MicroRNA Applications in Marine Biology
- 25 Downloads
Purpose of Review
MicroRNAs (miRNAs) are single-stranded, short (~ 22 nt) non-coding RNAs that control gene expression in most metazoan taxa. These vital post-transcriptional regulators are emerging as a novel class of relatively well-conserved biomarkers useful to molecular ecologists working on non-model marine organisms. The purpose of this review is to provide researchers with a brief background on miRNAs and to explore recent applications in marine biology.
MiRNA datasets have been broadly employed in studies concerning commercially important species (oysters and crustaceans), phylogenetics (particularly deep evolutionary splits), and environmental stressor responses (temperature and salinity). Most progress has been made in the characterization of cnidarian miRNAs and bivalve and crustacean immune-related miRNAs. The use of miRNAs in phylogenetics is still under debate due to the secondary loss of miRNAs in some lineages, but they have been successfully applied in the resolution of deep evolutionary splits. Finally, miRNAs have been investigated in abiotic stress responses, but data interpretation is limited by the high number of species-specific miRNAs detected in these studies. Improvements in miRNA database curation and functional annotation should provide more confidence in their use.
Due to their evolutionary conservation, resilience to degradation, and amenable bioinformatics workflows, miRNAs are a powerful molecular tool in marine genomics. MiRNA investigations regarding environmental stress response will be particularly useful due to their potential to reveal physiological alterations and disease. Thus, they may be ultimately utilized as bio-indicators of environmental health.
KeywordsMarine invertebrates Epigenetics Ecological genomics Phylogenomics Epigenomics
We are grateful to Dr. Michelle Penn-Marshall (Vice President for Research and Associate Provost) and Dr. Deidre Gibson (Chair, Department of Marine and Environmental Sciences) at Hampton University for logistical support. We also thank Nefertiti Smith and Isaiah Milton for assistance with acquiring literature used in this review.
This work was funded by Hampton University Faculty Research Awards to C. Bonin and E. Lewallen. Additionally, the National Oceanic and Atmospheric Administration Living Marine Resources Cooperative Science Center provided funds for the preparation of this manuscript (NOAA-LMRCSC-FY2016; Award #NA16SEC4810007).
Compliance with Ethical Standards
Conflict of Interest
All authors declare no conflict of interest.
Human and Animal Rights and Informed Consent
This article does not involve human or animal subject studies performed by the authors.
- 1.Lee RC, Feinbaum RL, Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell. 1993;75(5):843–54.Google Scholar
- 2.Reinhart BJ, et al. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature. 2000;403(6772):901–6.Google Scholar
- 12.Fraune S, Forêt S, Reitzel AM. Using Nematostella vectensis to study the interactions between genome, epigenome, and bacteria in a changing environment. Front Mar Sci. 2016;3:148.Google Scholar
- 23.Waiho K, et al. Gonadal microRNA expression profiles and their potential role in sex differentiation and gonadal maturation of mud crab Scylla paramamosain. Mar Biotechnol (NY). 2019;21(3):320–34.Google Scholar
- 25.Jiao Y, et al. Identification and characterization of microRNAs in pearl oyster Pinctada martensii by Solexa deep sequencing. Mar Biotechnol (NY). 2014;16(1):54–62.Google Scholar
- 63.Campbell LI, Rota-Stabelli O, Edgecombe GD, Marchioro T, Longhorn SJ, Telford MJ, et al. MicroRNAs and phylogenomics resolve the relationships of Tardigrada and suggest that velvet worms are the sister group of Arthropoda. Proc Natl Acad Sci U S A. 2011;108(38):15920–4.PubMedPubMedCentralGoogle Scholar
- 69.Gleason LU. Applications and future directions for population transcriptomics in marine invertebrates. Curr Mol Biol Rep. 2019;5(3):116–27.Google Scholar
- 71.van Wijnen AJ, et al. MicroRNA functions in osteogenesis and dysfunctions in osteoporosis. Curr Osteopor Rep. 2013;11(2):72–82.Google Scholar
- 72.Sonna LA, et al. Invited review: Effects of heat and cold stress on mammalian gene expression. J Appl Physiol (1985). 2002;92(4):1725–42.Google Scholar
- 73.Sørensen JG, Kristensen TN, Loeschcke V. The evolutionary and ecological role of heat shock proteins. Ecol Lett. 2003;6(11):1025–37.Google Scholar
- 87.Makarova JA, Shkurnikov MU, Wicklein D, Lange T, Samatov TR, Turchinovich AA, et al. Intracellular and extracellular microRNA: an update on localization and biological role. Prog Histochem Cytochem. 2016;51(3–4):33–49.Google Scholar