Dual Functional Roles of Molecular Beacon As a MicroRNA Detector and Inhibitor

Overview

Journal J Biol Chem

Specialty Biochemistry

Date 2017 Jan 20

PMID 28100783

Citations 4

Authors

Wai Ming Li

Ching-Man Chan

Andrew L Miller

Chow H Lee

Affiliations

Soon will be listed here.

Abstract

MicroRNAs are essential in many cellular processes. The ability to detect microRNAs is important for understanding its function and biogenesis. This study is aimed at using a molecular beacon to detect miR-430 in developing zebrafish embryos as a proof of principle. miR-430 is crucial for the clearance of maternal mRNA during maternal zygotic transition in embryonic development. Despite its known function, the temporal and spatial expression of miR-430 remains unclear. We used various imaging techniques, including laser scanning confocal microscopy, spinning disk, and lightsheet microscopy, to study the localization of miR-430 and any developmental defects possibly caused by the molecular beacon. Our results show that miR-430 is expressed early in development and is localized in distinct cytoplasmic granules where its target mRNA can be detected. We also show that the designed molecular beacon can inhibit the function of miR-430 and cause developmental defect in the brain, notochord, heart, and kidney, depending on the delivery site within the embryo, suggesting that miR-430 plays a diverse role in embryonic morphogenesis. When compared with morpholino, molecular beacon is 2 orders of magnitude more potent in inhibiting miR-430. Thus, our results reveal that in addition to being used as a valuable tool for the detection of microRNAs , molecular beacons can also be employed to inhibit microRNAs in a specific manner.

Citing Articles

miR-430 microRNA Family in Fishes: Molecular Characterization and Evolution.

Jimenez-Ruiz C, de la Herran R, Robles F, Navajas-Perez R, Cross I, Rebordinos L Animals (Basel). 2023; 13(15).

PMID: 37570208 PMC: 10417697. DOI: 10.3390/ani13152399.

Zebrafish neuromesodermal progenitors undergo a critical state transition .

Toh K, Saunders D, Verd B, Steventon B iScience. 2022; 25(10):105216.

PMID: 36274939 PMC: 9579027. DOI: 10.1016/j.isci.2022.105216.

A cell cycle-coordinated Polymerase II transcription compartment encompasses gene expression before global genome activation.

Hadzhiev Y, Qureshi H, Wheatley L, Cooper L, Jasiulewicz A, Van Nguyen H Nat Commun. 2019; 10(1):691.

PMID: 30741925 PMC: 6370886. DOI: 10.1038/s41467-019-08487-5.

Enhancing the Therapeutic Delivery of Oligonucleotides by Chemical Modification and Nanoparticle Encapsulation.

Sun Y, Zhao Y, Zhao X, Lee R, Teng L, Zhou C Molecules. 2017; 22(10).

PMID: 29027965 PMC: 6158866. DOI: 10.3390/molecules22101724.

References

Wienholds E, Kloosterman W, Miska E, Alvarez-Saavedra E, Berezikov E, de Bruijn E . MicroRNA expression in zebrafish embryonic development. Science. 2005; 309(5732):310-1. DOI: 10.1126/science.1114519. View

Kato Y, Miyaki S, Yokoyama S, Omori S, Inoue A, Horiuchi M . Real-time functional imaging for monitoring miR-133 during myogenic differentiation. Int J Biochem Cell Biol. 2009; 41(11):2225-31. PMC: 2806093. DOI: 10.1016/j.biocel.2009.04.018. View

Stenvang J, Petri A, Lindow M, Obad S, Kauppinen S . Inhibition of microRNA function by antimiR oligonucleotides. Silence. 2012; 3(1):1. PMC: 3306207. DOI: 10.1186/1758-907X-3-1. View

Lebreton A, Tomecki R, Dziembowski A, Seraphin B . Endonucleolytic RNA cleavage by a eukaryotic exosome. Nature. 2008; 456(7224):993-6. DOI: 10.1038/nature07480. View

Kang W, Cho Y, Chae J, Lee J, Choi K, Kim S . Molecular beacon-based bioimaging of multiple microRNAs during myogenesis. Biomaterials. 2010; 32(7):1915-22. DOI: 10.1016/j.biomaterials.2010.11.007. View

Ritland Politz J, Zhang F, Pederson T . MicroRNA-206 colocalizes with ribosome-rich regions in both the nucleolus and cytoplasm of rat myogenic cells. Proc Natl Acad Sci U S A. 2006; 103(50):18957-62. PMC: 1748159. DOI: 10.1073/pnas.0609466103. View

Kimmel C, Warga R, Schilling T . Origin and organization of the zebrafish fate map. Development. 1990; 108(4):581-94. DOI: 10.1242/dev.108.4.581. View

Liao J, Ma L, Guo Y, Zhang Y, Zhou H, Shao P . Deep sequencing of human nuclear and cytoplasmic small RNAs reveals an unexpectedly complex subcellular distribution of miRNAs and tRNA 3' trailers. PLoS One. 2010; 5(5):e10563. PMC: 2871053. DOI: 10.1371/journal.pone.0010563. View

Sleep E, Boue S, Jopling C, Raya M, Raya A, Izpisua Belmonte J . Transcriptomics approach to investigate zebrafish heart regeneration. J Cardiovasc Med (Hagerstown). 2010; 11(5):369-80. DOI: 10.2459/JCM.0b013e3283375900. View

10.

Ko H, Lee J, Lee Y, Gu H, Ali B, Al-Khedhairy A . Bioimaging of the microRNA-294 expression-dependent color change in cells by a dual fluorophore-based molecular beacon. Chem Commun (Camb). 2015; 51(11):2159-61. DOI: 10.1039/c4cc08898k. View

11.

Kato Y, Sawata S, Inoue A . A lentiviral vector encoding two fluorescent proteins enables imaging of adenoviral infection via adenovirus-encoded miRNAs in single living cells. J Biochem. 2009; 147(1):63-71. DOI: 10.1093/jb/mvp144. View

12.

Tyagi S, Kramer F . Molecular beacons: probes that fluoresce upon hybridization. Nat Biotechnol. 1996; 14(3):303-8. DOI: 10.1038/nbt0396-303. View

13.

Bazzini A, Lee M, Giraldez A . Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish. Science. 2012; 336(6078):233-7. PMC: 3547538. DOI: 10.1126/science.1215704. View

14.

Thatcher E, Bond J, Paydar I, Patton J . Genomic organization of zebrafish microRNAs. BMC Genomics. 2008; 9:253. PMC: 2427041. DOI: 10.1186/1471-2164-9-253. View

15.

Wei C, Salichos L, Wittgrove C, Rokas A, Patton J . Transcriptome-wide analysis of small RNA expression in early zebrafish development. RNA. 2012; 18(5):915-29. PMC: 3334700. DOI: 10.1261/rna.029090.111. View

16.

Place R, Li L, Pookot D, Noonan E, Dahiya R . MicroRNA-373 induces expression of genes with complementary promoter sequences. Proc Natl Acad Sci U S A. 2008; 105(5):1608-13. PMC: 2234192. DOI: 10.1073/pnas.0707594105. View

17.

Salmanidis M, Pillman K, Goodall G, Bracken C . Direct transcriptional regulation by nuclear microRNAs. Int J Biochem Cell Biol. 2014; 54:304-11. DOI: 10.1016/j.biocel.2014.03.010. View

18.

Rosa A, Spagnoli F, Brivanlou A . The miR-430/427/302 family controls mesendodermal fate specification via species-specific target selection. Dev Cell. 2009; 16(4):517-27. DOI: 10.1016/j.devcel.2009.02.007. View

19.

Hwang H, Wentzel E, Mendell J . A hexanucleotide element directs microRNA nuclear import. Science. 2007; 315(5808):97-100. DOI: 10.1126/science.1136235. View

20.

Zeng L, Carter A, Childs S . miR-145 directs intestinal maturation in zebrafish. Proc Natl Acad Sci U S A. 2009; 106(42):17793-8. PMC: 2764920. DOI: 10.1073/pnas.0903693106. View