Integrated analyses of zebrafish miRNA and mRNA expression profiles identify miR-29b and miR-223 as potential regulators of optic nerve regeneration.
BACKGROUND
Unlike mammals, zebrafish have the ability to regenerate damaged parts of their central nervous system (CNS) and regain functionality of the affected area. A better understanding of the molecular mechanisms involved in zebrafish regeneration may therefore provide insight into how CNS repair might be induced in mammals. Although many studies have described differences in gene expression in zebrafish during CNS regeneration, the regulatory mechanisms underpinning the differential expression of these genes have not been examined.


RESULTS
We used microarrays to analyse and integrate the mRNA and microRNA (miRNA) expression profiles of zebrafish retina after optic nerve crush to identify potential regulatory mechanisms that underpin central nerve regeneration. Bioinformatic analysis identified 3 miRNAs and 657 mRNAs that were differentially expressed after injury. We then combined inverse correlations between our miRNA expression and mRNA expression, and integrated these findings with target predictions from TargetScan Fish to identify putative miRNA-gene target pairs. We focused on two over-expressed miRNAs (miR-29b and miR-223), and functionally validated seven of their predicted gene targets using RT-qPCR and luciferase assays to confirm miRNA-mRNA binding. Gene ontology analysis placed the miRNA-regulated genes (eva1a, layna, nefmb, ina, si:ch211-51a6.2, smoc1, sb:cb252) in key biological processes that included cell survival/apoptosis, ECM-cytoskeleton signaling, and heparan sulfate proteoglycan binding,


CONCLUSIONS
Our results suggest a key role for miR-29b and miR-223 in zebrafish regeneration. The identification of miRNA regulation in a zebrafish injury model provides a framework for future studies in which to investigate not only the cellular processes required for CNS regeneration, but also how these mechanisms might be regulated to promote successful repair and return of function in the injured mammalian brain.
Experimental and Regenerative Neurosciences, School of Animal Biology; University of Western Australia, Crawley, 6009, , WA, Australia. paula.fuller@uwa.edu.au.
Paula I
PI
Fuller-Carter
McCusker Charitable Foundation Bioinformatics Centre, Telethon Kids Institute, University of Western Australia, 6008, Subiaco, WA, Australia. Kim.Carter@telethonkids.org.au.
Kim W
KW
Carter
Centre for Biostatistics, Telethon Kids Institute, University of Western Australia, 6008, Subiaco, WA, Australia. Denise.Anderson@telethonkids.org.au.
Denise
D
Anderson
School of Physiology, Anatomy and Human Biology, University of Western Australia, Crawley, 6009, , WA, Australia. alan.harvey@uwa.edu.au.|West Australian Neuroscience Research Institute (WANRI), QEII Medical Centre, Verdun Street, Nedlands, 6009, Western Australia. alan.harvey@uwa.edu.au.
Alan R
AR
Harvey
Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, Nedlands, 6008, WA, Australia. keith.giles@nyumc.org.|Current address: Ronald O. Perelman Department of Dermatology, New York University School of Medicine, New York, NY, 10016, USA. keith.giles@nyumc.org.
Keith M
KM
Giles
Experimental and Regenerative Neurosciences, School of Animal Biology; University of Western Australia, Crawley, 6009, , WA, Australia. jennifer.rodger@uwa.edu.au.|West Australian Neuroscience Research Institute (WANRI), QEII Medical Centre, Verdun Street, Nedlands, 6009, Western Australia. jennifer.rodger@uwa.edu.au.
Jennifer
J
Rodger
D000818:Animals; D019295:Computational Biology / Q000379:methods; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods; D053263:Gene Regulatory Networks; D008297:Male; D035683:MicroRNAs / Q000235:genetics*; D009416:Nerve Regeneration; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D009900:Optic Nerve / Q000502:physiology; D020221:Optic Nerve Injuries / Q000235:genetics*; D015027:Zebrafish / Q000235:genetics* / Q000502:physiology
D035683:MicroRNAs; C000599690:microRNA-223, zebrafish; C000607227:microRNA-29, zebrafish