et al. Dose-dependent differential mRNA target selection and regulation by let-7a-7f and miR-17-92 cluster microRNAs. RNA Biol 2012; 9(10): 1275-87.
[31]
Witwer KW, McAlexander MA, Queen SE, Adams RJ. Real-time quantitative PCR and droplet digital PCR for plant miRNAs in mammalian blood provide little evidence for general uptake of dietary miRNAs: limited evidence for general uptake of dietary plant xenomiRs. RNA Biol 2013; 10: 1080-6.
[32]
Kang W, Bang-Berthelsen CH, Holm A. Survey of 800+ data sets from human tissue and body fluid reveals xenomiRs are likely artifacts. RNA 2017; 23: 433-45.
[33]
Witwer KW. Alternative miRNAs? human sequences misidentified as plant miRNAs in plant studies and in human plasma. F1000 Res 2018; 7: 244.

Rights & Permissions Print Cite
Article Metrics
47
6
© 2024 Bentham Science Publishers | Privacy Policy